subject:(Aptamer)

Wake Forest University

1. Stuart, Christopher H. USE OF DNA APTAMERS FOR TARGETED DELIVERY OF CHEMOTHERAPEUTIC AGENTS.

Degree: 2016, Wake Forest University

► The development of safe and efficacious chemotherapeutics has been the goal of cancer researchers for decades. Many different methods have been used to pursue this… (more)

Subjects/Keywords: Aptamer

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APA (6^th Edition):

Stuart, C. H. (2016). USE OF DNA APTAMERS FOR TARGETED DELIVERY OF CHEMOTHERAPEUTIC AGENTS. (Thesis). Wake Forest University. Retrieved from http://hdl.handle.net/10339/59294

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stuart, Christopher H. “USE OF DNA APTAMERS FOR TARGETED DELIVERY OF CHEMOTHERAPEUTIC AGENTS.” 2016. Thesis, Wake Forest University. Accessed February 19, 2020. http://hdl.handle.net/10339/59294.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stuart, Christopher H. “USE OF DNA APTAMERS FOR TARGETED DELIVERY OF CHEMOTHERAPEUTIC AGENTS.” 2016. Web. 19 Feb 2020.

Vancouver:

Stuart CH. USE OF DNA APTAMERS FOR TARGETED DELIVERY OF CHEMOTHERAPEUTIC AGENTS. [Internet] [Thesis]. Wake Forest University; 2016. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10339/59294.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stuart CH. USE OF DNA APTAMERS FOR TARGETED DELIVERY OF CHEMOTHERAPEUTIC AGENTS. [Thesis]. Wake Forest University; 2016. Available from: http://hdl.handle.net/10339/59294

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Oregon State University

2. Hutanu, Daniela. Synthesis and characterization of novel stationary phases for small scale liquid chromatographic separations of proteins and nanoparticles.

Degree: PhD, Chemistry, 2008, Oregon State University

URL: http://hdl.handle.net/1957/8223

► The emerging field of nanotechnology strictly requires the micro-scaling of the available separation technology and the design of novel devices for separations of molecules of… (more)

▼ The emerging field of nanotechnology strictly requires the micro-scaling of the available separation technology and the design of novel devices for separations of molecules of interest. The separation of proteins and nanoparticles is challenging due to their relatively large size, non-specific adherence to surfaces and instability in many solvents. This dissertation presents the synthesis and characterization of novel stationary phases for use in separations of proteins or nanoparticles in both capillary and microchip formats. In order to separate blood proteins with high specificity, a DNA aptamer selected for α-thrombin was employed as an affinity component of the stationary phases. Silica surfaces and organic monoliths were modified with the aptamer via an azlactone linkage and have demonstrated highly efficient separations of thrombin from a mixture in the microscale. The high efficiency of the protein separation (HETP = 276 μm, RS = 1.7) is comparable with macroscale results using antibodies as the affinity factor. Novel hybrid inorganic-organic polysilsesquioxane stationary phases were synthesized by way of surfactant templated polymerization of bridged alcoxy-silyl ethane monomers, in presence of sodium hydroxide. The novel materials were successful in size exclusion separation of polystyrene standards with molecular diameters of 0.3-2.4 nm. A hybrid inorganic-organic polysilsesquioxane sorbent also proved useful for small scale separations of triphenyl phosphine protected gold nanoparticles, based on a sorptive mechanism instead of a size exclusion mechanism. Polysilsesquioxanes were easily synthesized in-situ inside fused silica capillary columns and PMMA microchip channels in order to facilitate integration with a micro-reactor. The novel stationary phases proved efficient for separation of proteins and nanoparticles in the micro-scale format and can further be utilized for online purification and separation of these difficult compounds. Advisors/Committee Members: REMCHO, VINCENT T. (advisor), INGLE, JAMES (committee member).

Subjects/Keywords: APTAMER; Nanotechnology

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APA (6^th Edition):

Hutanu, D. (2008). Synthesis and characterization of novel stationary phases for small scale liquid chromatographic separations of proteins and nanoparticles. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/8223

Chicago Manual of Style (16^th Edition):

Hutanu, Daniela. “Synthesis and characterization of novel stationary phases for small scale liquid chromatographic separations of proteins and nanoparticles.” 2008. Doctoral Dissertation, Oregon State University. Accessed February 19, 2020. http://hdl.handle.net/1957/8223.

MLA Handbook (7^th Edition):

Hutanu, Daniela. “Synthesis and characterization of novel stationary phases for small scale liquid chromatographic separations of proteins and nanoparticles.” 2008. Web. 19 Feb 2020.

Vancouver:

Hutanu D. Synthesis and characterization of novel stationary phases for small scale liquid chromatographic separations of proteins and nanoparticles. [Internet] [Doctoral dissertation]. Oregon State University; 2008. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/1957/8223.

Council of Science Editors:

Hutanu D. Synthesis and characterization of novel stationary phases for small scale liquid chromatographic separations of proteins and nanoparticles. [Doctoral Dissertation]. Oregon State University; 2008. Available from: http://hdl.handle.net/1957/8223

University of Ottawa

3. Al-Youssef, Nadia. The Selection of Aptamers to CD20 and Their Application as Inhibitors of Complement Dependent Cytotoxicity .

Degree: 2015, University of Ottawa

URL: http://hdl.handle.net/10393/33182

► CD20 is an important oncological B-cell marker. Immunotherapy, using anti-CD20 antibodies, has revolutionized the treatment of B-cell cancers. Aptamers are highly specific DNA ligands, raised… (more)

Subjects/Keywords: aptamer; CD20

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APA (6^th Edition):

Al-Youssef, N. (2015). The Selection of Aptamers to CD20 and Their Application as Inhibitors of Complement Dependent Cytotoxicity . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/33182

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Al-Youssef, Nadia. “The Selection of Aptamers to CD20 and Their Application as Inhibitors of Complement Dependent Cytotoxicity .” 2015. Thesis, University of Ottawa. Accessed February 19, 2020. http://hdl.handle.net/10393/33182.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Al-Youssef, Nadia. “The Selection of Aptamers to CD20 and Their Application as Inhibitors of Complement Dependent Cytotoxicity .” 2015. Web. 19 Feb 2020.

Vancouver:

Al-Youssef N. The Selection of Aptamers to CD20 and Their Application as Inhibitors of Complement Dependent Cytotoxicity . [Internet] [Thesis]. University of Ottawa; 2015. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10393/33182.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Al-Youssef N. The Selection of Aptamers to CD20 and Their Application as Inhibitors of Complement Dependent Cytotoxicity . [Thesis]. University of Ottawa; 2015. Available from: http://hdl.handle.net/10393/33182

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Urbana-Champaign

4. Akki, Spurti Umesh. Selecting DNA aptamers for 17β-estradiol.

Degree: MS, 0231, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/42165

► 17β-estradiol (E2) is a potent estrogen that has been widely documented in water resources. It falls under the category of endocrine disrupting compounds (EDCs), and… (more)

Subjects/Keywords: DNA aptamer; estradiol

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APA (6^th Edition):

Akki, S. U. (2013). Selecting DNA aptamers for 17β-estradiol. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/42165

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Akki, Spurti Umesh. “Selecting DNA aptamers for 17β-estradiol.” 2013. Thesis, University of Illinois – Urbana-Champaign. Accessed February 19, 2020. http://hdl.handle.net/2142/42165.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Akki, Spurti Umesh. “Selecting DNA aptamers for 17β-estradiol.” 2013. Web. 19 Feb 2020.

Vancouver:

Akki SU. Selecting DNA aptamers for 17β-estradiol. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2013. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/2142/42165.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Akki SU. Selecting DNA aptamers for 17β-estradiol. [Thesis]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/42165

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

5. Chen, Niancao. Programmable Nanomaterials for Detoxification.

Degree: PhD, Bioengineering, 2014, Penn State University

URL: https://etda.libraries.psu.edu/catalog/23701

► Exogenous chemicals (e.g., drugs) and endogenous signaling molecules (e.g., growth factors) are important for the treatment of human diseases and the maintenance of a normal… (more)

▼ Exogenous chemicals (e.g., drugs) and endogenous signaling molecules (e.g., growth factors) are important for the treatment of human diseases and the maintenance of a normal metabolism in the body. However, they can cause severe or fatal toxicity problems when their concentrations in the body exceed certain ranges1–3. To mitigate their toxic effects on the body, a myriad of antidotes have been developed. Of them, nanoparticles (e.g., liposomes) have recently attracted the most attention because nanoparticles can act as a sink to sequester toxic molecules more efficiently 4,5. Despite their promise, most nanoparticles have relatively low affinity in sequestering target molecules and slow sequestration rates. Moreover, currently available nanoparticle antidotes cannot be actively regulated to control their capability of sequestering target molecules. As a result, when nanoparticles are applied to sequester endogenous signaling molecules, these molecules may be over eliminated, which can also cause severe effects or even fatality. Thus, it is important that nanoparticle antidotes provide molecularly controllable target sequestration, which has never been studied before. This dissertation research explores the concept of bidirectional molecular recognition control for the development of an open, programmable nanoscale antidote. This nanoscale antidote can not only sequester target molecules effectively and rapidly, but also release target molecules via molecular interactions on demand. To construct the antidote, DNA oligonucleotides were used as programmable building blocks and affinity ligands (i.e., nucleic acid aptamer) for the synthesis of both linear and branched affinity DNA polymers (DPs). A magnetic nanoparticle was used as a nanoscaffold to support the growth of the DPs on its surface. Each repeating unit of the DP has the capability of target sequestration. The sequestration functionality of this programmable nanoparticle antidote was evaluated by using both a small molecule drug and large molecule protein. This novel antidote was also examined by evaluating its capabilities in mitigating the biological effects of the drug and the protein. Moreover the reversing of target sequestration via molecular regulation was validated. This dissertation has four major chapters. In Chapter 1, current strategies for developing nanoparticle-based antidotes are systematically reviewed. In Chapter 2, the synthesis of affinity DNA polymer-functionalized nanoparticles is introduced. In Chapter 3, the functionalities of the programmable antidote for detoxification is demonstrated in vitro. In Chapter 4, the ability to program the function of the antidote via molecular regulation is validated. The data suggest that this antidote can sequester both small molecules and large proteins. Importantly, this antidote can be programmed via strand displacement to control the molecular sequestration. The success of this study has opened a new avenue for the development of antidotes for safe and effective detoxification of either endogenous…

Subjects/Keywords: Aptamer; Nanoparticle; detoxification

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APA (6^th Edition):

Chen, N. (2014). Programmable Nanomaterials for Detoxification. (Doctoral Dissertation). Penn State University. Retrieved from https://etda.libraries.psu.edu/catalog/23701

Chicago Manual of Style (16^th Edition):

Chen, Niancao. “Programmable Nanomaterials for Detoxification.” 2014. Doctoral Dissertation, Penn State University. Accessed February 19, 2020. https://etda.libraries.psu.edu/catalog/23701.

