subject:(RNA Synthesis)

Brock University

1. Tram, Kha. (A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides .

Degree: Centre for Biotechnology, 2011, Brock University

URL: http://hdl.handle.net/10464/3377

► (A) Solid phase synthesis of oligonucleotides are well documented and are extensively studied as the demands continue to rise with the development of antisense, anti-gene,… (more)

Subjects/Keywords: Oligonucleotides – Synthesis.; Fluorimetry; RNA – Synthesis

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APA (6^th Edition):

Tram, K. (2011). (A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides . (Thesis). Brock University. Retrieved from http://hdl.handle.net/10464/3377

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):

Tram, Kha. “(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides .” 2011. Thesis, Brock University. Accessed January 23, 2021. http://hdl.handle.net/10464/3377.

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

MLA Handbook (7^th Edition):

Tram, Kha. “(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides .” 2011. Web. 23 Jan 2021.

Vancouver:

Tram K. (A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides . [Internet] [Thesis]. Brock University; 2011. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10464/3377.

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

Council of Science Editors:

Tram K. (A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides . [Thesis]. Brock University; 2011. Available from: http://hdl.handle.net/10464/3377

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

Georgia State University

2. Chen, Xinghua. SYNTHESIS OF 2SeU-RNAs AND RNA SQUARES.

Degree: MS, Chemistry, 2016, Georgia State University

URL: https://scholarworks.gsu.edu/chemistry_theses/93

► In this paper, an improved method^[1] for the chemical synthesis of ^2SeU-RNA was reported using a streamlined strategy employs 2'-O-Thiomopholine-4-carbothioate protecting group. And… (more)

Subjects/Keywords: 2SeU-RNA synthesis; Self-assembling; RNA square

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APA (6^th Edition):

Chen, X. (2016). SYNTHESIS OF 2SeU-RNAs AND RNA SQUARES. (Thesis). Georgia State University. Retrieved from https://scholarworks.gsu.edu/chemistry_theses/93

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):

Chen, Xinghua. “SYNTHESIS OF 2SeU-RNAs AND RNA SQUARES.” 2016. Thesis, Georgia State University. Accessed January 23, 2021. https://scholarworks.gsu.edu/chemistry_theses/93.

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

MLA Handbook (7^th Edition):

Chen, Xinghua. “SYNTHESIS OF 2SeU-RNAs AND RNA SQUARES.” 2016. Web. 23 Jan 2021.

Vancouver:

Chen X. SYNTHESIS OF 2SeU-RNAs AND RNA SQUARES. [Internet] [Thesis]. Georgia State University; 2016. [cited 2021 Jan 23]. Available from: https://scholarworks.gsu.edu/chemistry_theses/93.

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

Council of Science Editors:

Chen X. SYNTHESIS OF 2SeU-RNAs AND RNA SQUARES. [Thesis]. Georgia State University; 2016. Available from: https://scholarworks.gsu.edu/chemistry_theses/93

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

Oregon State University

3. Nielsen, Brent L. Purification and characterization of R. meliloti RNA polymerase from wild type and mutant strains, and the role of the enzyme in the specificity of in vitro transcription of nitrogen fixation genes.

Degree: PhD, Microbiology, 1985, Oregon State University

URL: http://hdl.handle.net/1957/40706

Subjects/Keywords: RNA – Synthesis

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APA (6^th Edition):

Nielsen, B. L. (1985). Purification and characterization of R. meliloti RNA polymerase from wild type and mutant strains, and the role of the enzyme in the specificity of in vitro transcription of nitrogen fixation genes. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/40706

Chicago Manual of Style (16^th Edition):

Nielsen, Brent L. “Purification and characterization of R. meliloti RNA polymerase from wild type and mutant strains, and the role of the enzyme in the specificity of in vitro transcription of nitrogen fixation genes.” 1985. Doctoral Dissertation, Oregon State University. Accessed January 23, 2021. http://hdl.handle.net/1957/40706.

MLA Handbook (7^th Edition):

Nielsen, Brent L. “Purification and characterization of R. meliloti RNA polymerase from wild type and mutant strains, and the role of the enzyme in the specificity of in vitro transcription of nitrogen fixation genes.” 1985. Web. 23 Jan 2021.

Vancouver:

Nielsen BL. Purification and characterization of R. meliloti RNA polymerase from wild type and mutant strains, and the role of the enzyme in the specificity of in vitro transcription of nitrogen fixation genes. [Internet] [Doctoral dissertation]. Oregon State University; 1985. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1957/40706.

Council of Science Editors:

Nielsen BL. Purification and characterization of R. meliloti RNA polymerase from wild type and mutant strains, and the role of the enzyme in the specificity of in vitro transcription of nitrogen fixation genes. [Doctoral Dissertation]. Oregon State University; 1985. Available from: http://hdl.handle.net/1957/40706

Michigan State University

4. Desrosiers, Ronald Charles, 1948-. The synthesis and methylation of messenger RNA in Novikoff hepatoma cells.

Degree: PhD, Department of Biochemistry, 1975, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:21052

Subjects/Keywords: RNA – Synthesis

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APA (6^th Edition):

Desrosiers, Ronald Charles, 1. (1975). The synthesis and methylation of messenger RNA in Novikoff hepatoma cells. (Doctoral Dissertation). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:21052

Chicago Manual of Style (16^th Edition):

Desrosiers, Ronald Charles, 1948-. “The synthesis and methylation of messenger RNA in Novikoff hepatoma cells.” 1975. Doctoral Dissertation, Michigan State University. Accessed January 23, 2021. http://etd.lib.msu.edu/islandora/object/etd:21052.

MLA Handbook (7^th Edition):

Desrosiers, Ronald Charles, 1948-. “The synthesis and methylation of messenger RNA in Novikoff hepatoma cells.” 1975. Web. 23 Jan 2021.

Vancouver:

Desrosiers, Ronald Charles 1. The synthesis and methylation of messenger RNA in Novikoff hepatoma cells. [Internet] [Doctoral dissertation]. Michigan State University; 1975. [cited 2021 Jan 23]. Available from: http://etd.lib.msu.edu/islandora/object/etd:21052.

Council of Science Editors:

Desrosiers, Ronald Charles 1. The synthesis and methylation of messenger RNA in Novikoff hepatoma cells. [Doctoral Dissertation]. Michigan State University; 1975. Available from: http://etd.lib.msu.edu/islandora/object/etd:21052

Michigan State University

5. Eschenfeldt, William Herman. Ribonucleic acid synthesis in isolated mouse myeloma nuclei.

Degree: PhD, Department of Microbiology and Public Health, 1978, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:39890

Subjects/Keywords: RNA – Synthesis

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APA (6^th Edition):

Eschenfeldt, W. H. (1978). Ribonucleic acid synthesis in isolated mouse myeloma nuclei. (Doctoral Dissertation). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:39890

Chicago Manual of Style (16^th Edition):

Eschenfeldt, William Herman. “Ribonucleic acid synthesis in isolated mouse myeloma nuclei.” 1978. Doctoral Dissertation, Michigan State University. Accessed January 23, 2021. http://etd.lib.msu.edu/islandora/object/etd:39890.

MLA Handbook (7^th Edition):

Eschenfeldt, William Herman. “Ribonucleic acid synthesis in isolated mouse myeloma nuclei.” 1978. Web. 23 Jan 2021.

Vancouver:

Eschenfeldt WH. Ribonucleic acid synthesis in isolated mouse myeloma nuclei. [Internet] [Doctoral dissertation]. Michigan State University; 1978. [cited 2021 Jan 23]. Available from: http://etd.lib.msu.edu/islandora/object/etd:39890.

Council of Science Editors:

Eschenfeldt WH. Ribonucleic acid synthesis in isolated mouse myeloma nuclei. [Doctoral Dissertation]. Michigan State University; 1978. Available from: http://etd.lib.msu.edu/islandora/object/etd:39890

University of Missouri – Columbia

6. Shebl, Bassem. The influence of mRNA secondary structures on ribosome conformational dynamics.

Degree: 2016, University of Missouri – Columbia

URL: http://hdl.handle.net/10355/62520

► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Synthesizing proteins in the cell is a critical aspect of life. Protein synthesis is a… (more)

▼ [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Synthesizing proteins in the cell is a critical aspect of life. Protein synthesis is a complicated process and involve highly functional machines at a molecular level. The ribosome is the molecular machine that translate coded sequences of nucleic acids into functional proteins. Understanding how ribosomes function is key to understanding protein synthesis / translation. We focus our work on ribosomes from bacterial cells. This allows us to study much simpler systems and extrapolate our knowledge to higher levels. One key challenge in the field is to be able to isolate a high quantity of good and active ribosomes out of the cell to study it in a controlled environment. Classically known methods involve extensive resources, high technical expertise, and a week of preparation. We developed a one-step protocol to purify ribosomes that are more active than the ones purified from classical methods. This developed technique saves time and money and results in much higher amounts of product. This approach also makes the technique approachable to a wider community of scientists and researchers. The same methodology could be applied towards purifying other molecular machines in the cells. Using these ribosomes, we wanted to investigate how the ribosomes function in cells when faced with specific signals. These signals are utilized by the cells to control protein synthesis. However, in dome diseased cells and for some viruses, normal protein synthesis is overridden by the invaders to produce faulty proteins that could result in a wide range of diseases such as Alzheimer and others. In this study, we investigated how the ribosome functions in the presence of such signals and how close do they need to be to the ribosome to affect protein synthesis. This allows us to design drugs to mimic or inhibit such changes thus fixing faulty protein production or sometimes induce it to inhibit protein synthesis in bacterial cells and as such designing and producing novel drugs. Advisors/Committee Members: Cornish, Peter V. (advisor).

Subjects/Keywords: Proteins – Synthesis; Messenger RNA; Ribosomes

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APA (6^th Edition):

Shebl, B. (2016). The influence of mRNA secondary structures on ribosome conformational dynamics. (Thesis). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/62520

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):

Shebl, Bassem. “The influence of mRNA secondary structures on ribosome conformational dynamics.” 2016. Thesis, University of Missouri – Columbia. Accessed January 23, 2021. http://hdl.handle.net/10355/62520.

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

MLA Handbook (7^th Edition):

Shebl, Bassem. “The influence of mRNA secondary structures on ribosome conformational dynamics.” 2016. Web. 23 Jan 2021.