MLA Handbook (7^th Edition):

Chen, Niancao. “Programmable Nanomaterials for Detoxification.” 2014. Web. 19 Feb 2020.

Vancouver:

Chen N. Programmable Nanomaterials for Detoxification. [Internet] [Doctoral dissertation]. Penn State University; 2014. [cited 2020 Feb 19]. Available from: https://etda.libraries.psu.edu/catalog/23701.

Council of Science Editors:

Chen N. Programmable Nanomaterials for Detoxification. [Doctoral Dissertation]. Penn State University; 2014. Available from: https://etda.libraries.psu.edu/catalog/23701

University of Houston

6. Adhikari, Meena 1979-. Aptamers and Phage as Tools for the Development of Novel and Sensitive Point-of-Care Diagnostics.

Degree: Biology and Biochemistry, Department of, 2014, University of Houston

URL: http://hdl.handle.net/10657/1898

► Immunochromatographic lateral flow assays (LFAs) represent a well-established point-of-care diagnostic analytical method for the primary testing of diverse samples. The sensitivity of conventional LFAs that… (more)

▼ Immunochromatographic lateral flow assays (LFAs) represent a well-established point-of-care diagnostic analytical method for the primary testing of diverse samples. The sensitivity of conventional LFAs that use the standard colored nanoparticles as reporters lags behind the more elaborate laboratory techniques, such as plaque counting, PCR or ELISA. To address this issue, we have introduced an innovative approach that utilizes functionalized M13 bacteriophage nanoparticles as reporters in the lateral flow diagnostic system. M13 phage offers a multitude of binding sites on its major coat protein pVIII for reporter enzymes, and for affinity agents specific for the target of interest. Furthermore we employed SAM-AviTag phage, derivatives of phage M13 in which the N-terminus of the tail protein pIII is replaced by the enzymatically-biotinylatable AviTag peptide (GLNDIFEAQKIEWHE). The lysine residue (K) in the AviTag is a substrate for biotinylation by the E. coli biotin ligase (birA) enzyme. Using streptavidin or Neutravidin, any biotinylated affinity agent can then easily be linked to these enzymatically-biotinylated phage particles. Viral nanoparticles were functionalized with target-specific antibodies and multiple copies of an enzymatic reporter (horseradish peroxidase). These particles were successfully integrated into a lateral-flow immunochromatographic assay detecting MS2 virus, a model for viral pathogens. The limit of detection of the assay was 10⁴ MS2/mL, 1000-fold more sensitive than the conventional gold nanoparticle lateral flow assays, and results could easily be evaluated, even without advanced lab instruments. Aptamers are short, library-selected nucleic acid molecules that can recognize and bind to pre-selected targets with high affinity and selectivity. They have been used as recognition elements in a variety of applications. We screened for DNA aptamers specific to the murine anti-lysozyme antibody, HyHEL-5. During the validation process, however, the originally selected aptamers did not show successful binding. As an alternative, literature DNA aptamers were employed to construct phage displaying aptamers and HRP, which were used as LFA reporters. We describe the first modification of bacteriophage particles with aptamers as bio-recognition elements, and demonstrate their use in ultrasensitive lateral flow assays detecting IgE and PBP2a (Penicillin binding protein) of Staphylococcus aureus. Advisors/Committee Members: Willson, Richard C. (advisor), Fox, George E. (committee member), Gao, Xiaolian (committee member), Williams, Cecilia M. (committee member), Bikram, Malavosklish (committee member).

Subjects/Keywords: Aptamer; Phage; LFA

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APA (6^th Edition):

Adhikari, M. 1. (2014). Aptamers and Phage as Tools for the Development of Novel and Sensitive Point-of-Care Diagnostics. (Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/1898

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Adhikari, Meena 1979-. “Aptamers and Phage as Tools for the Development of Novel and Sensitive Point-of-Care Diagnostics.” 2014. Thesis, University of Houston. Accessed February 19, 2020. http://hdl.handle.net/10657/1898.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Adhikari, Meena 1979-. “Aptamers and Phage as Tools for the Development of Novel and Sensitive Point-of-Care Diagnostics.” 2014. Web. 19 Feb 2020.

Vancouver:

Adhikari M1. Aptamers and Phage as Tools for the Development of Novel and Sensitive Point-of-Care Diagnostics. [Internet] [Thesis]. University of Houston; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10657/1898.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Adhikari M1. Aptamers and Phage as Tools for the Development of Novel and Sensitive Point-of-Care Diagnostics. [Thesis]. University of Houston; 2014. Available from: http://hdl.handle.net/10657/1898

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Victoria University of Wellington

7. Li, Shiwei. Selection and characterisation of single-stranded DNA aptamers for triclosan.

Degree: 2016, Victoria University of Wellington

URL: http://hdl.handle.net/10063/5017

► Triclosan (TCS) is a chlorinated organic compound which, due to its antibacterial properties in vitro, has found widespread usages in many medical and consumer products… (more)

▼ Triclosan (TCS) is a chlorinated organic compound which, due to its antibacterial properties in vitro, has found widespread usages in many medical and consumer products such as textiles, plastics and personal care products. Humans are directly and chronically exposed to TCS via dermal and mucosal contact from the use of TCS-formulated products such as soap and toothpaste. TCS is classified as an environmental contaminant by the European Union Water Framework Directive, whose mandatory goal is to develop new and simple-to-use analytical methodologies capable of measuring low concentrations of TCS and that are suitable for high-throughput detection. Synthetically-derived single-stranded oligonucleotides, also known as aptamers, are superior candidates for the development of sensitive and high-throughput biosensing strategies. Biosensors utilising aptamers as molecular recognition elements have showed great promise in a variety of diagnostic and therapeutic applications, especially for the detection of small molecular weight organic compounds such as TCS. The aim of this thesis was to develop aptamers as new capture reagents for TCS, as the first step towards the development of an alternative, user-friendly, diagnostic technique for monitoring TCS in both environmental and biological samples. The objectives of the thesis were to: [i] produce by in vitro selection procedures, TCS binding single-stranded DNA (ssDNA) aptamers; [ii] characterise the selected aptamers and determine their equilibrium dissociation constant (Kd) values and; [iii] evaluate the applicability of the selected aptamers in a biosensing platform. To achieve these objectives, ssDNA aptamers capable of binding TCS were generated in vitro using a sequential approach known as systematic evolution of ligands by exponential enrichment (SELEX). An affinity column-based SELEX strategy together with a variety of SELEX modifications such as negative and counter selections, real-time amplification and fluorescence quantification were explored for finding TCS specific aptamers. A total of 20 TCS aptamers, ten from 8 rounds of a basic-SELEX procedure, and the other ten from 10 rounds of a revised-SELEX procedure were generated. In general, these aptamers showed acceptable levels of sensitivity and specificity to TCS, and the best binding aptamer demonstrated a Kd value of 378 nM. The Kd value is comparable to published Kd values for compounds that share similar chemical structures to TCS. In addition, a novel fluorescent-based imaging method was developed in this dissertation. The method developed provides an alternative approach for monitoring SELEX progression and has the potential to simplify the way to characterise the binding properties of an aptamer to its cognate target. The utility of this method was compared with commonly used methods such as dot blot and fluorescent binding assays. The performance of the new imaging method was superior to the existing methods in terms of accuracy, simplicity and reproducibility. Furthermore, the best binding TCS… Advisors/Committee Members: McNatty, Kenneth.

Subjects/Keywords: Aptamer; Triclosan; Aptasensor

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APA (6^th Edition):

Li, S. (2016). Selection and characterisation of single-stranded DNA aptamers for triclosan. (Doctoral Dissertation). Victoria University of Wellington. Retrieved from http://hdl.handle.net/10063/5017

Chicago Manual of Style (16^th Edition):

Li, Shiwei. “Selection and characterisation of single-stranded DNA aptamers for triclosan.” 2016. Doctoral Dissertation, Victoria University of Wellington. Accessed February 19, 2020. http://hdl.handle.net/10063/5017.

MLA Handbook (7^th Edition):

Li, Shiwei. “Selection and characterisation of single-stranded DNA aptamers for triclosan.” 2016. Web. 19 Feb 2020.

Vancouver:

Li S. Selection and characterisation of single-stranded DNA aptamers for triclosan. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2016. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10063/5017.

Council of Science Editors:

Li S. Selection and characterisation of single-stranded DNA aptamers for triclosan. [Doctoral Dissertation]. Victoria University of Wellington; 2016. Available from: http://hdl.handle.net/10063/5017

University of Southern California

8. Sutch, Brian Thomas. Computational prediction and analysis of protein-RNA interfaces.

Degree: PhD, Pharmaceutical Sciences, 2010, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/385424/rec/1549

► Protein-RNA complexes play a central role in many biological processes, including translation, mRNA stabilization, ribosome formation, and viral packaging. The investigation of short nucleic acid… (more)

Subjects/Keywords: protein-RNA; interface solvation; aptamer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sutch, B. T. (2010). Computational prediction and analysis of protein-RNA interfaces. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/385424/rec/1549

Chicago Manual of Style (16^th Edition):

Sutch, Brian Thomas. “Computational prediction and analysis of protein-RNA interfaces.” 2010. Doctoral Dissertation, University of Southern California. Accessed February 19, 2020. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/385424/rec/1549.