Vancouver:

Shebl B. The influence of mRNA secondary structures on ribosome conformational dynamics. [Internet] [Thesis]. University of Missouri – Columbia; 2016. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10355/62520.

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

Council of Science Editors:

Shebl B. The influence of mRNA secondary structures on ribosome conformational dynamics. [Thesis]. University of Missouri – Columbia; 2016. Available from: http://hdl.handle.net/10355/62520

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

University of Lethbridge

7. University of Lethbridge. Faculty of Arts and Science. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation .

Degree: 2019, University of Lethbridge

URL: http://hdl.handle.net/10133/5666

► Cap-dependent translation drives the global synthesis of proteins. Under stress conditions global protein production is attenuated, yet the translation of ATF4 is upregulated through uORF-… (more)

Subjects/Keywords: Messenger RNA; Proteins – Synthesis; Ribosomes

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APA (6^th Edition):

Science, U. o. L. F. o. A. a. (2019). Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation . (Thesis). University of Lethbridge. Retrieved from http://hdl.handle.net/10133/5666

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):

Science, University of Lethbridge. Faculty of Arts and. “Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation .” 2019. Thesis, University of Lethbridge. Accessed January 23, 2021. http://hdl.handle.net/10133/5666.

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

MLA Handbook (7^th Edition):

Science, University of Lethbridge. Faculty of Arts and. “Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation .” 2019. Web. 23 Jan 2021.

Vancouver:

Science UoLFoAa. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation . [Internet] [Thesis]. University of Lethbridge; 2019. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10133/5666.

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

Council of Science Editors:

Science UoLFoAa. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation . [Thesis]. University of Lethbridge; 2019. Available from: http://hdl.handle.net/10133/5666

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

University of Arizona

8. Moore, Keith Edwin, 1931-. THE REGULATION OF RNA SYNTHESIS IN YEAST .

Degree: 1969, University of Arizona

URL: http://hdl.handle.net/10150/287446

Subjects/Keywords: RNA – Synthesis.; Yeast.

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APA (6^th Edition):

Moore, Keith Edwin, 1. (1969). THE REGULATION OF RNA SYNTHESIS IN YEAST . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/287446

Chicago Manual of Style (16^th Edition):

Moore, Keith Edwin, 1931-. “THE REGULATION OF RNA SYNTHESIS IN YEAST .” 1969. Doctoral Dissertation, University of Arizona. Accessed January 23, 2021. http://hdl.handle.net/10150/287446.

MLA Handbook (7^th Edition):

Moore, Keith Edwin, 1931-. “THE REGULATION OF RNA SYNTHESIS IN YEAST .” 1969. Web. 23 Jan 2021.

Vancouver:

Moore, Keith Edwin 1. THE REGULATION OF RNA SYNTHESIS IN YEAST . [Internet] [Doctoral dissertation]. University of Arizona; 1969. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10150/287446.

Council of Science Editors:

Moore, Keith Edwin 1. THE REGULATION OF RNA SYNTHESIS IN YEAST . [Doctoral Dissertation]. University of Arizona; 1969. Available from: http://hdl.handle.net/10150/287446

Vanderbilt University

9. -5241-5959. Improving Immune Checkpoint Blockade Efficacy Through the Design and Optimization of 5'-Triphosphate RNA Loaded Nanoparticles.

Degree: PhD, Chemical Engineering, 2020, Vanderbilt University

URL: http://hdl.handle.net/1803/10111

► Here, I develop and then further optimize 3pRNA-NPs: a nanoparticle delivery platform capable of activating the innate immune system through engagement of the cytosolic pattern… (more)

▼ Here, I develop and then further optimize 3pRNA-NPs: a nanoparticle delivery platform capable of activating the innate immune system through engagement of the cytosolic pattern recognition receptor RIG-I. Both targeting cytosolic receptors as well as utilizing RNA therapeutics are met with historic barriers to efficacy, including RNA degradation, poor cellular uptake, endosomolytic recycling, and lysosomal degradation. 3pRNA-NPs utilize pH responsive, membrane destabilizing polymers electrostatically complexed to the RIG-I agonist 5'ppp dsRNA, to overcome these barriers, drastically increasing the magnitude of the innate immune response. First, we use an already established pH-responsive membrane destabilizing polymer to formulate 3pRNA-NPs. We find that these particles are capable of inducing an immunostimulatory response, including the production of immune activating cytokines and T-cell recruiting chemokines in both murine colon cancer cells in addition to murine myeloid cells that comprise a typical tumor microenvironment. Furthermore, we found that 3pRNA-NP treatment also caused murine cancer cell death. We administer a combinatorial therapy comprising these 3pRNA-NPs in conjunction with anti-PD-1 in a murine colon cancer model and find that the combinatorial treatment resulted in redcued tumor burden as well as 3 tumor-free mice that resisted tumor rechallenge. In order to further optimize 3pRNA-NPs, we synthesize a series of pH-responsive polymers for formulations. We establish a relationship between polymer composition and pH-responsive properties across two parameters: hydrophobic monomer side chain length and second block composition. Next, we evaluate the ability of these series polymers to enhance the immune response of 5'ppp dsRNA, and further investigate four lead polymers capable of vastly enhancing 5'ppp dsRNA treatment. Although these polymers behave similarly, we find that NPs comprising 5'ppp dsRNA complexed with the series polymer “P-b-DA450” demonstrate enhanced stability and immunostimulatory response in murine breast tumors. While 3pRNA-NP dose and treatment regimen remain to be optimized for maximum therapeutic benefit, these studies demonstrate the importance of carrier design in immunotherapeutic targeting and set the stage for future investigation into the development of new delivery technologies for this promising class of innate immune agonist. Advisors/Committee Members: Wilson, John T (advisor).

Subjects/Keywords: RIG-I; RNA delivery; Polymer Synthesis; 5' Triphosphate RNA; Cancer Immunotherapy

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APA (6^th Edition):

-5241-5959. (2020). Improving Immune Checkpoint Blockade Efficacy Through the Design and Optimization of 5'-Triphosphate RNA Loaded Nanoparticles. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10111

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-5241-5959. “Improving Immune Checkpoint Blockade Efficacy Through the Design and Optimization of 5'-Triphosphate RNA Loaded Nanoparticles.” 2020. Doctoral Dissertation, Vanderbilt University. Accessed January 23, 2021. http://hdl.handle.net/1803/10111.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-5241-5959. “Improving Immune Checkpoint Blockade Efficacy Through the Design and Optimization of 5'-Triphosphate RNA Loaded Nanoparticles.” 2020. Web. 23 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-5241-5959. Improving Immune Checkpoint Blockade Efficacy Through the Design and Optimization of 5'-Triphosphate RNA Loaded Nanoparticles. [Internet] [Doctoral dissertation]. Vanderbilt University; 2020. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1803/10111.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-5241-5959. Improving Immune Checkpoint Blockade Efficacy Through the Design and Optimization of 5'-Triphosphate RNA Loaded Nanoparticles. [Doctoral Dissertation]. Vanderbilt University; 2020. Available from: http://hdl.handle.net/1803/10111

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Columbia University

10. Bailey, Nevette Adia. Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity.

Degree: 2019, Columbia University

URL: https://doi.org/10.7916/d8-qsnc-d250

► Ribosomes are universally conserved macromolecular machines found within all living cells that catalyze protein synthesis, one of nature’s most fundamental processes. Ribosomes synthesize proteins, which… (more)

▼ Ribosomes are universally conserved macromolecular machines found within all living cells that catalyze protein synthesis, one of nature’s most fundamental processes. Ribosomes synthesize proteins, which are polymeric chains of amino acids, by incorporating the amino acids one at a time via aminoacylated-transfer RNAs (aa-tRNAs), based on translation of the sequence of triplet- nucleotide codons presented by the messenger RNA (mRNA) template that is a direct readout of genomic DNA. Recent biochemical, structural, dynamic, and computational studies have uncovered large-scale conformational changes of the ribosome, its tRNA substrates, and the additional protein translation factors that play important roles in regulating protein synthesis, especially during the elongation phase of translation when the bulk of each protein is synthesized. How the ribosome, its translation elongation factors, tRNAs, and mRNA physically coordinate and regulate the movements of the tRNAs carrying amino acids into, through, and out of the ribosome remains one of the more fundamental questions in the mechanistic studies of protein synthesis. A complete understanding of the conformational dynamics of ribosomal complexes will improve our knowledge of how translation is regulated, including how ribosome-targeting antibiotics regulate translation elongation, and will provide crucial information for designing next-generation antibiotics. In this thesis I have investigated the conformational dynamics of the ribosome during the elongation phase of protein synthesis at the single-molecule level using single-molecule fluorescence resonance energy transfer (smFRET) microscopy experiments. Specifically, I have studied ribosomal dynamics during the elongation phase of translation in the presence of a tRNAPro in the context of an mRNA that has the propensity to shift out of the reading frame. My studies have revealed information about the mechanistic and regulatory functions of the posttranscriptional modifications of tRNAPro in a context in which the ribosomal complex has the propensity to undergo non-programmed +1-frameshifting, in which the tRNA-mRNA base pairing shifts one base toward the 3’ end of the mRNA, and if unchecked, leads to the synthesis of a polypeptide with a completely different sequence of amino acids. My data suggests that in this context, the mechanism underlying non-programmed +1-frameshifting involves the tRNA shifting out of frame prior to the tRNA being accommodated in the P site, i.e. either while the tRNA is in the A site, or more likely, during translocation of the tRNA from the A site to the P site, and not while the tRNA is already occupying the P site, as previously proposed.

Subjects/Keywords: Biophysics; Ribosomes; Proteins – Synthesis; Genetic translation; Messenger RNA; Transfer RNA

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APA (6^th Edition):

Bailey, N. A. (2019). Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/d8-qsnc-d250

Chicago Manual of Style (16^th Edition):

Bailey, Nevette Adia. “Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity.” 2019. Doctoral Dissertation, Columbia University. Accessed January 23, 2021. https://doi.org/10.7916/d8-qsnc-d250.

MLA Handbook (7^th Edition):

Bailey, Nevette Adia. “Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity.” 2019. Web. 23 Jan 2021.

Vancouver:

Bailey NA. Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity. [Internet] [Doctoral dissertation]. Columbia University; 2019. [cited 2021 Jan 23]. Available from: https://doi.org/10.7916/d8-qsnc-d250.