MLA Handbook (7^th Edition):

Sutch, Brian Thomas. “Computational prediction and analysis of protein-RNA interfaces.” 2010. Web. 19 Feb 2020.

Vancouver:

Sutch BT. Computational prediction and analysis of protein-RNA interfaces. [Internet] [Doctoral dissertation]. University of Southern California; 2010. [cited 2020 Feb 19]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/385424/rec/1549.

Council of Science Editors:

Sutch BT. Computational prediction and analysis of protein-RNA interfaces. [Doctoral Dissertation]. University of Southern California; 2010. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/385424/rec/1549

Cornell University

9. Szeto, Kylan. Development And Characterization Of High-Throughput Methods And Technologies For In Vitro Rna Aptamer Selections .

Degree: 2014, Cornell University

URL: http://hdl.handle.net/1813/37086

► Aptamers are an emerging class of molecules that are valued for their ability to bind with high affinity and specificity to a desired target. These… (more)

▼ Aptamers are an emerging class of molecules that are valued for their ability to bind with high affinity and specificity to a desired target. These DNA or RNA ligands can be synthesized easily in the lab making them much more stable, reproducible, and cost-effective than other affinity reagents such as antibodies. These molecules possess a diverse and versatile set of abilities upon binding, making them useful not only in biotechnology and diagnostics, but also in therapeutics. Aptamers are typically generated through an in vitro process called SELEX (Systematic Evolution of Ligands by EXponential Enrichment). SELEX is an iterative process whereby a library of random sequences is exposed to a target, and bound sequences are selected and amplified making a pool enriched for improved binding over the original library. This process can be repeated until the best binding sequence dominates the pool. In this way, aptamers can be generated to nearly any conceivable target or molecule, overcoming the immunological limitations in generating antibodies. By manipulating the conditions within this selection process, aptamers can also be generated to bind in non-physiological environments, giving them the ability to perform in diverse applications. To help accelerate the discovery of aptamers, we developed a modular microcolumn technology that decreases reagent consumption, while permitting multiplex SELEX, allowing for more sophisticated selection schemes. By characterizing aptamer enrichments for all the available parameters, we have significantly increased the selection efficiency, while illustrating the failures of simple binding theories to non-classical modes of selection. We have also demonstrated the power of high-throughput sequencing for early identification of aptamers before they fully converge. This was used to validate a new method which optimizes selection time over individual selection cycle efficiencies. Surprisingly, our results also show the new method significantly improves selection efficiency, bringing into question some common beliefs derived from SELEX theory. Finally, we scaled our microcolumn technology to an automatable 96-well microplate format, and demonstrated its utility by characterizing and validating specific, non-specific, and background binding behavior of several RNA aptamers. The results reveal binding behaviors that fundamentally limit the performance and sensitivity of aptamer selections. Advisors/Committee Members: Lis, John T (committeeMember), Zipfel, Warren R. (committeeMember), Muller, David Anthony (committeeMember).

Subjects/Keywords: Aptamer; high-throughput; SELEX

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APA (6^th Edition):

Szeto, K. (2014). Development And Characterization Of High-Throughput Methods And Technologies For In Vitro Rna Aptamer Selections . (Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/37086

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Szeto, Kylan. “Development And Characterization Of High-Throughput Methods And Technologies For In Vitro Rna Aptamer Selections .” 2014. Thesis, Cornell University. Accessed February 19, 2020. http://hdl.handle.net/1813/37086.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Szeto, Kylan. “Development And Characterization Of High-Throughput Methods And Technologies For In Vitro Rna Aptamer Selections .” 2014. Web. 19 Feb 2020.

Vancouver:

Szeto K. Development And Characterization Of High-Throughput Methods And Technologies For In Vitro Rna Aptamer Selections . [Internet] [Thesis]. Cornell University; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/1813/37086.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Szeto K. Development And Characterization Of High-Throughput Methods And Technologies For In Vitro Rna Aptamer Selections . [Thesis]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/37086

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

McMaster University

10. Shang, Jieting. MONITORING YEAST tRNA ADSORPTION BY QCM-D: AN OPPORTUNITY FOR OPTIMIZATION OF APTAMER SELECTION CONDITIONS.

Degree: MASc, 2014, McMaster University

URL: http://hdl.handle.net/11375/16365

►

RNA aptamers that bind to a wide range of targets with high affinity and specificity have been identified via the in vitro systematic evolution of… (more)

▼

RNA aptamers that bind to a wide range of targets with high affinity and specificity have been identified via the in vitro systematic evolution of ligands by exponential enrichment (SELEX). However, the process is quite unpredictable due in part to binding that occurs not only on the targets themselves but also on any of the other functional groups, moieties, or surfaces. Recent modelling work has shown that this level of “background binding” is a key parameter in the performance of aptamer selection processes. One strategy to minimize the amount of background binding is to pre-block those possible binding sites with a non-amplifiable nucleic acid molecule, such as yeast tRNA. It is also known that binding buffer conditions have strong effect on the binding affinity of nucleic acids. However, there are no detailed studies and little quantitative information available to guide the design of aptamer selection processes. In this study, the binding ability of yeast tRNA, which has comparable size with most RNA aptamer libraries, on both silicon dioxide and poly (ethylene terephthalate glycol) (PET-G) surfaces was studied using Quartz Crystal Microbalance with Dissipation (QCM-D). Silicon dioxide surface is a commonly used substrate for QCM-D tests on the adsorption behaviour of different nucleic acid. PET-G is a commonly used polymer substrate for the fabrication of microfluidic devices, which are advanced techniques for aptamer selection. The presence of specific divalent cations, for example Mg2+ over Ca2+, in binding buffers greatly enhanced the binding of yeast tRNA on silicon dioxide surfaces and PET-G surfaces. Proper NaCl concentration (100 mM) and MgCl2 concentration (5 mM) is necessary to enhance yeast tRNA binding on both surfaces. Yeast tRNA binding ability on silicon dioxide surfaces show more dependence on binding buffer pH than on PET-G surfaces.

Thesis

Master of Applied Science (MASc)

Advisors/Committee Members: Latulippe, David, Chemical Engineering.

Subjects/Keywords: QCM-D; aptamer; RNA; SELEX

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APA (6^th Edition):

Shang, J. (2014). MONITORING YEAST tRNA ADSORPTION BY QCM-D: AN OPPORTUNITY FOR OPTIMIZATION OF APTAMER SELECTION CONDITIONS. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/16365

Chicago Manual of Style (16^th Edition):

Shang, Jieting. “MONITORING YEAST tRNA ADSORPTION BY QCM-D: AN OPPORTUNITY FOR OPTIMIZATION OF APTAMER SELECTION CONDITIONS.” 2014. Masters Thesis, McMaster University. Accessed February 19, 2020. http://hdl.handle.net/11375/16365.

MLA Handbook (7^th Edition):

Shang, Jieting. “MONITORING YEAST tRNA ADSORPTION BY QCM-D: AN OPPORTUNITY FOR OPTIMIZATION OF APTAMER SELECTION CONDITIONS.” 2014. Web. 19 Feb 2020.

Vancouver:

Shang J. MONITORING YEAST tRNA ADSORPTION BY QCM-D: AN OPPORTUNITY FOR OPTIMIZATION OF APTAMER SELECTION CONDITIONS. [Internet] [Masters thesis]. McMaster University; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/11375/16365.

Council of Science Editors:

Shang J. MONITORING YEAST tRNA ADSORPTION BY QCM-D: AN OPPORTUNITY FOR OPTIMIZATION OF APTAMER SELECTION CONDITIONS. [Masters Thesis]. McMaster University; 2014. Available from: http://hdl.handle.net/11375/16365

University of Ottawa

11. Bushnik, Evan. Partially Robotic Selection of Aptamers to Red Blood Cell Protein Glycophorin A .

Degree: 2018, University of Ottawa

URL: http://hdl.handle.net/10393/38175

► Aptamers are small DNA ligands that have been manually selected to strongly and specifically bind a target of interest. These molecules may prove superior to… (more)

Subjects/Keywords: Aptamer; Glycophorin; Blood; Emulsion

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APA (6^th Edition):

Bushnik, E. (2018). Partially Robotic Selection of Aptamers to Red Blood Cell Protein Glycophorin A . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/38175

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Bushnik, Evan. “Partially Robotic Selection of Aptamers to Red Blood Cell Protein Glycophorin A .” 2018. Thesis, University of Ottawa. Accessed February 19, 2020. http://hdl.handle.net/10393/38175.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Bushnik, Evan. “Partially Robotic Selection of Aptamers to Red Blood Cell Protein Glycophorin A .” 2018. Web. 19 Feb 2020.

Vancouver:

Bushnik E. Partially Robotic Selection of Aptamers to Red Blood Cell Protein Glycophorin A . [Internet] [Thesis]. University of Ottawa; 2018. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10393/38175.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Bushnik E. Partially Robotic Selection of Aptamers to Red Blood Cell Protein Glycophorin A . [Thesis]. University of Ottawa; 2018. Available from: http://hdl.handle.net/10393/38175

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Guelph

12. Van Riesen, Abigail. Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer .

Degree: 2016, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10018

► A number of non-natural nucleic acid monomers were synthesized and employed in a model system in an effort to demonstrate the potential for expanding the… (more)

Subjects/Keywords: aptamer; G-quadruplex; thrombin; fluorescence

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APA (6^th Edition):

Van Riesen, A. (2016). Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer . (Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10018

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Van Riesen, Abigail. “Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer .” 2016. Thesis, University of Guelph. Accessed February 19, 2020. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10018.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Van Riesen, Abigail. “Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer .” 2016. Web. 19 Feb 2020.