Council of Science Editors:

Bailey NA. Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity. [Doctoral Dissertation]. Columbia University; 2019. Available from: https://doi.org/10.7916/d8-qsnc-d250

University of Oxford

11. York, Ashley D. A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase.

Degree: PhD, 2014, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879

► The segmented negative-sense vRNA genome of influenza A virus is replicated via a complementary RNA (cRNA) intermediate by the viral RNA-dependent RNA polymerase (RdRP). The… (more)

Subjects/Keywords: 572.8; Biochemistry; Biology; Microbiology; Viruses; influenza; RNA polymerase; RNA synthesis

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APA (6^th Edition):

York, A. D. (2014). A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879

Chicago Manual of Style (16^th Edition):

York, Ashley D. “A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase.” 2014. Doctoral Dissertation, University of Oxford. Accessed January 23, 2021. http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879.

MLA Handbook (7^th Edition):

York, Ashley D. “A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase.” 2014. Web. 23 Jan 2021.

Vancouver:

York AD. A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase. [Internet] [Doctoral dissertation]. University of Oxford; 2014. [cited 2021 Jan 23]. Available from: http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879.

Council of Science Editors:

York AD. A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase. [Doctoral Dissertation]. University of Oxford; 2014. Available from: http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879

Duke University

12. Donlic, Anita. Insights, Assays, and Strategies for Small Molecule-Based Modulation of the MALAT1 RNA Triple Helix .

Degree: 2020, Duke University

URL: http://hdl.handle.net/10161/20851

► Recent discoveries of myriad of endogenous RNA transcripts that do not code for proteins has led to a paradigm shift in our understanding of… (more)

▼ Recent discoveries of myriad of endogenous RNA transcripts that do not code for proteins has led to a paradigm shift in our understanding of human biology. As the subsequent “RNA revolution” continues to elucidate the disease-related functions and structures of mammalian non-coding RNA molecules, interest in developing small molecule probes and drug leads for these targets is on the rise. For example, the long non-coding RNA MALAT1 (Metastasis-Associated-Lung-Adenocarcinoma-Transcript-1) is overexpressed in and is critical for metastasis in a variety of cancers. A recently characterized triple helix structure at the 3'-end of MALAT1 was shown to be pivotal in stabilizing the transcript, and deletions or a single base substitution - proposed to destabilize this structure - led to a significant decrease in MALAT1 accumulation. While this unique structure represents a novel opportunity for therapeutic intervention, there is a gap in knowledge regarding effective strategies for targeting RNA in general and, in particular, triple helices. Towards elucidating these principles, this work takes a three-pronged approach: i) synthesis and evaluation of scaffold-based small molecule libraries to deduce fundamental ligand-triple helix recognition principles, ii) development of robust and high-throughput screening assays to discover functional probes, and iii) structural characterization of the MALAT1 triple helix conformational landscape for small molecule-based regulation. In the first area, we have discovered first small molecule ligands for the MALAT1 triple helix and gained insights into the role of three-dimensional small molecule shape and intramolecular interactions in binding events. Additionally, we established a correlation between ligand-induced thermal stabilization and prevention of exonucleolytic degradation of this target and elucidated binding properties of ligands with triplex-stabilizing functions. In the second area, we developed a high-throughput screening (HTS) technique based on differential scanning fluorimetry and curated an RNA-targeted library to identify novel small molecules with a destabilizing effect on the triple helix. Such thermal melting profiles were predictive of accelerated degradation profiles of the triple helix, thereby providing a robust discovery tool for identifying functional small molecule modulators of this target. In the third area, we conducted chemical probing experiments to characterize secondary structures that may exist in equilibrium with the triple helix and hence represent attractive targets for small molecule stabilization. Together, this work has and will continue to build a set of small molecule tools, rapid assays, and novel design strategies to enable chemical biology-based interrogation of the MALAT1 triple helix role in cancer biology. This knowledge and tools can be utilized to interrogate the protective mechanism of the MALAT1 triple helix, to identify and develop therapeutic leads, as well as to apply these strategies for the study of other… Advisors/Committee Members: Hargrove, Amanda E (advisor).

Subjects/Keywords: Chemistry; Biochemistry; assays; MALAT1; RNA; RNA recognition; small molecule; synthesis

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APA (6^th Edition):

Donlic, A. (2020). Insights, Assays, and Strategies for Small Molecule-Based Modulation of the MALAT1 RNA Triple Helix . (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/20851

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):

Donlic, Anita. “Insights, Assays, and Strategies for Small Molecule-Based Modulation of the MALAT1 RNA Triple Helix .” 2020. Thesis, Duke University. Accessed January 23, 2021. http://hdl.handle.net/10161/20851.

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

MLA Handbook (7^th Edition):

Donlic, Anita. “Insights, Assays, and Strategies for Small Molecule-Based Modulation of the MALAT1 RNA Triple Helix .” 2020. Web. 23 Jan 2021.

Vancouver:

Donlic A. Insights, Assays, and Strategies for Small Molecule-Based Modulation of the MALAT1 RNA Triple Helix . [Internet] [Thesis]. Duke University; 2020. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10161/20851.

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

Council of Science Editors:

Donlic A. Insights, Assays, and Strategies for Small Molecule-Based Modulation of the MALAT1 RNA Triple Helix . [Thesis]. Duke University; 2020. Available from: http://hdl.handle.net/10161/20851

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

Rutgers University

13. Veliath, Elizabeth, 1971-. Synthesis and characterization of C8 analogs of c-di-GMP; new synthetic method for 5’-capped oligoribonucleotides.

Degree: PhD, Chemistry and Chemical Biology, 2011, Rutgers University

URL: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000057711

►

This research is centered on two projects of biological importance composed of RNA –based compounds: C8 analogs of cyclic diguanosine monophosphate (c-di-GMP) and 5’-capped oligoribonucleotides.… (more)

▼

This research is centered on two projects of biological importance composed of RNA –based compounds: C8 analogs of cyclic diguanosine monophosphate (c-di-GMP) and 5’-capped oligoribonucleotides. c-di-GMP is an important bacterial second messenger molecule that is critical for the transition between a biofilm-protected sessile state and a virulent, single cellular motile state in species like V. Cholerae and S.Typhimurium. The synthesis and solution phase structural analysis of a family of C8-modified analogs is described. Starting from unmodified c-di-GMP, elaboration at the C8 position of both guanine moieties of c-di-GMP resulted in the bromo, thio, methylthio, phenyl, and meta-acetylphenyl analogs. Biophysical studies of all five compounds was performed using 1D and (1H, 31P, 13C) and 2D (DOSY, HMBC/HMQC) NMR to ascertain the level of G-quadruplex formation. It was found that only c-di-Br-GMP as the K+ salt form adopts the formation of higher order complexes containing guanine quartet structures. All analogs have an NMR-visible amino resonance that is most prominent at low temperatures due to protection from exchange by the self-stacking, and that disappears at elevated temperatures, which does not occur in with the 8-bromo-GMP monomer illustrating the special structural characteristics of the symmetric dimer. Capped RNA has a unique 5’-end structure containing a terminal N7-methylated guanosine that is joined via a triphosphate bridge to the 5’-OH of all eukaryotic mRNAs. This structure plays a vital role in regulating RNA maturation, processing, transport and translation, but capped RNA is extremely difficult to synthesize chemically due to its instability. A new protection strategy was devised that uses a lipophilic dimethoxytrityl (DMT) group on the amino group of the N7-methylated guanine activated capping reagent. This allows efficient purification of the final capped RNA on reverse-phase HPLC. Additionally, the DMT group increases the capping reagent solubility in organic solvents which improves the final coupling step. The synthetic method is general to include a variety of mixed sequence oligonucleotides, and is compatible with reverse-phase HPLC. This method has been used to synthesize and purify the unmodified cap structure m7GpppG, the individual diastereomers of the α-thiophosphate analog m7Gppp(s)G, m7GpppT8 and mixed sequences of m7Gppp-(2’-O-Me-GAUGC), m7Gppp-(2’-O-Me-GAUGC)2, m7Gppp-(2’- O-Me-GUAUC)4 and m7Gppp-(GUAUC)4.

Advisors/Committee Members: Jones, Roger A (chair), Lee, Jeehiun K (internal member), Williams, Lawrence J (internal member), LaVoie, Edmond J (outside member).

Subjects/Keywords: RNA – Synthesis; Nucleic acids – Synthesis; Cyclic guanylic acid

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APA (6^th Edition):

Veliath, Elizabeth, 1. (2011). Synthesis and characterization of C8 analogs of c-di-GMP; new synthetic method for 5’-capped oligoribonucleotides. (Doctoral Dissertation). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000057711

Chicago Manual of Style (16^th Edition):

Veliath, Elizabeth, 1971-. “Synthesis and characterization of C8 analogs of c-di-GMP; new synthetic method for 5’-capped oligoribonucleotides.” 2011. Doctoral Dissertation, Rutgers University. Accessed January 23, 2021. http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000057711.

MLA Handbook (7^th Edition):

Veliath, Elizabeth, 1971-. “Synthesis and characterization of C8 analogs of c-di-GMP; new synthetic method for 5’-capped oligoribonucleotides.” 2011. Web. 23 Jan 2021.

Vancouver:

Veliath, Elizabeth 1. Synthesis and characterization of C8 analogs of c-di-GMP; new synthetic method for 5’-capped oligoribonucleotides. [Internet] [Doctoral dissertation]. Rutgers University; 2011. [cited 2021 Jan 23]. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000057711.

Council of Science Editors:

Veliath, Elizabeth 1. Synthesis and characterization of C8 analogs of c-di-GMP; new synthetic method for 5’-capped oligoribonucleotides. [Doctoral Dissertation]. Rutgers University; 2011. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000057711

University of Arizona

14. Bullaro, Joseph Carava, 1936-. THE RELATIONSHIP OF RNA SYNTHESIS TO PROTEIN SYNTHESIS, DURING URACIL STARVATION, IN A URACIL REQUIRING STRAIN OF SACCHAROMYCES CEREVISIAE .

Degree: 1970, University of Arizona

URL: http://hdl.handle.net/10150/287552

Subjects/Keywords: RNA – Synthesis.; Proteins – Synthesis.; Uracil.