Vancouver:

Van Riesen A. Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer . [Internet] [Thesis]. University of Guelph; 2016. [cited 2020 Feb 19]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10018.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Van Riesen A. Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer . [Thesis]. University of Guelph; 2016. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10018

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Guelph

13. Fadock, Kaila. Aryl-Deoxyguanosine Probes: Application in G-Quadruplex Forming Aptamers .

Degree: 2016, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/9869

► Aptamers are laboratory created single-strands of DNA or RNA that have been designed to bind to a specific target with high affinity and specificity, and… (more)

▼ Aptamers are laboratory created single-strands of DNA or RNA that have been designed to bind to a specific target with high affinity and specificity, and are gaining popularity over antibody detection due to their economical and ethical advantages. With recent developments in the field of aptamer technology, the desire for fluorescent probes that can be incorporated within an oligonucleotide strand, without disrupting it's activity, has increased. Addition of an aryl group at the C8 site of deoxyguanosine (dG) affords addition products (adducts) which can have a variety of fluorescence capabilities. These fluorescent nucleosides have been known to be sensitive to their solvent environment, base stacking, and H-bonding interactions, making them ideal candidates for development as fluorescent probes within aptamers. Aside from possessing fluorescence capabilities, the formation of a C8-aryl-dG adduct alters the conformational preference of the nucleoside. The probes are known to prefer the -syn¬-conformation, where rotation about its glycosidic bond minimizes steric interactions with the bulky aromatic group. This conformational preference can be exploited to influence the stability of a folded aptamer, and probe the structural features of the aptamer-target complex. A common folded motif within aptamers is the G-quadruplex (GQ). Insertion of probes within the core structure of the GQ has been fairly limited to date because current probes available are not able to be inserted in the place of a dG base, without disruption of the folded structure. The C8-aryl-dG probes presented in this thesis stabilize the folded GQ when placed within a syn-G, and have been optimized within a duplex to GQ exchange detection platform with thrombin binding aptamer (TBA). The utility of these probes were highlighted with insertion of 8-(2"-thienyl)-dG within the ochratoxin A aptamer to determine its structural properties, as well as probing the structural polymorphism of the human telomeric repeat sequence (HTelo). In order to create a series of probes that could be excited by visible light, further probe development was applied towards the creation of a series of push-pull adducts that contained molecular-rotor light switching abilities. Advisors/Committee Members: Manderville, Richard (advisor).

Subjects/Keywords: oligonucleotides; quadruplex; adduct; deoxyguanosine; aptamer

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APA (6^th Edition):

Fadock, K. (2016). Aryl-Deoxyguanosine Probes: Application in G-Quadruplex Forming Aptamers . (Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/9869

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fadock, Kaila. “Aryl-Deoxyguanosine Probes: Application in G-Quadruplex Forming Aptamers .” 2016. Thesis, University of Guelph. Accessed February 19, 2020. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/9869.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fadock, Kaila. “Aryl-Deoxyguanosine Probes: Application in G-Quadruplex Forming Aptamers .” 2016. Web. 19 Feb 2020.

Vancouver:

Fadock K. Aryl-Deoxyguanosine Probes: Application in G-Quadruplex Forming Aptamers . [Internet] [Thesis]. University of Guelph; 2016. [cited 2020 Feb 19]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/9869.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fadock K. Aryl-Deoxyguanosine Probes: Application in G-Quadruplex Forming Aptamers . [Thesis]. University of Guelph; 2016. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/9869

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Texas State University – San Marcos

14. Navarro, Renato S. Click-Chemistry Based Molecularly Responsive Hydrogel as Biodegradable Scaffolds for 3-D Cell Culture: Design and Preparation of Building Blocks.

Degree: MS, Chemistry, 2014, Texas State University – San Marcos

URL: https://digital.library.txstate.edu/handle/10877/6898

► According to the American Cancer Society, every year over one million Americans are diagnosed with one of the recognized forms of cancer. Cancer metastasis is… (more)

▼ According to the American Cancer Society, every year over one million Americans are diagnosed with one of the recognized forms of cancer. Cancer metastasis is associated with poor patient prognosis. In order to better understand how cancer grows and metastasizes, researchers are interested in the development of platforms that could model the environment of tumor tissue and enable the study of the effect of cancer cell-secreted molecules on cell replication, extracellular matrix remodeling, and cell migration leading to metastasis. Due to their tissue-like properties, hydrogels have the ability to serve as such model systems by providing a three-dimensional scaffold in which cancerous cells could be cultured and studied. Hydrogels are formed from physically or chemically cross-linked hydrophilic polymers that form insoluble networks. Due to their high water content, hydrogels have mechanical properties that are similar to those of tissue; therefore, hydrogels could become ideal platforms for the study of cell growth and migration. The long-term goal of this work is to develop a hydrogel system that is molecularly responsive and can be synthesized at physiological conditions that could be used as a model the study of cancer cell growth. In order to achieve this goal, in this work we focused on: (1) the development of an aptamer complex to be used as crosslinker within the hydrogel network that is responsive towards the cancer cell-secreted protein vascular endothelium growth factor (VEGF), (2) the development of methods for the synthesis of hydrogels under mild conditions via copper-free click chemistry, and (3) the integration of cell adhesive properties to the hydrogels through a cyclo-Arginine-Glycine-Aspartic Acid (cRGD) peptide that mimics fibrin and collagen, some of the most abundant protein components of the extracellular matrix. The aptamer complex was designed to be able to hybridize a physiological conditions but denature in the presence of the molecular target VEGF, yielding a system that is responsive and degradable. Through the use of copper-free click chemistry, the hydrogels could be synthesized in the absence of toxins like free radicals, metals, and ultraviolet light that are typically used in polymerization reactions but that have deleterious effects on cells. The bioorthogonal reaction between azide and dibenzylcyclooctyne utilized in the copper-free click chemistry reaction between azide and dibenzylcyclooctyne utilized in the copper-free click chemistry reaction is able to rapidly link polymeric precursors, thus providing a method for immediate the encapsulation of cancer cells within the hydrogel scaffold. The encapsulated cells are then able to interact with the mimicry peptide cRGD and signal the cells to begin growing and proliferating. In doing so, a hydrogel that is molecular responsive, nontoxic, and capable of encapsulating cells is fashioned in order to serve as three-dimensional platform for their study. Chapter 1 provides a background on the various concepts on which the proposed… Advisors/Committee Members: Betancourt, Tania (advisor), Corina, Maeder (committee member), Brittain, William (committee member).

Subjects/Keywords: Biomaterials; Cell culture; Aptamer

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APA (6^th Edition):

Navarro, R. S. (2014). Click-Chemistry Based Molecularly Responsive Hydrogel as Biodegradable Scaffolds for 3-D Cell Culture: Design and Preparation of Building Blocks. (Masters Thesis). Texas State University – San Marcos. Retrieved from https://digital.library.txstate.edu/handle/10877/6898

Chicago Manual of Style (16^th Edition):

Navarro, Renato S. “Click-Chemistry Based Molecularly Responsive Hydrogel as Biodegradable Scaffolds for 3-D Cell Culture: Design and Preparation of Building Blocks.” 2014. Masters Thesis, Texas State University – San Marcos. Accessed February 19, 2020. https://digital.library.txstate.edu/handle/10877/6898.

MLA Handbook (7^th Edition):

Navarro, Renato S. “Click-Chemistry Based Molecularly Responsive Hydrogel as Biodegradable Scaffolds for 3-D Cell Culture: Design and Preparation of Building Blocks.” 2014. Web. 19 Feb 2020.

Vancouver:

Navarro RS. Click-Chemistry Based Molecularly Responsive Hydrogel as Biodegradable Scaffolds for 3-D Cell Culture: Design and Preparation of Building Blocks. [Internet] [Masters thesis]. Texas State University – San Marcos; 2014. [cited 2020 Feb 19]. Available from: https://digital.library.txstate.edu/handle/10877/6898.

Council of Science Editors:

Navarro RS. Click-Chemistry Based Molecularly Responsive Hydrogel as Biodegradable Scaffolds for 3-D Cell Culture: Design and Preparation of Building Blocks. [Masters Thesis]. Texas State University – San Marcos; 2014. Available from: https://digital.library.txstate.edu/handle/10877/6898

University of Arizona

15. Li, Zhen. POROUS PHOSPHOLIPID NANOSHELL PROTECTED APTAMER SENSOR FOR URINE MERCURY DETECTION .

Degree: 2010, University of Arizona

URL: http://hdl.handle.net/10150/193450

► Mercury exposure has been related to neurological diseases and poisoning. Quantification of mercury in biological fluids, such as serum or urine is an important diagnostic… (more)

Subjects/Keywords: aptamer; mercury; phospholipids; sensor; vesicles

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APA (6^th Edition):

Li, Z. (2010). POROUS PHOSPHOLIPID NANOSHELL PROTECTED APTAMER SENSOR FOR URINE MERCURY DETECTION . (Masters Thesis). University of Arizona. Retrieved from http://hdl.handle.net/10150/193450

Chicago Manual of Style (16^th Edition):

Li, Zhen. “POROUS PHOSPHOLIPID NANOSHELL PROTECTED APTAMER SENSOR FOR URINE MERCURY DETECTION .” 2010. Masters Thesis, University of Arizona. Accessed February 19, 2020. http://hdl.handle.net/10150/193450.

MLA Handbook (7^th Edition):

Li, Zhen. “POROUS PHOSPHOLIPID NANOSHELL PROTECTED APTAMER SENSOR FOR URINE MERCURY DETECTION .” 2010. Web. 19 Feb 2020.

Vancouver:

Li Z. POROUS PHOSPHOLIPID NANOSHELL PROTECTED APTAMER SENSOR FOR URINE MERCURY DETECTION . [Internet] [Masters thesis]. University of Arizona; 2010. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10150/193450.

Council of Science Editors:

Li Z. POROUS PHOSPHOLIPID NANOSHELL PROTECTED APTAMER SENSOR FOR URINE MERCURY DETECTION . [Masters Thesis]. University of Arizona; 2010. Available from: http://hdl.handle.net/10150/193450

Georgia Tech

16. Dunaway, Adam Blake. Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets.

Degree: MS, Materials Science and Engineering, 2014, Georgia Tech

URL: http://hdl.handle.net/1853/54310

► Deoxyribonucleic acid (DNA) aptamers are oligonucleotides with high specificity and affinity for non-nucleotide targets ranging from molecular species to cellular proteins. Their high affinity, rapid… (more)

Subjects/Keywords: DNA; Aptamer; Colloid; VEGF; Ampicillin

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APA (6^th Edition):

Dunaway, A. B. (2014). Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/54310

Chicago Manual of Style (16^th Edition):

Dunaway, Adam Blake. “Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets.” 2014. Masters Thesis, Georgia Tech. Accessed February 19, 2020. http://hdl.handle.net/1853/54310.

MLA Handbook (7^th Edition):

Dunaway, Adam Blake. “Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets.” 2014. Web. 19 Feb 2020.

Vancouver:

Dunaway AB. Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets. [Internet] [Masters thesis]. Georgia Tech; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/1853/54310.

Council of Science Editors:

Dunaway AB. Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets. [Masters Thesis]. Georgia Tech; 2014. Available from: http://hdl.handle.net/1853/54310

17. Ray, Judhajeet. Aptamer sensors for live-cell imaging of Pol II promoter activity.

Degree: 2014, Iowa State University

URL: https://lib.dr.iastate.edu/etd/14283

► Development of multicellular organisms depends on spatial and temporal expression of certain genes. The spatio-temporal control is achieved by several factors involved in the key… (more)

Subjects/Keywords: Biochemistry; Aptamer; Imaging; Transcription; Biochemistry

11 more images…

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APA (6^th Edition):

Ray, J. (2014). Aptamer sensors for live-cell imaging of Pol II promoter activity. (Thesis). Iowa State University. Retrieved from https://lib.dr.iastate.edu/etd/14283

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ray, Judhajeet. “Aptamer sensors for live-cell imaging of Pol II promoter activity.” 2014. Thesis, Iowa State University. Accessed February 19, 2020. https://lib.dr.iastate.edu/etd/14283.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ray, Judhajeet. “Aptamer sensors for live-cell imaging of Pol II promoter activity.” 2014. Web. 19 Feb 2020.

Vancouver:

Ray J. Aptamer sensors for live-cell imaging of Pol II promoter activity. [Internet] [Thesis]. Iowa State University; 2014. [cited 2020 Feb 19]. Available from: https://lib.dr.iastate.edu/etd/14283.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ray J. Aptamer sensors for live-cell imaging of Pol II promoter activity. [Thesis]. Iowa State University; 2014. Available from: https://lib.dr.iastate.edu/etd/14283

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Technology, Sydney

18. Wood, MA. A novel approach to latent fingermark detection using aptamer-based reagents.

Degree: 2014, University of Technology, Sydney

URL: http://hdl.handle.net/10453/24200

► Research into latent fingermark detection and visualisation has taken many paths over the years as researchers and practitioners explore numerous methods to improve existing reagents.… (more)

▼ Research into latent fingermark detection and visualisation has taken many paths over the years as researchers and practitioners explore numerous methods to improve existing reagents. The majority of past research has resulted in providing small, incremental improvements to existing techniques. Currently, some researchers have opted to seek more transformational improvements in detection sensitivity, selectivity and visualisation. One such area being investigated is utilising immunology to target proteins, amino acids and drug metabolites in the latent fingermark deposit. Research to date has indicated that antibodies have great potential in providing these transformational improvements due to their ability to bind to certain fingermark components with high sensitivity and selectivity. Following on from the antibody research, aptamers have been highlighted as the next potential immunogenic technique for several reasons, including reduced health and safety issues, lower cost, greater sensitivity and selectivity, and ease of design and versatility. Aptamers are specifically selected oligonucleotides comprised of either ribonucleic acid (RNA) or single-stranded deoxyribonucleic acid (ssDNA). Due to the selection strategies employed, aptamers can be designed to target most molecules and bind to them with detection limits in the sub-micromolar to nanomolar ranges. Although aptamers have been successfully used in a variety of highly sensitive and selective detection devices, they have not been investigated for use in the detection and visualisation of latent fingermarks prior to this project. Initially, this project focussed on aptamers targeting amino acids as a means of visualising latent fingermarks. However, it was found that strong, non-specific interactions occurred with both the aptamer and the fluorescent tag, resulting in a lack of success with this approach. In order to address these issues, aptamers selected to the protein lysozyme were used on fingermarks placed on both PVDF and plain white copier paper. Lysozyme was selected as it was found to be a component in human sweat, while aptamers selected to lysozyme, with binding affinities in the nanomolar range were available. It was found that the aptamer-based reagents possessed high levels of sensitivity with the clear detection of lysozyme at very low concentrations (1 ng). Latent fingermarks from various donors were able to be detected on both substrates, with primary and secondary level detail being clearly visible. Results, however, were very inconsistent, with marks older than a couple of days being difficult to detect. This was found to be due to the degradation of lysozyme in the latent fingermark. Unfortunately, aptamers to other, possibly more suitable, fingermark components that would circumvent this problem were not available for this project. Despite the difficulties encountered, this project has, for the first time, demonstrated the potential of detecting and visualising latent fingermarks with an aptamer-based reagent. The study has laid the…

Subjects/Keywords: Fingermark.; Forensics.; Aptamer.; Detection.; Identification.

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APA (6^th Edition):

Wood, M. (2014). A novel approach to latent fingermark detection using aptamer-based reagents. (Thesis). University of Technology, Sydney. Retrieved from http://hdl.handle.net/10453/24200

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wood, MA. “A novel approach to latent fingermark detection using aptamer-based reagents.” 2014. Thesis, University of Technology, Sydney. Accessed February 19, 2020. http://hdl.handle.net/10453/24200.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wood, MA. “A novel approach to latent fingermark detection using aptamer-based reagents.” 2014. Web. 19 Feb 2020.

Vancouver:

Wood M. A novel approach to latent fingermark detection using aptamer-based reagents. [Internet] [Thesis]. University of Technology, Sydney; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10453/24200.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wood M. A novel approach to latent fingermark detection using aptamer-based reagents. [Thesis]. University of Technology, Sydney; 2014. Available from: http://hdl.handle.net/10453/24200

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Boise State University

19. Burden, Steven J. The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals.

Degree: 2019, Boise State University

URL: https://scholarworks.boisestate.edu/td/1627

► Fluorogenic aptamers are emerging as useful molecular tools to track RNA molecules in cells and as a platform for fluorescent biosensors. The recently developed RNA… (more)

Subjects/Keywords: RNA; aptamer; fluorogenic aptamer; Other Biochemistry, Biophysics, and Structural Biology

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APA (6^th Edition):

Burden, S. J. (2019). The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals. (Thesis). Boise State University. Retrieved from https://scholarworks.boisestate.edu/td/1627

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Burden, Steven J. “The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals.” 2019. Thesis, Boise State University. Accessed February 19, 2020. https://scholarworks.boisestate.edu/td/1627.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Burden, Steven J. “The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals.” 2019. Web. 19 Feb 2020.

Vancouver:

Burden SJ. The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals. [Internet] [Thesis]. Boise State University; 2019. [cited 2020 Feb 19]. Available from: https://scholarworks.boisestate.edu/td/1627.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Burden SJ. The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals. [Thesis]. Boise State University; 2019. Available from: https://scholarworks.boisestate.edu/td/1627

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Edinburgh

20. Kasturiarachchi, Jagath Chandana. Bio-oligomers as antibacterial agents and strategies for bacterial detection.

Degree: PhD, 2014, University of Edinburgh

URL: http://hdl.handle.net/1842/10030

► In this thesis I examined the potential of Bio-Oligomers such as peptoids, peptides and aptamers, as therapeutic and diagnostic entities. Therapeutic Bio-Oligomers; A series of… (more)

▼ In this thesis I examined the potential of Bio-Oligomers such as peptoids, peptides and aptamers, as therapeutic and diagnostic entities. Therapeutic Bio-Oligomers; A series of peptoid analogs have been designed and synthesised using solid phase synthesis. These peptoids have been subjected to biological evaluation to determine structure-activity relationships that define their antimicrobial activity. In total 13 peptoids were synthesised. Out of 13 different peptoids, only one peptoid called Tosyl-Octyl-Peptoid (TOP) demonstrated significant broad-spectrum bactericidal activity. TOP kills bacteria under non-dividing and dividing conditions. The Minimum Inhibitory Concentrations (MIC) values of TOP for S. epidermidis, E. coli and Klebsiella were 20 μM, whereas Methicillin-resistant Staphylococcus aureus (MRSA) and Methicillin-sensitive Staphylococcus aureus (MSSA) were 40 μM. The highest MIC values were observed for Pseudomonas aeruginosa (PAO1) at 80 μM. The selectivity ratio (SR) or Therapeutic index (TI) was calculated, by dividing the 10% haemolysis activity (5 mM) by the median of the MIC (50 μM) yielding a TI for TOP as 100. This TI is well above previously reported peptidomimetics TI of around 20. TOP demonstrates selective bacterial killing in co-culture systems and intracellular bacterial killing activity. Diagnostic Bio-Oligomers; In the second part of my thesis, I investigated aptamer and peptide-based molecular probes to detect MRSA. As well as screening aptamers and peptide probes against whole MRSA, I over-expressed and purified PBP2A protein. This purified protein was used as a target for aptamer and peptide probes to detect MRSA. Two different aptamer libraries were initially screened for utility. In-vitro conditions for SELEX were optimised. Biopanning with a phage derived peptides was also performed. Target sequences for both methods were identified and chemically synthesised. Evaluation of fluorescently labelled sequences with flow cytometry and confocal imaging showed no specificity for MRSA detection with either method. The Bio-Oligomers and the in-vitro selection methodology require further refinement to improve diagnostic utility.

Subjects/Keywords: 616.9; antibacterial drugs; imaging; aptamer; peptide; peptoid

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APA (6^th Edition):

Kasturiarachchi, J. C. (2014). Bio-oligomers as antibacterial agents and strategies for bacterial detection. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/10030

Chicago Manual of Style (16^th Edition):

Kasturiarachchi, Jagath Chandana. “Bio-oligomers as antibacterial agents and strategies for bacterial detection.” 2014. Doctoral Dissertation, University of Edinburgh. Accessed February 19, 2020. http://hdl.handle.net/1842/10030.

MLA Handbook (7^th Edition):

Kasturiarachchi, Jagath Chandana. “Bio-oligomers as antibacterial agents and strategies for bacterial detection.” 2014. Web. 19 Feb 2020.