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

APA (6^th Edition):

Bullaro, Joseph Carava, 1. (1970). THE RELATIONSHIP OF RNA SYNTHESIS TO PROTEIN SYNTHESIS, DURING URACIL STARVATION, IN A URACIL REQUIRING STRAIN OF SACCHAROMYCES CEREVISIAE . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/287552

Chicago Manual of Style (16^th Edition):

Bullaro, Joseph Carava, 1936-. “THE RELATIONSHIP OF RNA SYNTHESIS TO PROTEIN SYNTHESIS, DURING URACIL STARVATION, IN A URACIL REQUIRING STRAIN OF SACCHAROMYCES CEREVISIAE .” 1970. Doctoral Dissertation, University of Arizona. Accessed January 23, 2021. http://hdl.handle.net/10150/287552.

MLA Handbook (7^th Edition):

Bullaro, Joseph Carava, 1936-. “THE RELATIONSHIP OF RNA SYNTHESIS TO PROTEIN SYNTHESIS, DURING URACIL STARVATION, IN A URACIL REQUIRING STRAIN OF SACCHAROMYCES CEREVISIAE .” 1970. Web. 23 Jan 2021.

Vancouver:

Bullaro, Joseph Carava 1. THE RELATIONSHIP OF RNA SYNTHESIS TO PROTEIN SYNTHESIS, DURING URACIL STARVATION, IN A URACIL REQUIRING STRAIN OF SACCHAROMYCES CEREVISIAE . [Internet] [Doctoral dissertation]. University of Arizona; 1970. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10150/287552.

Council of Science Editors:

Bullaro, Joseph Carava 1. THE RELATIONSHIP OF RNA SYNTHESIS TO PROTEIN SYNTHESIS, DURING URACIL STARVATION, IN A URACIL REQUIRING STRAIN OF SACCHAROMYCES CEREVISIAE . [Doctoral Dissertation]. University of Arizona; 1970. Available from: http://hdl.handle.net/10150/287552

University of British Columbia

15. Johnston, Julie Catherine. In vitro translation of cucumber necrosis virus RNA.

Degree: MS- MSc, Plant Science, 1989, University of British Columbia

URL: http://hdl.handle.net/2429/28969

► The in vitro translation products directed by cucumber necrosis virus (CNV) RNA were analyzed in both rabbit reticulocyte lysate and wheat germ extract cell-free translation… (more)

▼ The in vitro translation products directed by cucumber necrosis virus (CNV) RNA were analyzed in both rabbit reticulocyte lysate and wheat germ extract cell-free translation systems. In rabbit reticulocyte lysates, one major protein of ca. 33 Mr was produced. In wheat germ extracts, four proteins of ca. 41, 33, 21 and 20 Mr were produced. Hybrid-arrested translation (HART) studies using synthetic CNV antisense RNA corresponding to the entire CNV genome demonstrated that the four major proteins synthesized from CNV virion RNA in wheat germ extracts are virus-specific translation products. The genomic locations of the CNV in vitro translation products were determined using a number of experimental approaches including: (1) HART using antisense RNA corresponding to selected regions of the CNV genome; (2) in vitro translation of synthetic messenger-sense CNV transcripts; (3) immunoprecipitation of in vitro translation products with CNV polyclonal antisera and (4) in vitro translation of size-fractionated CNV virion RNA. Together, these experiments demonstrated that the ca. 33 Mr protein is derived from the 5' proximal coding region, the ca. 41 Mr protein is derived from an internal coding region, and that at least one but probably both of the ca. 20 and 21 Mr proteins are derived from the 3' terminal coding region(s) of the CNV genome. In addition, immunoprecipitation experiments provided further evidence that the ca. 41 Mr protein is the viral coat protein. The size, number, and genomic locations of the CNV in vitro translation products reported here are in agreement with those predicted from nucleotide sequence data (Rochon & Tremaine, 1989). The natural template for the expression of downstream cistrons in the CNV genome was investigated by in vitro translation of sucrose fractionated CNV virion RNA as well as in vitro translation of messenger-sense synthetic transcripts. These studies indicate that in vitro, both subgenomic and genomic-length CNV RNA molecules may act as templates for the synthesis of the ca. 41,21 and 20 Mr proteins as well as the ca. 33 Mr protein.

Subjects/Keywords: RNA – Synthesis; Proteins – Synthesis

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APA (6^th Edition):

Johnston, J. C. (1989). In vitro translation of cucumber necrosis virus RNA. (Masters Thesis). University of British Columbia. Retrieved from http://hdl.handle.net/2429/28969

Chicago Manual of Style (16^th Edition):

Johnston, Julie Catherine. “In vitro translation of cucumber necrosis virus RNA.” 1989. Masters Thesis, University of British Columbia. Accessed January 23, 2021. http://hdl.handle.net/2429/28969.

MLA Handbook (7^th Edition):

Johnston, Julie Catherine. “In vitro translation of cucumber necrosis virus RNA.” 1989. Web. 23 Jan 2021.

Vancouver:

Johnston JC. In vitro translation of cucumber necrosis virus RNA. [Internet] [Masters thesis]. University of British Columbia; 1989. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/2429/28969.

Council of Science Editors:

Johnston JC. In vitro translation of cucumber necrosis virus RNA. [Masters Thesis]. University of British Columbia; 1989. Available from: http://hdl.handle.net/2429/28969

16. Da Silva, Laura. Synthèse d'ARN en conditions prébiotiques : RNA synthesis in prebiotic conditions.

Degree: Docteur es, Sciences de la vie et de la santé, 2016, Université Paris-Saclay (ComUE)

URL: http://www.theses.fr/2016SACLS487

►

L'une des questions essentielles concernant l'origine de la vie est de comprendre les étapes de l'évolution ayant permis le passage d’une chimie prébiotique complexe aux… (more)

▼

L'une des questions essentielles concernant l'origine de la vie est de comprendre les étapes de l'évolution ayant permis le passage d’une chimie prébiotique complexe aux premières étapes biologiques. Les constituants cellulaires actuels nous permettent de suivre le lien des produits chimiques aux métabolites biochimiques, de l'ancien au monde moderne. De nombreuses preuves soutiennent l'hypothèse du "monde à ARN" stipulant qu’au début de l'évolution de la vie, l'ARN était responsable à la fois du stockage et du transfert de l'information génétique mais aussi de la catalyse de réactions biochimiques. Dans cette thèse, j’ai étudié la synthèse non-enzymatique d’ARN dans des conditions prébiotiques. Ces conditions simulent les processus hydrothermaux qui se produisent dans les sources chaudes hydrothermales modernes et étaient vraisemblablement omniprésentes sur la Terre primitive. J’ai ensuite recherché les conditions optimales permettant la synthèse de longs polymères d’ARN et montré que la présence d’une matrice cristalline augmente de manière significative le rendement et la longueur des polymères synthétisés. Enfin, j’ai examiné la stabilité des polymères nouvellement synthétisés dans ces conditions hydrothermales and comparé la dégradation par dépurination des nucléotides et polymères en présence des deux agents organisateurs favorisant la polymérisation, soit des phospholipides, soit des sels cristallins. Nous avons conclu que, bien que la décomposition des nucléotides ait lieu dans ces conditions, des nucléotides puriques sont toujours disponibles pour participer à la synthèse de polymères et que la présence de phospholipides protège les nucléotides contre la dégradation.

One remaining crucial point in the early life history is to understand how evolution passed from complex prebiotic chemistry to simple biology. Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. A substantial weight of evidence supports the “RNA world” hypothesis stipulating that the earliest forms of life passed through a phase in which RNA served both for the storage and transfer of genetic information and for the catalysis of biochemical reactions. In this thesis, we studied the non-enzymatic synthesis of RNA under simulated prebiotic conditions. These conditions simulated hydrothermal processes that commonly occur in volcanic hydrothermal fields today and were presumably ubiquitous on the primitive Earth. We then looked for optimal conditions allowing synthesis of long RNA-like polymers and showed that the presence of crystalline matrix significantly increases the yield and length of synthesized polymers. Finally, we investigated the stability of the synthesized polymers under hydrothermal conditions and compared the degradation by depurination of nucleotides and polymers in the presence of two organsing agents that promotes polymerisation, either phospholipids or salts crystals. We concluded that although decomposition of nucleotides occurs in these simulated…

Advisors/Committee Members: Maurel, Marie-Christine (thesis director), Deamer, David W (thesis director).

Subjects/Keywords: Conditions hydrothermales; Monde à ARN; Synthèse d'ARN; Hydrothermal fields; RNA world; RNA synthesis

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

APA (6^th Edition):

Da Silva, L. (2016). Synthèse d'ARN en conditions prébiotiques : RNA synthesis in prebiotic conditions. (Doctoral Dissertation). Université Paris-Saclay (ComUE). Retrieved from http://www.theses.fr/2016SACLS487

Chicago Manual of Style (16^th Edition):

Da Silva, Laura. “Synthèse d'ARN en conditions prébiotiques : RNA synthesis in prebiotic conditions.” 2016. Doctoral Dissertation, Université Paris-Saclay (ComUE). Accessed January 23, 2021. http://www.theses.fr/2016SACLS487.

MLA Handbook (7^th Edition):

Da Silva, Laura. “Synthèse d'ARN en conditions prébiotiques : RNA synthesis in prebiotic conditions.” 2016. Web. 23 Jan 2021.

Vancouver:

Da Silva L. Synthèse d'ARN en conditions prébiotiques : RNA synthesis in prebiotic conditions. [Internet] [Doctoral dissertation]. Université Paris-Saclay (ComUE); 2016. [cited 2021 Jan 23]. Available from: http://www.theses.fr/2016SACLS487.

Council of Science Editors:

Da Silva L. Synthèse d'ARN en conditions prébiotiques : RNA synthesis in prebiotic conditions. [Doctoral Dissertation]. Université Paris-Saclay (ComUE); 2016. Available from: http://www.theses.fr/2016SACLS487

Kennesaw State University

17. Diatta, Diane. Small Angle X-ray Scattering study of conformational changes in steroid responsive activator (SRA) RNA upon binding with suppressor protein SHARP.