Vancouver:

Kasturiarachchi JC. Bio-oligomers as antibacterial agents and strategies for bacterial detection. [Internet] [Doctoral dissertation]. University of Edinburgh; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/1842/10030.

Council of Science Editors:

Kasturiarachchi JC. Bio-oligomers as antibacterial agents and strategies for bacterial detection. [Doctoral Dissertation]. University of Edinburgh; 2014. Available from: http://hdl.handle.net/1842/10030

University of Louisville

21. Choi, Enid W. Tumor-targeting aptamers for the treatment of prostate cancer.

Degree: PhD, 2011, University of Louisville

URL: 10.18297/etd/245 ; https://ir.library.louisville.edu/etd/245

► Prostate cancer is the most common type diagnosed among men in the United States. Random oligodeoxynucleotide (ODN) libraries are used to generate DNA aptamers by… (more)

Subjects/Keywords: Aptamer; Cancer stem cell; Chemotherapy; Prostate cancer

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APA (6^th Edition):

Choi, E. W. (2011). Tumor-targeting aptamers for the treatment of prostate cancer. (Doctoral Dissertation). University of Louisville. Retrieved from 10.18297/etd/245 ; https://ir.library.louisville.edu/etd/245

Chicago Manual of Style (16^th Edition):

Choi, Enid W. “Tumor-targeting aptamers for the treatment of prostate cancer.” 2011. Doctoral Dissertation, University of Louisville. Accessed February 19, 2020. 10.18297/etd/245 ; https://ir.library.louisville.edu/etd/245.

MLA Handbook (7^th Edition):

Choi, Enid W. “Tumor-targeting aptamers for the treatment of prostate cancer.” 2011. Web. 19 Feb 2020.

Vancouver:

Choi EW. Tumor-targeting aptamers for the treatment of prostate cancer. [Internet] [Doctoral dissertation]. University of Louisville; 2011. [cited 2020 Feb 19]. Available from: 10.18297/etd/245 ; https://ir.library.louisville.edu/etd/245.

Council of Science Editors:

Choi EW. Tumor-targeting aptamers for the treatment of prostate cancer. [Doctoral Dissertation]. University of Louisville; 2011. Available from: 10.18297/etd/245 ; https://ir.library.louisville.edu/etd/245

University of Minnesota

22. Brumann Clemente, Ana Paula. DNA Nanotechnology: Developing and Analyzing a New Tool for Sensing Allergens.

Degree: MS, Food Science, 2016, University of Minnesota

URL: http://hdl.handle.net/11299/190614

► Allergens are a major problem especially concerning public health and economy. There are more than 150 foods that can initiate allergic reactions, these reactions can… (more)

▼ Allergens are a major problem especially concerning public health and economy. There are more than 150 foods that can initiate allergic reactions, these reactions can elicit a mild response or a dangerous life threatening condition and in some extreme cases death. Milk and milk ingredients are one of the 8 foods that are responsible for about 90% of all food related allergic reactions. Food containing undeclared allergens in the label are misbranded and adulterated, and in accordance with the FSMA law must be recalled. It is estimated that the food industry can spend up to $10 millions dollars in direct costs from a recall. It was hypothesized that aptamer-amphiphile, a synthesis product from ssDNA aptamer and a hydrocarbon tale, in conjunction with liquid-crystal could be used as a sensor for detection of -lactoglobulin, an allergenic whey protein. The sensor was based on the self-alignment properties of liquid crystals based on the environment that it is exposed and on the capabilities of DNA aptamers to specific binding to targets. Results of this work showed that the aptamer-amphiphile of choice, amphiphile synthesized without a spacer between the DNA head group and the hydrocabon tail, had a great affinity to target, Kd= 45 ± 1.68 nM. In addition to it, it was possible to demonstrate that the interaction of the aptamer-amphiphile with the target protein, -lactoglobulin, using the sensor assembly resulted in images that can be easily identified under the polarizing microscope, sensor exposed to the aptamer-amphiphile alone gave a black image, once the protein was introduced the image was bright. Furthermore, the sensor developed has a limit of detection of 18.4ng of -lactoglobulin. It was also able to selectively identify the target protein, since when aptamer-amphiphile supported on the sensor was exposed to a random protein the image did not change as it did with -lactoglobulin. In conclusion, this sensor developed proves the concept that aptamer-amphiphile and the liquid crystal can potentially be used as a sensor technique in food plants to detect allergens in food contact surfaces.

Subjects/Keywords: Allergens; Aptamer; Liquid Crystal; Milk allergen

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APA (6^th Edition):

Brumann Clemente, A. P. (2016). DNA Nanotechnology: Developing and Analyzing a New Tool for Sensing Allergens. (Masters Thesis). University of Minnesota. Retrieved from http://hdl.handle.net/11299/190614

Chicago Manual of Style (16^th Edition):

Brumann Clemente, Ana Paula. “DNA Nanotechnology: Developing and Analyzing a New Tool for Sensing Allergens.” 2016. Masters Thesis, University of Minnesota. Accessed February 19, 2020. http://hdl.handle.net/11299/190614.

MLA Handbook (7^th Edition):

Brumann Clemente, Ana Paula. “DNA Nanotechnology: Developing and Analyzing a New Tool for Sensing Allergens.” 2016. Web. 19 Feb 2020.

Vancouver:

Brumann Clemente AP. DNA Nanotechnology: Developing and Analyzing a New Tool for Sensing Allergens. [Internet] [Masters thesis]. University of Minnesota; 2016. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/11299/190614.

Council of Science Editors:

Brumann Clemente AP. DNA Nanotechnology: Developing and Analyzing a New Tool for Sensing Allergens. [Masters Thesis]. University of Minnesota; 2016. Available from: http://hdl.handle.net/11299/190614

Louisiana State University

23. Boyapati, Vamsi Krishna. Study of complex RNA function modulated by small molecules: the development of RNA directed small molecule library and probing the S-adenosyl methionine discrimination between on and off conformational states of the SAM-I riboswitch.

Degree: PhD, 2011, Louisiana State University

URL: etd-11082011-165455 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2172

► RNA recently remained unexploited and is now drawing interest as a potential drug target. The methodology and available drug libraries for RNA targeting/screening are in… (more)

▼ RNA recently remained unexploited and is now drawing interest as a potential drug target. The methodology and available drug libraries for RNA targeting/screening are in rudimentary stages. The interactions made by ligands with RNA can be explored for RNA based drug development. The dissertation is composed of 4 chapters. The first chapter focuses on the structural features of RNA and the attempts made to target RNA previously. The second chapter focuses on the development of a small molecule library enriched with substructures derived from RNA binding ligands. For this study a fragment-based approach (fragment based approach is detailed in chapter 2) is used in order to accommodate the conformational flexibility of RNA. The library molecules are used for screening against suitable RNA targets using NMR. We identified at least 5 ligands out of which 2 are novel ligands binding to the ribosomal 16s rRNA. The third chapter is focused on the role of small molecules in inducing conformational changes in an RNA genetic regulatory element called the S-Adenosyl methionine (SAM) SAM-I riboswitch. The mechanistic features of the SAM-I riboswitch to understand the basis for specificity and discrimination and its gene regulation mechanism are reported. To address the conformational dynamics Bacillus subtilis and Thermoanearobacter tencongenesis SAM-I riboswitches in response to SAM binding several conformer mimics are designed, synthesized and characterized using NMR, equilibrium dialysis, and inline probing. The study shows that apart from the conserved residues of the binding pocket, residues downstream of the binding pocket are involved in detecting SAM and assist the binding of SAM to the riboswitch with weak affinity. Our data highlights the capacity of a so-called antiterminator helix from the expression platform to assist the formation of a partial P1 helix of the aptamer domain. A stable P1 is involved in recognition and tight binding of SAM. Our in vitro experiments suggest that the riboswitch could switch from an unbound conformation to tightly SAM bound structure through weakly binding intermediate structures in the presence of the small molecule SAM. The future directions are included in the fourth chapter along with the conclusions.

Subjects/Keywords: RIBOSWITCH; SAM; AT; APTAMER; SMALL MOLECULE

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APA (6^th Edition):

Boyapati, V. K. (2011). Study of complex RNA function modulated by small molecules: the development of RNA directed small molecule library and probing the S-adenosyl methionine discrimination between on and off conformational states of the SAM-I riboswitch. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-11082011-165455 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2172

Chicago Manual of Style (16^th Edition):

Boyapati, Vamsi Krishna. “Study of complex RNA function modulated by small molecules: the development of RNA directed small molecule library and probing the S-adenosyl methionine discrimination between on and off conformational states of the SAM-I riboswitch.” 2011. Doctoral Dissertation, Louisiana State University. Accessed February 19, 2020. etd-11082011-165455 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2172.

MLA Handbook (7^th Edition):

Boyapati, Vamsi Krishna. “Study of complex RNA function modulated by small molecules: the development of RNA directed small molecule library and probing the S-adenosyl methionine discrimination between on and off conformational states of the SAM-I riboswitch.” 2011. Web. 19 Feb 2020.

Vancouver:

Boyapati VK. Study of complex RNA function modulated by small molecules: the development of RNA directed small molecule library and probing the S-adenosyl methionine discrimination between on and off conformational states of the SAM-I riboswitch. [Internet] [Doctoral dissertation]. Louisiana State University; 2011. [cited 2020 Feb 19]. Available from: etd-11082011-165455 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2172.

Council of Science Editors:

Boyapati VK. Study of complex RNA function modulated by small molecules: the development of RNA directed small molecule library and probing the S-adenosyl methionine discrimination between on and off conformational states of the SAM-I riboswitch. [Doctoral Dissertation]. Louisiana State University; 2011. Available from: etd-11082011-165455 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2172

Louisiana State University

24. Bai, Wei. Bio-imprinted hydro-gels (BIGS) for protein and virus detection.

Degree: PhD, Chemistry, 2014, Louisiana State University

URL: etd-04102014-101643 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3795

► Detection of bio-markers at low concentration is becoming a more and more important topic in scientific research due to its importance in applications crucially related… (more)

Subjects/Keywords: hydrogel; aptamer; protein; virus; molecular recognition

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APA (6^th Edition):

Bai, W. (2014). Bio-imprinted hydro-gels (BIGS) for protein and virus detection. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-04102014-101643 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3795

Chicago Manual of Style (16^th Edition):

Bai, Wei. “Bio-imprinted hydro-gels (BIGS) for protein and virus detection.” 2014. Doctoral Dissertation, Louisiana State University. Accessed February 19, 2020. etd-04102014-101643 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3795.