Degree: MSCB, Chemistry, 2019, Kennesaw State University

URL: https://digitalcommons.kennesaw.edu/mscs_etd/27

► ABSTRACT Differentiation and proliferation are known to be influenced by steroid stimulation. The steroid receptor activator (SRA) RNA is a large RNA transcript indicated… (more)

Subjects/Keywords: SEC-SAXS; STR7 RNA; protein purification; RNA synthesis and Electroelution; Ab initio beads modeling; Chemistry

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APA (6^th Edition):

Diatta, D. (2019). Small Angle X-ray Scattering study of conformational changes in steroid responsive activator (SRA) RNA upon binding with suppressor protein SHARP. (Thesis). Kennesaw State University. Retrieved from https://digitalcommons.kennesaw.edu/mscs_etd/27

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):

Diatta, Diane. “Small Angle X-ray Scattering study of conformational changes in steroid responsive activator (SRA) RNA upon binding with suppressor protein SHARP.” 2019. Thesis, Kennesaw State University. Accessed January 23, 2021. https://digitalcommons.kennesaw.edu/mscs_etd/27.

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

MLA Handbook (7^th Edition):

Diatta, Diane. “Small Angle X-ray Scattering study of conformational changes in steroid responsive activator (SRA) RNA upon binding with suppressor protein SHARP.” 2019. Web. 23 Jan 2021.

Vancouver:

Diatta D. Small Angle X-ray Scattering study of conformational changes in steroid responsive activator (SRA) RNA upon binding with suppressor protein SHARP. [Internet] [Thesis]. Kennesaw State University; 2019. [cited 2021 Jan 23]. Available from: https://digitalcommons.kennesaw.edu/mscs_etd/27.

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

Council of Science Editors:

Diatta D. Small Angle X-ray Scattering study of conformational changes in steroid responsive activator (SRA) RNA upon binding with suppressor protein SHARP. [Thesis]. Kennesaw State University; 2019. Available from: https://digitalcommons.kennesaw.edu/mscs_etd/27

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

Boston University

18. Cressey, Tessa. RNA synthesis initiation by the nonsegmented negative-sense RNA virus polymerases.

Degree: PhD, Microbiology, 2020, Boston University

URL: http://hdl.handle.net/2144/39385

► Nonsegmented negative-sense RNA viruses (nsNSVs) include the human pathogens respiratory syncytial virus (RSV) and Ebola virus (EBOV). The genomes of these viruses are replicated and… (more)

▼ Nonsegmented negative-sense RNA viruses (nsNSVs) include the human pathogens respiratory syncytial virus (RSV) and Ebola virus (EBOV). The genomes of these viruses are replicated and transcribed by a virus-encoded RNA dependent RNA polymerase (RdRp). The RdRps of nsNSVs initiate RNA synthesis in a primer-independent (de novo) manner. RSV RdRp initiates replication opposite the uridine at template position 1 (T1U) and transcription opposite the cytidine at template position 3 (T3C). The EBOV RdRp initiation site(s) was not known. We sought to better understand nsNSV RNA synthesis initiation by investigating the factors affecting initiation including promoter sequence, initiating NTPs, and RdRp structural determinants. We investigated the importance of promoter sequence for ebolavirus RNA synthesis initiation. Most nsNSVs have complementary genomic ends, however published ebolavirus sequences lack complementarity. We sequenced ebolavirus genomic termini and discovered the 3′ end has sequence variability and an overhang compared to the 5′ end of the replication product. Characterization of promoter sequence requirements for initiation revealed ebolavirus RdRp initiates internally (T2C) in contrast to most nsNSV RdRps, including RSV RdRp which initiates replication from T1U . We investigated the role of promoter sequence along with initiating NTPs for RSV RNA synthesis initiation. We showed that initiation by the RSV RdRp at T1U and T3C occurred independently of each other with the same RdRp selecting the two sites. Site selection could be modulated by the relative concentrations of ATP versus GTP. RSV template mutation analysis indicated the RdRp could bind ATP and CTP, or GTP, independently of template nucleotides. The data suggest a model in which the RdRps innate affinity for particular NTPs, coupled with a repeating sequence element within the promoter, allows precise initiation of replication at T1U or transcription at T3C. Other RNA virus polymerases utilize a priming residue to form base stacking interactions with the initiating NTP and stabilize the initiation complex. The RSV RdRp priming residue has not been described. Our data suggest RSV RdRp large subunit L proline 1261 is involved in initiation from T1U and T3C, but not RNA elongation. Alanine substitution analysis revealed the initiation defect at T3C, but not T1U, was partially rescued by increasing initiating NTP levels. These data suggest proline 1261 is the RSV priming residue and is more strictly required for terminal initiation (T1U) than internal initiation (T3C). The nsNSV have divergent initiation mechanisms and better understanding will aid in rational antiviral and vaccine design. Advisors/Committee Members: Fearns, Rachel (advisor).

Subjects/Keywords: Virology; Nonsegmented negative sense RNA virus polymerase; Priming loop; RdRp; RNA synthesis initiation

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APA (6^th Edition):

Cressey, T. (2020). RNA synthesis initiation by the nonsegmented negative-sense RNA virus polymerases. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/39385

Chicago Manual of Style (16^th Edition):

Cressey, Tessa. “RNA synthesis initiation by the nonsegmented negative-sense RNA virus polymerases.” 2020. Doctoral Dissertation, Boston University. Accessed January 23, 2021. http://hdl.handle.net/2144/39385.

MLA Handbook (7^th Edition):

Cressey, Tessa. “RNA synthesis initiation by the nonsegmented negative-sense RNA virus polymerases.” 2020. Web. 23 Jan 2021.

Vancouver:

Cressey T. RNA synthesis initiation by the nonsegmented negative-sense RNA virus polymerases. [Internet] [Doctoral dissertation]. Boston University; 2020. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/2144/39385.

Council of Science Editors:

Cressey T. RNA synthesis initiation by the nonsegmented negative-sense RNA virus polymerases. [Doctoral Dissertation]. Boston University; 2020. Available from: http://hdl.handle.net/2144/39385

University of Arizona

19. Summerton, James Edward, 1944-. FUNCTIONAL COMPARTMENTATION OF RIBONUCLEIC ACID PRECURSORS IN ESCHERICHIA COLI .

Degree: 1973, University of Arizona

URL: http://hdl.handle.net/10150/288066

Subjects/Keywords: RNA – Metabolism.; Escherichia coli.; RNA – Synthesis.

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

APA (6^th Edition):

Summerton, James Edward, 1. (1973). FUNCTIONAL COMPARTMENTATION OF RIBONUCLEIC ACID PRECURSORS IN ESCHERICHIA COLI . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/288066

Chicago Manual of Style (16^th Edition):

Summerton, James Edward, 1944-. “FUNCTIONAL COMPARTMENTATION OF RIBONUCLEIC ACID PRECURSORS IN ESCHERICHIA COLI .” 1973. Doctoral Dissertation, University of Arizona. Accessed January 23, 2021. http://hdl.handle.net/10150/288066.

MLA Handbook (7^th Edition):

Summerton, James Edward, 1944-. “FUNCTIONAL COMPARTMENTATION OF RIBONUCLEIC ACID PRECURSORS IN ESCHERICHIA COLI .” 1973. Web. 23 Jan 2021.

Vancouver:

Summerton, James Edward 1. FUNCTIONAL COMPARTMENTATION OF RIBONUCLEIC ACID PRECURSORS IN ESCHERICHIA COLI . [Internet] [Doctoral dissertation]. University of Arizona; 1973. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10150/288066.

Council of Science Editors:

Summerton, James Edward 1. FUNCTIONAL COMPARTMENTATION OF RIBONUCLEIC ACID PRECURSORS IN ESCHERICHIA COLI . [Doctoral Dissertation]. University of Arizona; 1973. Available from: http://hdl.handle.net/10150/288066

University of British Columbia

20. Chase, Randal. A study of tRNA biosynthesis in Escherichia coli.

Degree: PhD, Biochemistry and Molecular Biology, 1974, University of British Columbia

URL: http://hdl.handle.net/2429/18942

► Escherichia coli was grown in the presence of amino acid analogues or in the absence of required amino acids. The tRNAs. were isolated and characterized.… (more)

▼ Escherichia coli was grown in the presence of amino acid analogues or in the absence of required amino acids. The tRNAs. were isolated and characterized. Numerous changes were observed in the total tRNA acceptance for particular amino acids although in no instance did these changes occur for amino acids corresponding to the adverse growth condition. The isoacceptor patterns for particular labelled aminoacyl-tRNAs were determined on the anion exchanger RPC-5. Novel isoacceptor tRNAs were observed under several growth conditions. Significant changes in tRNA isoacceptor distributions were noted. In certain instances it appeared that changes in total amino acid acceptance could be explained in terms of the increased or decreased synthesis of particular tRNA isoacceptors while for other tRNAs it seemed that changes occurred in the synthesis of all isoacceptors for a particular amino acid such that the relative amounts of isoacceptors remained constant even when total amino acid acceptance changed considerably. E. coli was grown over a wide temperature range, 17°C to 44°C, and the tRNA isolated and characterized. Novel tRNA isoacceptors were observed at both high and low growth temperatures for most but not all tRNAs. It was shown that the same isoacceptors could be formed at both extremes of temperature. Preliminary results suggest that the novel isoacceptors are formed as the result of a temperature aggravation of a nutritional problem at extremes of growth temperature. One of the novel tRNA isoacceptors formed under a variety of adverse growth conditions, tRNA3[sup Val] , was purified and partially characterized. The results are consistent with tRNA3[sup Val] being an undermodified precursor of the major isoacceptor tRNA₁[sup Val]. E. coli str[sup D] was grown and the tRNA isolated and characterized. Major differences in the amino acid acceptances for several tRNAs were observed. These changes were accomplished without any significant changes in the relative isoacceptor distributions as determined by RPC-5 chromatography. Gel electrophoretic analysis was performed on tRNA from cells grown at extremes of growth temperature. Significant differences were observed in the 5S region; there was an accumulation of material in cells grown at low temperature and a decrease of material in cells grown at high temperature.

Subjects/Keywords: RNA – biosynthesis; RNA – Synthesis; Escherichia coli

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

APA (6^th Edition):

Chase, R. (1974). A study of tRNA biosynthesis in Escherichia coli. (Doctoral Dissertation). University of British Columbia. Retrieved from http://hdl.handle.net/2429/18942

Chicago Manual of Style (16^th Edition):

Chase, Randal. “A study of tRNA biosynthesis in Escherichia coli.” 1974. Doctoral Dissertation, University of British Columbia. Accessed January 23, 2021. http://hdl.handle.net/2429/18942.

MLA Handbook (7^th Edition):

Chase, Randal. “A study of tRNA biosynthesis in Escherichia coli.” 1974. Web. 23 Jan 2021.

Vancouver:

Chase R. A study of tRNA biosynthesis in Escherichia coli. [Internet] [Doctoral dissertation]. University of British Columbia; 1974. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/2429/18942.

Council of Science Editors:

Chase R. A study of tRNA biosynthesis in Escherichia coli. [Doctoral Dissertation]. University of British Columbia; 1974. Available from: http://hdl.handle.net/2429/18942

University of British Columbia

21. Webb, Vera Ann B. In vivo in vitro synthesis of ribosomal RNA in bacillus subtilis.

Degree: PhD, Microbiology and Immunology, 1988, University of British Columbia

URL: http://hdl.handle.net/2429/29448

► The work presented explored the in vivo and in vitro synthesis of ribosomal RNA in the Gram positive, spore-forming bacterium Bacillus subtilis. The investigation began… (more)

▼ The work presented explored the in vivo and in vitro synthesis of ribosomal RNA in the Gram positive, spore-forming bacterium Bacillus subtilis. The investigation began with a study of rRNA synthesis in B. subtilis during steady state growth and under nutritional shift-up conditions. The percent of transcription which is ribosomal RNA was measured by hybridization of pulse labeled RNA to a specific DNA probe carrying the 3' end of the 23S RNA gene. The fractional rate of ribosomal RNA synthesis increased with cellular growth rate, and showed a rapid increase after a nutritional shift up. RNA synthesis during infection with an amber mutant of bacteriophage SP01 was also examined. Infected cells continued to synthesize rRNA at the preinfection rate, but could not respond to media enrichment by increasing the percent rRNA-synthesis. The latter study suggested the existence of a specific RNA polymerase that transcribed ribosomal RNA genes. The conclusions from the in vivo study led to an analysis of rRNA transcription in vitro. The isolation of the putative ribosomal RNA specific RNA polymerase was attempted by affinity chromatography on cellulose complexed with plasmid DNA containing the promoter region of the B. subtilis rrnB rRNA operon, and by sedimentation through a glycerol gradient. No difference in activity profile was observed when transcription activity at the rRNA tandem promoters was compared to activity at a non-ribosomal promoter. Since in vivo analysis of the control of rRNA synthesis in Escherichia coli suggested that regulation occurs at the level of transcription initiation, in vitro transcription initiation at the B. subtilis rRNA promoters was investigated using the single round transcription assay. Initial rates of transcription were different at each of the two tandem promoters of the B. subtilis rrnB operon: the upstream promoter, PI, initiated slowly, while the downstream promoter, P2, initiated faster. In addition, transcription initiation at the two promoters appeared to be linked. The formation of a heparin resistant complex at the PI promoter affected the stability of the heparin resistant complex formed at the P2 promoter. The kinetics of transcription initiation at the tandem rRNA promoters were examined using the tau plot analysis. RNA polymerase had a high affinity for both rRNA promoters, but the rate of initiation at these promoters was relatively slow when compared to non-ribosomal promoters. Finally, transcription initiation on two artificial tandem promoter constructs was compared with initiation on the native tandem promoter construct. In general, PI was shown to have a positive effect on transcription from downstream promoters, but had specific effects on different promoters.

Subjects/Keywords: RNA, Ribosomal; RNA – Synthesis; Bacillus subtilis

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

APA (6^th Edition):

Webb, V. A. B. (1988). In vivo in vitro synthesis of ribosomal RNA in bacillus subtilis. (Doctoral Dissertation). University of British Columbia. Retrieved from http://hdl.handle.net/2429/29448

Chicago Manual of Style (16^th Edition):

Webb, Vera Ann B. “In vivo in vitro synthesis of ribosomal RNA in bacillus subtilis.” 1988. Doctoral Dissertation, University of British Columbia. Accessed January 23, 2021. http://hdl.handle.net/2429/29448.

MLA Handbook (7^th Edition):

Webb, Vera Ann B. “In vivo in vitro synthesis of ribosomal RNA in bacillus subtilis.” 1988. Web. 23 Jan 2021.

Vancouver:

Webb VAB. In vivo in vitro synthesis of ribosomal RNA in bacillus subtilis. [Internet] [Doctoral dissertation]. University of British Columbia; 1988. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/2429/29448.

Council of Science Editors:

Webb VAB. In vivo in vitro synthesis of ribosomal RNA in bacillus subtilis. [Doctoral Dissertation]. University of British Columbia; 1988. Available from: http://hdl.handle.net/2429/29448

University of Rochester

22. Spitale, Robert C. (1982 - ). Chemical and structural analysis of RNA-based gene regulation.

Degree: PhD, 2011, University of Rochester

URL: http://hdl.handle.net/1802/14557

► Non-protein coding RNA (ncRNA), once thought to be a functional spectator in biological systems have recently been recharacterized as a critical component of many essential… (more)

▼ Non-protein coding RNA (ncRNA), once thought to be a functional spectator in biological systems have recently been recharacterized as a critical component of many essential life processes. Due to the emergent pervasiveness of these vital biomolecules, structure/function studies aimed at elucidating their molecular basis of action are becoming increasingly important to the scientific community. To that end, this thesis is aimed at understanding the chemical and structural basis of function in ncRNA macromolecules, and to compare their molecular basis of action with proteins. In order to accomplish this, the thesis focuses on two ncRNA macromolecules: the hairpin ribozyme and the PreQ1 riboswitch. The hairpin ribozyme is an autocatalytic RNA motif found in tobacco ringspot virus satellite RNA. It serves to process concatentated RNA transcripts during rolling-circle RNA. Unlike other catalytic RNA motifs, the hairpin ribozyme relies solely on the localized nucleobases of the catalytic core. This all-RNA based mode of catalysis makes it an ideal system to elucidate the chemical principles employed by RNA for rate acceleration. To shed light on the mode of activity of this RNA construct, a synergistic approach using organic synthesis, enzymology and X-ray crystallography has been undertaken. From these studies, we have begun to understand how this RNA uses substrate orientation and functional group complimentarity to initiate activity. Additionally, parallels between RNA and protein enzymes have been derived, highlighting similar mechanisms of RNA processing. The second goal of the thesis is aimed at understanding the mode of metabolite recognition in the PreQ1 riboswitch aptamer domain. The PreQ1 riboswitch aptamer domain functions to regulate bacterial genes encoding proteins that are critical for exogenous preQ1 uptake or de novo biosynthesis. Notably, the essential aptamer domain was characterized to be ~3-times smaller than other analogous purine-sensing riboswitches. To understand how PreQ1 is recognized by the aptamer, an examination was performed employing X-Ray crystallographic techniques; this study provided a molecular glimpse into the mode of metabolite recognition. From these studies, we have expanded the knowledge of structure-based functional RNA, and have been able to compare modes of metabolite recognition between RNA and protein macromolecules.

Subjects/Keywords: RNA; Ribozyme; Riboswitch; X-ray crystallography; Organic synthesis

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

APA (6^th Edition):

Spitale, R. C. (. -. ). (2011). Chemical and structural analysis of RNA-based gene regulation. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/14557

Chicago Manual of Style (16^th Edition):

Spitale, Robert C (1982 - ). “Chemical and structural analysis of RNA-based gene regulation.” 2011. Doctoral Dissertation, University of Rochester. Accessed January 23, 2021. http://hdl.handle.net/1802/14557.

MLA Handbook (7^th Edition):

Spitale, Robert C (1982 - ). “Chemical and structural analysis of RNA-based gene regulation.” 2011. Web. 23 Jan 2021.

Vancouver:

Spitale RC(-). Chemical and structural analysis of RNA-based gene regulation. [Internet] [Doctoral dissertation]. University of Rochester; 2011. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1802/14557.

Council of Science Editors:

Spitale RC(-). Chemical and structural analysis of RNA-based gene regulation. [Doctoral Dissertation]. University of Rochester; 2011. Available from: http://hdl.handle.net/1802/14557

University of Otago

23. Bernhardt, Harold Stephen. tRNA: Self-Assembly and the Dawn of Genetic Coding .

Degree: 2011, University of Otago

URL: http://hdl.handle.net/10523/559

► Transfer RNA (tRNA) is an ancient molecule with a myriad of functions in modern biology; however, its pre-eminent role is in the transfer of individual… (more)

▼ Transfer RNA (tRNA) is an ancient molecule with a myriad of functions in modern biology; however, its pre-eminent role is in the transfer of individual amino acids to the growing polypeptide chain in protein synthesis. The weight of both theoretical and experimental evidence points to a hairpin-duplication origin for tRNA, with Di Giulio arguing that the canonical intron insertion position in the anticodon loop marks the point at which the two hairpins were originally joined. I have discovered a molecular ‘signature’ in the anticodon loop sequences of contemporary tRNAsGly: a highly conserved CCA sequence that suggests the first anticodon (NCC for glycine) was derived from the 3'-terminal CCA of the upstream hairpin, and the first tRNA was tRNAGly. The relative lack of post- transcriptional modification in contemporary tRNAsGly suggests that this tRNA could have formed the necessary interactions that form the basis of the genetic code prior to the advent of protein modification enzymes. Such a scenario would appear to fit Crick’s frozen accident model for the origin of the genetic code, but in fact the presence of this particular sequence in the anticodon loop of the first tRNA may have been instrumental in the subsequent evolution of coded protein synthesis. I have hypothesized that the advent of the single-stranded anticodon loop allowed tRNAs to interact with single-stranded (regions of) RNAs in the RNA world, and these serendipitous binding partners bound to pairs of anticodon loops held in juxtaposition on an ancestral peptidyl transferase ribozyme catalysing noncoded peptide synthesis, the predecessor to the large ribosomal subunit RNA. This interaction would have tethered the two tRNAs, enhancing their binding to the peptidyl transferase and increasing the rate of peptide synthesis. I believe such a system evolved naturally into a system of coded protein synthesis, driven by selection for enhancement of synthesis of specific peptides. A similar model has been discussed very briefly by Christian de Duve in Blueprint for a Cell, and is supported by isolated experiments that demonstrate enhanced binding of tRNA to the Escherichia coli 50S ribosomal subunit (that contains the peptidyl transfer centre) in the presence of cognate oligonucleotides. According to my model, the small ribosomal subunit RNA evolved later as a decoding hairpin that functioned in trans, exerting control over the interaction between tRNAs and their binding partners (proto-mRNAs). I have also utilized tRNAGly from E. coli as a starting material for the creation of tRNA variants able to oligomerize or self-assemble, with the dual aims of exploring the possible role of self-assembly in the evolution of tRNA and for producing RNA building blocks that will form higher oligomers, ideally 3D arrays, at neutral pH, with potential nanotechnology applications. Site-directed mutagenesis of tRNAGly was used to create tRNA variants with additional complementarity in the T loop and other single-stranded regions, with the aim of enhancing their… Advisors/Committee Members: Tate, Warren P (advisor).