MLA Handbook (7^th Edition):

Bai, Wei. “Bio-imprinted hydro-gels (BIGS) for protein and virus detection.” 2014. Web. 19 Feb 2020.

Vancouver:

Bai W. Bio-imprinted hydro-gels (BIGS) for protein and virus detection. [Internet] [Doctoral dissertation]. Louisiana State University; 2014. [cited 2020 Feb 19]. Available from: etd-04102014-101643 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3795.

Council of Science Editors:

Bai W. Bio-imprinted hydro-gels (BIGS) for protein and virus detection. [Doctoral Dissertation]. Louisiana State University; 2014. Available from: etd-04102014-101643 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3795

University of California – Berkeley

25. Cho, Hansang. Biologically-inspired Microfluidic Platforms and Aptamer-based Nanobiosensors.

Degree: Bioengineering, 2010, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/23684207

► Recent advances in micro/nano- technologies have shown high potentials in the field of quantitative biology, biomedical science, and analytical chemistry. However, micro/nano fluidics still requires… (more)

▼ Recent advances in micro/nano- technologies have shown high potentials in the field of quantitative biology, biomedical science, and analytical chemistry. However, micro/nano fluidics still requires multi-layered structures, complex plumbing/tubing, and external equipments for large-scale applications and nanotechnology-based sensors demand high cost. Interestingly, nature has much simpler and more effective solutions. The goal of this dissertation is to develop novel microfluidic platforms and nanobiosensors inspired by biological systems.In this dissertation, I report the development of a biologically inspired bidirectional fluidic diode motivated by the xylem pores, which allows designing a functional large-scale microfluidic circuit and autonomous fluidic controls without any delegate efforts on fluid regulation. The biologically inspired bidirectional fluidic diode requires only a single-layered structure and a single pressure source to regulate flow in both directions through the entire platform. The operational conditions are precisely estimated based on the fully developed analytical model, which considers the hysteresis of contact angles and effects of fabrication limitations. To demonstrate its many possible applications, I show large-scale, spontaneous droplet-patterning and colonized cell-patterning programmed with the uni- and bi-directional fluidic diodes in the microfludic platform. In addition, inspired by target recognition in nature, an aptamer-based nanoplasmonic sensor, `aptasensor' is presented by detecting a coagulation protein, human α-thrombin. Also, I present an aptasensor targeting vascular endothelial growth factor-165 (VEGF165), a predominant and effective cancer biomarker for the diagnostics of various solid cancers. The integration of an aptasensor into a microfluidic platform is demonstrated by applying the VEGF165 aptasensor to detect secreted VEGF165 from breast cancer cells cultured in a microfluidic platform.I envision that elucidation of mechanisms underlying in biological systems will inspire to create new technologies for the application to precision biology, biotechnology, and medicine. Furthermore, the developed biologically inspired engineering will provide physical insights, analytical models, and useful tools for the better understanding of biological systems.

Subjects/Keywords: Biomedical engineering; aptamer; bioinspiration; microfluidics; plasmonics; sensor

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APA (6^th Edition):

Cho, H. (2010). Biologically-inspired Microfluidic Platforms and Aptamer-based Nanobiosensors. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/23684207

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cho, Hansang. “Biologically-inspired Microfluidic Platforms and Aptamer-based Nanobiosensors.” 2010. Thesis, University of California – Berkeley. Accessed February 19, 2020. http://www.escholarship.org/uc/item/23684207.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cho, Hansang. “Biologically-inspired Microfluidic Platforms and Aptamer-based Nanobiosensors.” 2010. Web. 19 Feb 2020.

Vancouver:

Cho H. Biologically-inspired Microfluidic Platforms and Aptamer-based Nanobiosensors. [Internet] [Thesis]. University of California – Berkeley; 2010. [cited 2020 Feb 19]. Available from: http://www.escholarship.org/uc/item/23684207.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cho H. Biologically-inspired Microfluidic Platforms and Aptamer-based Nanobiosensors. [Thesis]. University of California – Berkeley; 2010. Available from: http://www.escholarship.org/uc/item/23684207

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

26. Fomo, Gertrude. Ionophoric and aptameric recognition-modulated electroactive polyaniline films for the determination of tetrodotoxin .

Degree: 2014, University of the Western Cape

URL: http://hdl.handle.net/11394/4340

► Tetrodotoxin (TTX) is a nonpeptidic neurotoxin with a high rate of food poisoning mortality (60%) that has been associated with the consumption of diets from… (more)

▼ Tetrodotoxin (TTX) is a nonpeptidic neurotoxin with a high rate of food poisoning mortality (60%) that has been associated with the consumption of diets from puffer fish and mud snails harbouring TTX-producing bacteria. As this neurotoxin has no known antidote and could not be mitigated by cooking, the only way for safety appears to be the detection of TTX-contaminated fishes at the points of harvest and control. The overall aim of this study was to develop amperometric and impedimetric sensors for TTX based on ionophores and aptamer immobilised on the modified conducting electroactive polyaniline (PANI)/electrode. The undoped polyaniline and poly(4-styrenesulfonic acid) (PSSA) doped electroactive polyanilines were prepared in perchloric acid/acetonitrile and phosphoric acid respectively by electrochemical oxidative polymerisation. Two types of electropolymerisation were applied to prepare the neutral and p-doped PANI−PSSA films composites. The dynamic electroinactivity of TTX was studied which revealed that TTX is not electrochemically active on bare Au, GC, Pt, PG, Ni, Ti and BDD (Boron dopeddiamond) electrodes in acetate buffer pH 4.8. Using ion transfer voltammetry and UV-Vis analysis, the complexation of TTX with two neutral ionophores (sodium ionophore X (NaX) and dibenzo-18-crown6 (B18C6)) was investigated. The cyclic voltammograms (CVs) recorded from ion transfer voltammetry presented no redox peak and no increasing/decreasing current was observed which indicates that no TTX ions transfer from the liquid to the organic phase. In addition, the absorption spectra of the mixture of TTX/NaX and TTX/B18C6 presented the same absorption bands recorded for NaX and B18C6 respectively. Three absorptions bands at 250.4, 278.3, and 370.6 nm for NaX and two at 222.03 and 274.10 nm for B18C6 were observed before and after mixing TTX with NaX and TTX with B18C6 separately. No chemical reaction occurred between the TTX and both ionophores, therefore, sodium ionophore X and dibenzo-18-crown-6 did not form a complex with TTX. Thus, TTX ion sensor cannot be developed based on these two neutral compounds. The electrodynamics of the PANI and PANI−PSSA films electropolymerised on the bare precious metal electrodes were also investigated through various electrochemical techniques. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) studies in sodium phosphate (SPB) and acetate (OAc) buffer revealed that both neutral and p-doped films synthesized were thin (thickness L < 5 nm in acetate buffer and L < 10 nm in sodium phosphate buffer) film polymers. Advisors/Committee Members: Iwuoha, Emmanuel (advisor), Waryo, Tesfaye (advisor).

Subjects/Keywords: Aptasensor; Tetrodotoxin-aptamer; Tetrodotoxin; Ion transfer voltammetry

11 more images…

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APA (6^th Edition):

Fomo, G. (2014). Ionophoric and aptameric recognition-modulated electroactive polyaniline films for the determination of tetrodotoxin . (Thesis). University of the Western Cape. Retrieved from http://hdl.handle.net/11394/4340

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fomo, Gertrude. “Ionophoric and aptameric recognition-modulated electroactive polyaniline films for the determination of tetrodotoxin .” 2014. Thesis, University of the Western Cape. Accessed February 19, 2020. http://hdl.handle.net/11394/4340.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fomo, Gertrude. “Ionophoric and aptameric recognition-modulated electroactive polyaniline films for the determination of tetrodotoxin .” 2014. Web. 19 Feb 2020.

Vancouver:

Fomo G. Ionophoric and aptameric recognition-modulated electroactive polyaniline films for the determination of tetrodotoxin . [Internet] [Thesis]. University of the Western Cape; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/11394/4340.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fomo G. Ionophoric and aptameric recognition-modulated electroactive polyaniline films for the determination of tetrodotoxin . [Thesis]. University of the Western Cape; 2014. Available from: http://hdl.handle.net/11394/4340

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

NSYSU

27. Yin, Yao-De. The Utility of DNA Aptamers against Î²-Bungarotoxin as Sensors for Detecting Î²-Bungarotoxin, Coralyne and Heparin.

Degree: Master, Institute of Biomedical Sciences, 2018, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0528118-084541

► Aptamers are single-stranded DNA or RNA fragments that bind to targeted molecules via folding into specific structure. Thus, aptamers can be employed as aptasensors for… (more)

▼ Aptamers are single-stranded DNA or RNA fragments that bind to targeted molecules via folding into specific structure. Thus, aptamers can be employed as aptasensors for detecting targeted molecules. The aim of this study was to investigate the utility of DNA aptamers against Bungarus multicinctus (Taiwan banded krait) presynaptic neurotoxin Î²-bungarotoxin (Î²-Bgt) as biosensors. Four Î²-Bgt aptamers, Bgt1, Bgt2, Bgt3, and Bgt4 were synthesized according to previously published results. Electrophoretic mobility shift assay showed that Î²-Bgt reduced the electrophoretic mobility of the aptamers. Moreover, Î²-Bgt reduced fluorescence intensity of the aptamers labeled with 5'-end carboxyfluorescein (FAM) and 3'-end 4-([4-(dimethylamino)-phenyl]azo)-benzoic acid (Dabcyl). These results showed that the folded structure of aptamers changed upon binding with Î²-Bgt. Measurement of the changes in FAM fluorescence revealed that Î²-Bgt had the highest binding affinity for Bgt1 among the four aptamers. In contrast to palmatine and berberine, coralyne drastically reduced FAM fluorescence intensity of 5'-FAM-Bgt1 and 5'-FAM-Bgt1-3'-Dabcyl, suggesting the selectivity of the sensors for detecting coralyne. The limit of detection (LOD) of coralyne determined by 5'-FAM-Bgt1 and 5'-FAM-Bgt1-3'-Dabcyl were 0.034 Î¼M and 0.021 Î¼M, respectively. Furthermore, coralyne-5'-FAM-Bgt1 and coralyne-5'-FAM-Bgt1-3'-Dabcyl complexes were employed as turn-on fluorescent sensors for detecting Î²-Bgt and heparin. Î²-Bgt and heparin notably restored FAM fluorescence intensity of coralyne-5'-FAM-Bgt1 and coralyne-5'-FAM-Bgt1-3'-Dabcyl complexes. The LOD of Î²-Bgt measured by coralyne-5'-FAM-Bgt1 and coralyne-5'-FAM-Bgt1-3'-Dabcyl complexes were 3.57 nM and 2.74 nM, respectively; the LOD of heparin were 0.012 Î¼g/ml and 0.004 Î¼g/ml, respectively; and the LOD for heparin-spiked serum were 0.027 Î¼g/ml and 0.009 Î¼g/ml, respectively. The sensor system constructed by coralyne and Bgt1 showed a high selectivity for heparin detection than for other glycosaminoglycans including chondroitin sulfate and hyaluronic acid. Although the sensor system effectively differentiated Î²-Bgt from other purified snake venom proteins, it could not specifically detect Taiwan banded krait crude venom. Taken together, our data indicate that aptamer against Î²-Bgt can be used for constructing biosensors for detecting coralyne and heparin. However, the sensor system is unable to identify the crude venoms of different snake species via Î²-Bgt detection. Advisors/Committee Members: Bin-Nan Wu (chair), Long-Sen Chang (committee member), Ying-Jung Chen (chair).

Subjects/Keywords: DNA aptamer; Sensors; Heparin; Coralyne; Î²-Bungarotoxin

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APA (6^th Edition):

Yin, Y. (2018). The Utility of DNA Aptamers against Î²-Bungarotoxin as Sensors for Detecting Î²-Bungarotoxin, Coralyne and Heparin. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0528118-084541

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yin, Yao-De. “The Utility of DNA Aptamers against Î²-Bungarotoxin as Sensors for Detecting Î²-Bungarotoxin, Coralyne and Heparin.” 2018. Thesis, NSYSU. Accessed February 19, 2020. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0528118-084541.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yin, Yao-De. “The Utility of DNA Aptamers against Î²-Bungarotoxin as Sensors for Detecting Î²-Bungarotoxin, Coralyne and Heparin.” 2018. Web. 19 Feb 2020.

Vancouver:

Yin Y. The Utility of DNA Aptamers against Î²-Bungarotoxin as Sensors for Detecting Î²-Bungarotoxin, Coralyne and Heparin. [Internet] [Thesis]. NSYSU; 2018. [cited 2020 Feb 19]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0528118-084541.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yin Y. The Utility of DNA Aptamers against Î²-Bungarotoxin as Sensors for Detecting Î²-Bungarotoxin, Coralyne and Heparin. [Thesis]. NSYSU; 2018. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0528118-084541

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universitat Rovira i Virgili

28. Nadal Polo, Pedro. Selection, characterisation and analytical application of dna aptamer against the anaphylactic toxic allergen, b-conglutin, lup an 1.

Degree: Departament d'Enginyeria Química, 2012, Universitat Rovira i Virgili

URL: http://hdl.handle.net/10803/84036

► Lupin has recently been added to the list of allergens requiring mandatory advisory labelling on foodstuffs sold in the European Union, and since December 2008… (more)

▼ Lupin has recently been added to the list of allergens requiring mandatory advisory labelling on foodstuffs sold in the European Union, and since December 2008 all products containing even trace amounts of lupin must be labelled correctly. Lupin globulins consist of two major globulins called α-conglutin (11S and “legumin-like”) and β-conglutin (7S and “vicilin-like”), and another additional two globulins, γ-conglutin and δ-conglutin, which are present in lower amounts. β-conglutin is the only conglutin currently included in the list of the International Union of Immunological Societies (IUIS), designated as Lup an 1. The overall objective of these PhD is the selection of aptamers that can detect this allergen. Nucleic acid aptamers are synthetic ligands selected from vast combinatorial libraries through a process referred to as SELEX – Systematic Evolution of Ligand By Exponential Enrichment. Aptamers possess unique chemical and biochemical characteristics, such as: well known chemistry and remarkable stability, moreover, aptamers can be selected against virtually any target and in non-physiological conditions. In order to achieve the overall objective, a set of subobjectives will be achieved. The first of these involves the elucidation of protocols for the selective extraction of each of the lupin α, β, γ, and δ subunits, resulting in (i) protocols that can be used for selective extraction and isolation of the lupin α, β, γ, and δ proteins from food for subsequent analysis; (ii) standards that can be used in analytical assays and tools; and (iii) target that can be used for the selection of aptamers specific to the β-conglutin subunit. The core of the work is the selection of aptamers against the allergen Lup an 1 using a SELEX procedure, as well the preparation of protocols that can be used to monitor the evolution of aptamer selection. The functionality of the aptamer is demonstratedby exploiting it in an enzyme linked oligonucleotide assay as well as apta-PCR. Finally the resulting aptamer candidates that exhibit high affinity are fully characterised, truncated, and the structure of the final truncated aptamer is elucidated Advisors/Committee Members: [email protected] (authoremail), true (authoremailshow), O'Sullivan, Ciara (director), true (authorsendemail).

Subjects/Keywords: Aptamer; Selex; Lupin; 577; 663/664

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APA (6^th Edition):

Nadal Polo, P. (2012). Selection, characterisation and analytical application of dna aptamer against the anaphylactic toxic allergen, b-conglutin, lup an 1. (Thesis). Universitat Rovira i Virgili. Retrieved from http://hdl.handle.net/10803/84036

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nadal Polo, Pedro. “Selection, characterisation and analytical application of dna aptamer against the anaphylactic toxic allergen, b-conglutin, lup an 1.” 2012. Thesis, Universitat Rovira i Virgili. Accessed February 19, 2020. http://hdl.handle.net/10803/84036.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nadal Polo, Pedro. “Selection, characterisation and analytical application of dna aptamer against the anaphylactic toxic allergen, b-conglutin, lup an 1.” 2012. Web. 19 Feb 2020.

Vancouver:

Nadal Polo P. Selection, characterisation and analytical application of dna aptamer against the anaphylactic toxic allergen, b-conglutin, lup an 1. [Internet] [Thesis]. Universitat Rovira i Virgili; 2012. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/10803/84036.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nadal Polo P. Selection, characterisation and analytical application of dna aptamer against the anaphylactic toxic allergen, b-conglutin, lup an 1. [Thesis]. Universitat Rovira i Virgili; 2012. Available from: http://hdl.handle.net/10803/84036

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Cornell University

29. Meng, Hsien-Wei. Development Of Dna Aptamers By Cell-Selex Using Yeast Cell Surface Display .

Degree: 2014, Cornell University

URL: http://hdl.handle.net/1813/36083

► SELEX, the process of selecting aptamers, is often hampered by the difficulty of preparing target molecules in their native forms and by a lack of… (more)

Subjects/Keywords: Aptamer; Cell-SELEX; Yeast Surface Display

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Meng, H. (2014). Development Of Dna Aptamers By Cell-Selex Using Yeast Cell Surface Display . (Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/36083

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Meng, Hsien-Wei. “Development Of Dna Aptamers By Cell-Selex Using Yeast Cell Surface Display .” 2014. Thesis, Cornell University. Accessed February 19, 2020. http://hdl.handle.net/1813/36083.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Meng, Hsien-Wei. “Development Of Dna Aptamers By Cell-Selex Using Yeast Cell Surface Display .” 2014. Web. 19 Feb 2020.

Vancouver:

Meng H. Development Of Dna Aptamers By Cell-Selex Using Yeast Cell Surface Display . [Internet] [Thesis]. Cornell University; 2014. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/1813/36083.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Meng H. Development Of Dna Aptamers By Cell-Selex Using Yeast Cell Surface Display . [Thesis]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/36083

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

McMaster University

30. Tram, Kha. EXPLORING SYNTHETIC FUNCTIONAL DNA MOLECULES FOR BIOSENSOR DEVELOPMENT.

Degree: PhD, 2015, McMaster University

URL: http://hdl.handle.net/11375/16884

►

The development of the in vitro selection technique permits the creation of synthetic DNA molecules with ligand-binding capabilities (DNA aptamers), or abilities to catalyze chemical… (more)

Subjects/Keywords: DNAzyme; Aptamer; Biosensors; Functional Nucleic Acids

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tram, K. (2015). EXPLORING SYNTHETIC FUNCTIONAL DNA MOLECULES FOR BIOSENSOR DEVELOPMENT. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/16884

Chicago Manual of Style (16^th Edition):

Tram, Kha. “EXPLORING SYNTHETIC FUNCTIONAL DNA MOLECULES FOR BIOSENSOR DEVELOPMENT.” 2015. Doctoral Dissertation, McMaster University. Accessed February 19, 2020. http://hdl.handle.net/11375/16884.

MLA Handbook (7^th Edition):

Tram, Kha. “EXPLORING SYNTHETIC FUNCTIONAL DNA MOLECULES FOR BIOSENSOR DEVELOPMENT.” 2015. Web. 19 Feb 2020.

Vancouver:

Tram K. EXPLORING SYNTHETIC FUNCTIONAL DNA MOLECULES FOR BIOSENSOR DEVELOPMENT. [Internet] [Doctoral dissertation]. McMaster University; 2015. [cited 2020 Feb 19]. Available from: http://hdl.handle.net/11375/16884.

Council of Science Editors:

Tram K. EXPLORING SYNTHETIC FUNCTIONAL DNA MOLECULES FOR BIOSENSOR DEVELOPMENT. [Doctoral Dissertation]. McMaster University; 2015. Available from: http://hdl.handle.net/11375/16884

Open Access Theses and Dissertations