Subjects/Keywords: transfer RNA; evolution; origin genetic code; nanotechnology; origin protein synthesis

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

APA (6^th Edition):

Bernhardt, H. S. (2011). tRNA: Self-Assembly and the Dawn of Genetic Coding . (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/559

Chicago Manual of Style (16^th Edition):

Bernhardt, Harold Stephen. “tRNA: Self-Assembly and the Dawn of Genetic Coding .” 2011. Doctoral Dissertation, University of Otago. Accessed January 23, 2021. http://hdl.handle.net/10523/559.

MLA Handbook (7^th Edition):

Bernhardt, Harold Stephen. “tRNA: Self-Assembly and the Dawn of Genetic Coding .” 2011. Web. 23 Jan 2021.

Vancouver:

Bernhardt HS. tRNA: Self-Assembly and the Dawn of Genetic Coding . [Internet] [Doctoral dissertation]. University of Otago; 2011. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10523/559.

Council of Science Editors:

Bernhardt HS. tRNA: Self-Assembly and the Dawn of Genetic Coding . [Doctoral Dissertation]. University of Otago; 2011. Available from: http://hdl.handle.net/10523/559

University of Vienna

24. Heindl, Katrin. Roles of the novel 5'-Polynucleotide kinase NoI9 in ribosome synthesis.

Degree: 2010, University of Vienna

URL: http://othes.univie.ac.at/12007/

►

In einer sich teilenden Zelle nehmen ribosomale RNAs 80% der gesamten zellulären RNA ein. Sie sind die Hauptkomponente der Ribosomen, grossen Komplexen aus RNA und… (more)

▼

In einer sich teilenden Zelle nehmen ribosomale RNAs 80% der gesamten zellulären RNA ein. Sie sind die Hauptkomponente der Ribosomen, grossen Komplexen aus RNA und Proteinen, die als “Protein-Fabriken” der Zelle eine zentrale Aufgabe ausüben. Die korrekte und effiziente Biosynthese der ribosomalen RNA ist daher grundlegend für jede Zelle. Im Nukleolus werden drei der vier ribosomalen RNAs (rRNAs), 18S, 5.8S und 28S, gemeinsam von der RNA Polymerase I zu einem einzelnen polyzistronen Precursor transkribiert. In einer geordneten Aufeinanderfolge von endo- und exonukleo-lytischen Aktivitäten maturieren diese rRNAs und werden letztendlich gemeinsam mit der 5S rRNA und einer Vielzahl von ribosomalen Proteinen zum Ribosom zusammengefügt. Während meiner Doktorarbeit habe ich die erste nukleoläre Polynukleotid-Kinase Nol9/Grc3 identifiziert und ihre Funktion studiert. Nol9/Grc3 ist in zweierlei Hinsicht an der Maturierung von ribosomalen RNAs beteiligt: 1. S. cerevisiae Grc3 ist essenziell für eine effiziente Beendigung der Transkription von rRNA Genen als Teil des Rat1-abhängigen ‘Torpedo-Mechanismus” und somit wesentlich für die rasche Wiederverwendung der RNA Polymerase I. 2. Humanes Nol9 hat eine Funktion bei der Prozessierung der 5.8S und 28S ribosomalen RNA aus ihrem gemeinsamen Precursor, möglicherweise in einem Xrn2-abhängigen Prozessierungsschritt. Diese Ergebnisse beleuchten ein moegliches Zusammenspiel der Polynukleotid-Kinase Nol9/Grc3 und der 5’-3’ Exonuklease Xrn2/Rat1. Berücksichtigt man die wachsenden Berichte über zusätzliche Aufgaben des Nukleolus im RNA Metabolismus abseits der Maturierung ribosomaler RNA und die Aktivitaet von Nol9/Grc3 an sowohl einzel- als auch doppelsträngigen RNA- und DNA-Substraten, zeichnen sich mögliche weitere Funktionen für die Polynukleotid-Kinase Nol9/Grc3 ab.

In a dividing cell, about 80% of the cellular RNA consist of ribosomal RNAs (rRNAs), the core components of the ribosomes. Efficient protein production relies on the sufficient availability of ribosomes; therefore indefectible rRNA processing is fundamental to every cell. The 18S, 5.8S and 28S rRNAs are transcribed in the nucleolus by RNA polymerase I as a single polycistronic precursor RNA and liberated by a complex series of endo- and exonucleolytic cleavage events. Eventually, they are assembled together with the 5S rRNA and a plethora of ribosomal proteins to form the ribosomes. In my PhD work, I identified the first nucleolar polynucleotide kinase Nol9/Grc3 and investigated its involvement in two different aspects of rRNA biogenesis: 1. RNA Polymerase I transcription termination; and 2. processing of the large subunit rRNAs. In yeast, Grc3 is essential for efficient transcription termination in the Rat1-dependent ‘torpedo mechanism’ thereby enabling rapid recycling of RNA polymerase I. In human cells, Nol9 is required for the processing of 5.8S and 28S rRNAs, the components of the large 60S ribosomal subunits, most likely at a Xrn2-dependent processing step. These findings intrigue a potential…

Subjects/Keywords: 42.13 Molekularbiologie; Kinase / rRNA / Ribosom; Polynucleotide kinase / ribosomal RNA / ribosome synthesis

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APA (6^th Edition):

Heindl, K. (2010). Roles of the novel 5'-Polynucleotide kinase NoI9 in ribosome synthesis. (Thesis). University of Vienna. Retrieved from http://othes.univie.ac.at/12007/

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):

Heindl, Katrin. “Roles of the novel 5'-Polynucleotide kinase NoI9 in ribosome synthesis.” 2010. Thesis, University of Vienna. Accessed January 23, 2021. http://othes.univie.ac.at/12007/.

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

MLA Handbook (7^th Edition):

Heindl, Katrin. “Roles of the novel 5'-Polynucleotide kinase NoI9 in ribosome synthesis.” 2010. Web. 23 Jan 2021.

Vancouver:

Heindl K. Roles of the novel 5'-Polynucleotide kinase NoI9 in ribosome synthesis. [Internet] [Thesis]. University of Vienna; 2010. [cited 2021 Jan 23]. Available from: http://othes.univie.ac.at/12007/.

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

Council of Science Editors:

Heindl K. Roles of the novel 5'-Polynucleotide kinase NoI9 in ribosome synthesis. [Thesis]. University of Vienna; 2010. Available from: http://othes.univie.ac.at/12007/

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

California State University – San Bernardino

25. Lin, Jared. CHARACTERIZING THE ROLE OF N TERMINUS OF INFLUENZA A NUCLEOPROTEIN FOR LOCATION AND VIRAL RNP ACTIVITY.

Degree: MSin Biology, Biology, 2018, California State University – San Bernardino

URL: https://scholarworks.lib.csusb.edu/etd/694

► The influenza viral ribonucleoprotein complexes (vRNPs) are responsible for viral RNA synthesis. Each vRNP is comprised of one vRNA segment, the viral RNA dependent… (more)

▼ The influenza viral ribonucleoprotein complexes (vRNPs) are responsible for viral RNA synthesis. Each vRNP is comprised of one vRNA segment, the viral RNA dependent RNA polymerase complex (RdRP), and multiple copies of nucleoprotein (NP). NP serves as scaffold in formation of vRNPs, but also regulates vRNP activity. The N-terminus of NP contains a nonconventional nuclear localization signal (NLS1) essential for initial vRNP nuclear import, but also interacts with host RNA helicases to enhance viral RNA replication in the nucleus. NP contains at least one additional NLS sequence, with bioinformatics revealing a third NLS in some NP proteins. Published yeast-two hybrid results indicate that the first 20 amino acids of NP can sufficiently bind with cellular protein UAP56. Suggesting the interaction of NP-UAP56 can be a major mechanism of how NP involve in viral replication. Thus, to examine the role of the N-terminus of NP aside from its vRNP nuclear localization activity N-terminal 20 amino acid deletion mutants with or without the addition of the conventional NLS from SV-40 T-antigen were constructed, termed del20NLS-NP and del20-NP. Nuclear localization of vRNPs with these constructs was assessed by GFP expression and western blotting. All these constructs exhibit nuclear localization, consistent with NLS1 being utilized for vRNP localization but not NP localization and vRNP formation in the nucleus. Furthermore, qPCR results demonstrated decreased vRNA synthesis activity, exacerbated as the vRNA template is lengthened in both plasmids, consistent with a lack of interaction with host RNA helicases. Interestingly, del20-NP vRNP activity is less severe than del20NLS-NP, suggesting perturbations of the N-terminus disrupt vRNP activity. To narrow down the region responsible for vRNA expression defect, del10-NP was constructed. GFP expression displayed similar activity between del10-NP and WT-NP with del20-NP showing a severe defection, suggesting NP amino acids 11-20 might be the major region responsible for the vRNA synthesis defect. However, sucrose density gradient results do not support the published interaction between NP and UAP56 in 293T cells. These results support the N-terminal region, potentially amino acids 11-20 of NP, is playing the important role in efficient viral gene expression during virus replication especially as vRNA template lengthen, and that the NLS1 of NP is not essential for NP/vRNP nuclear localization in our reconstituted vRNP assay. Advisors/Committee Members: Newcomb, Laura.

Subjects/Keywords: Influenza; Nucleoprotein; NLS; UAP56; GFP expression; viral RNA synthesis; Virology

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

APA (6^th Edition):

Lin, J. (2018). CHARACTERIZING THE ROLE OF N TERMINUS OF INFLUENZA A NUCLEOPROTEIN FOR LOCATION AND VIRAL RNP ACTIVITY. (Thesis). California State University – San Bernardino. Retrieved from https://scholarworks.lib.csusb.edu/etd/694

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):

Lin, Jared. “CHARACTERIZING THE ROLE OF N TERMINUS OF INFLUENZA A NUCLEOPROTEIN FOR LOCATION AND VIRAL RNP ACTIVITY.” 2018. Thesis, California State University – San Bernardino. Accessed January 23, 2021. https://scholarworks.lib.csusb.edu/etd/694.

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

MLA Handbook (7^th Edition):

Lin, Jared. “CHARACTERIZING THE ROLE OF N TERMINUS OF INFLUENZA A NUCLEOPROTEIN FOR LOCATION AND VIRAL RNP ACTIVITY.” 2018. Web. 23 Jan 2021.

Vancouver:

Lin J. CHARACTERIZING THE ROLE OF N TERMINUS OF INFLUENZA A NUCLEOPROTEIN FOR LOCATION AND VIRAL RNP ACTIVITY. [Internet] [Thesis]. California State University – San Bernardino; 2018. [cited 2021 Jan 23]. Available from: https://scholarworks.lib.csusb.edu/etd/694.

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

Council of Science Editors:

Lin J. CHARACTERIZING THE ROLE OF N TERMINUS OF INFLUENZA A NUCLEOPROTEIN FOR LOCATION AND VIRAL RNP ACTIVITY. [Thesis]. California State University – San Bernardino; 2018. Available from: https://scholarworks.lib.csusb.edu/etd/694

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

Uppsala University

26. Elkhalifa, Dina. Improvement of positive strand assay used in detecting positive and negative RNA of hepatitis E virus.

Degree: Women's and Children's Health, 2014, Uppsala University

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-218747

► Background: Hepatitis E (HEV) is a small, non-enveloped virus that belongs to the viral genus Hepevirus. HEV is a positive sense single-stranded RNA virus… (more)

Subjects/Keywords: Replication; false positivity; cDNA synthesis; transcribed RNA sample; MgCl2

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

APA (6^th Edition):

Elkhalifa, D. (2014). Improvement of positive strand assay used in detecting positive and negative RNA of hepatitis E virus. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-218747

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):

Elkhalifa, Dina. “Improvement of positive strand assay used in detecting positive and negative RNA of hepatitis E virus.” 2014. Thesis, Uppsala University. Accessed January 23, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-218747.

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

MLA Handbook (7^th Edition):

Elkhalifa, Dina. “Improvement of positive strand assay used in detecting positive and negative RNA of hepatitis E virus.” 2014. Web. 23 Jan 2021.

Vancouver:

Elkhalifa D. Improvement of positive strand assay used in detecting positive and negative RNA of hepatitis E virus. [Internet] [Thesis]. Uppsala University; 2014. [cited 2021 Jan 23]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-218747.

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

Council of Science Editors:

Elkhalifa D. Improvement of positive strand assay used in detecting positive and negative RNA of hepatitis E virus. [Thesis]. Uppsala University; 2014. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-218747

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

Michigan State University

27. Chaney, William G. The role of messenger RNA in nascent peptide chain accumulations.

Degree: PhD, Department of Biochemistry, 1979, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:42126

Subjects/Keywords: RNA; Peptides; Proteins – Synthesis

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

APA (6^th Edition):

Chaney, W. G. (1979). The role of messenger RNA in nascent peptide chain accumulations. (Doctoral Dissertation). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:42126

Chicago Manual of Style (16^th Edition):

Chaney, William G. “The role of messenger RNA in nascent peptide chain accumulations.” 1979. Doctoral Dissertation, Michigan State University. Accessed January 23, 2021. http://etd.lib.msu.edu/islandora/object/etd:42126.

MLA Handbook (7^th Edition):

Chaney, William G. “The role of messenger RNA in nascent peptide chain accumulations.” 1979. Web. 23 Jan 2021.

Vancouver:

Chaney WG. The role of messenger RNA in nascent peptide chain accumulations. [Internet] [Doctoral dissertation]. Michigan State University; 1979. [cited 2021 Jan 23]. Available from: http://etd.lib.msu.edu/islandora/object/etd:42126.

Council of Science Editors:

Chaney WG. The role of messenger RNA in nascent peptide chain accumulations. [Doctoral Dissertation]. Michigan State University; 1979. Available from: http://etd.lib.msu.edu/islandora/object/etd:42126

Michigan State University

28. Frederick, Robert John, 1944-. Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli.

Degree: PhD, 1976, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:40107

Subjects/Keywords: RNA – Synthesis; Bacteriophages; Escherichia coli

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APA (6^th Edition):

Frederick, Robert John, 1. (1976). Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli. (Doctoral Dissertation). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:40107

Chicago Manual of Style (16^th Edition):

Frederick, Robert John, 1944-. “Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli.” 1976. Doctoral Dissertation, Michigan State University. Accessed January 23, 2021. http://etd.lib.msu.edu/islandora/object/etd:40107.

MLA Handbook (7^th Edition):

Frederick, Robert John, 1944-. “Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli.” 1976. Web. 23 Jan 2021.

Vancouver:

Frederick, Robert John 1. Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli. [Internet] [Doctoral dissertation]. Michigan State University; 1976. [cited 2021 Jan 23]. Available from: http://etd.lib.msu.edu/islandora/object/etd:40107.

Council of Science Editors:

Frederick, Robert John 1. Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli. [Doctoral Dissertation]. Michigan State University; 1976. Available from: http://etd.lib.msu.edu/islandora/object/etd:40107

Michigan State University

29. Jolly, James Frederick, 1946-. The control of RNA transcription in bacteriophage gh-1-infected Pseudomonas putida.

Degree: PhD, Department of Biochemistry, 1976, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:40802

Subjects/Keywords: Genetic transcription; RNA – Synthesis

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

APA (6^th Edition):

Jolly, James Frederick, 1. (1976). The control of RNA transcription in bacteriophage gh-1-infected Pseudomonas putida. (Doctoral Dissertation). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:40802

Chicago Manual of Style (16^th Edition):

Jolly, James Frederick, 1946-. “The control of RNA transcription in bacteriophage gh-1-infected Pseudomonas putida.” 1976. Doctoral Dissertation, Michigan State University. Accessed January 23, 2021. http://etd.lib.msu.edu/islandora/object/etd:40802.

MLA Handbook (7^th Edition):

Jolly, James Frederick, 1946-. “The control of RNA transcription in bacteriophage gh-1-infected Pseudomonas putida.” 1976. Web. 23 Jan 2021.

Vancouver:

Jolly, James Frederick 1. The control of RNA transcription in bacteriophage gh-1-infected Pseudomonas putida. [Internet] [Doctoral dissertation]. Michigan State University; 1976. [cited 2021 Jan 23]. Available from: http://etd.lib.msu.edu/islandora/object/etd:40802.

Council of Science Editors:

Jolly, James Frederick 1. The control of RNA transcription in bacteriophage gh-1-infected Pseudomonas putida. [Doctoral Dissertation]. Michigan State University; 1976. Available from: http://etd.lib.msu.edu/islandora/object/etd:40802

Texas Tech University

30. Brantley, Kenny M. Estradiol regulation of uterine nucleolar RNA synthesis.

Degree: TTUHSC – Biochemistry and Molecular Genetics, 1993, Texas Tech University

URL: http://hdl.handle.net/2346/10636

► Administration of estradiol (E) to mature ovariectomized rats results in an early (4h) increase in nucleolar transcriptional activity above controls, this increase is totally due… (more)

▼ Administration of estradiol (E) to mature ovariectomized rats results in an early (4h) increase in nucleolar transcriptional activity above controls, this increase is totally due to an increased elongation rate of nascent transcripts. Salt extraction (150 mM NaCl) of isolated nucleoli eliminates the early stimulatory effect of E on nucleolar transcriptional activity. Addition of salt extracts obtained from uterine nucleoli of animals treated with E (4h) to nucleoli isolated from uteri of control animals resulted in increased transcriptional activity. The stimulation was due to an increased rate of elongation of nascent chains in uterine nucleoli. Treatment of animals with cycloheximide (eye) or actinomycin D (AD) eliminates the E induced stimulation and the stimulatory activity of salt extract from nucleoli isolated from E treated animals on control uterine nucleoli. Alkaline phosphatase treatment of nucleoli in vitro also is able to eliminate the E induced increase in transcriptional activity. Isolated uterine nucleoli and the salt extracts (E treated and control) contain active protein kinase(s), which are capable of in vitro phosphorylating a number of proteins in nucleoli isolated from control and E treated animals using ATP or GTP as substrate. In vivo E treatment results in the phosphorylation of a single protein with an apparent molecular weight of 105 kDa. Treatment of animals with AD or eye blocks the in vivo phosphorylation of a 105 kDa protein but not the in vitro phosphorylation, suggesting that the protein substrates and at least one of the endogenous nuclear kinase(s) are not the targets of the metabolic inhibitors. Decreased in vitro phosphorylation of a number of other proteins is also observed due to AD or eye treatment in vivo. In vitro treatment of nucleoli with camptothecin, a specific inhibitor of topoisomerase I, was capable of inhibiting the E induced increase in nucleolar RNA synthesis. Results showed that topoisomerase was necessary but not sufficient for the E induced increase in nucleolar RNA synthesis. Leupeptin, an inhibitor of the processing of nucleolin, a 105 kDa phosphoprotein, was also capable of inhibiting E induced increase in nucleolar RNA synthesis. These results point to a role of phosphorylation of the 105 kDa protein in the early E induced stimulation of nucleolar RNA transcriptional activity. Nucleolin is a possible candidate for the 105 kDa protein that is phosphorylated in vivo

Subjects/Keywords: Rats – Physiology; Estradiol; RNA – Synthesis

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

Brantley, K. M. (1993). Estradiol regulation of uterine nucleolar RNA synthesis. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/10636

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):

Brantley, Kenny M. “Estradiol regulation of uterine nucleolar RNA synthesis.” 1993. Thesis, Texas Tech University. Accessed January 23, 2021. http://hdl.handle.net/2346/10636.

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

MLA Handbook (7^th Edition):

Brantley, Kenny M. “Estradiol regulation of uterine nucleolar RNA synthesis.” 1993. Web. 23 Jan 2021.

Vancouver:

Brantley KM. Estradiol regulation of uterine nucleolar RNA synthesis. [Internet] [Thesis]. Texas Tech University; 1993. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/2346/10636.

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

Council of Science Editors:

Brantley KM. Estradiol regulation of uterine nucleolar RNA synthesis. [Thesis]. Texas Tech University; 1993. Available from: http://hdl.handle.net/2346/10636

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

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