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  • 1
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    Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-09
    Description: A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Structural biology: Aerial view of the HIV genome (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Al-Hashimi, Hashim M -- England -- Nature. 2009 Aug 6;460(7256):696-8. doi: 10.1038/460696a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661906" target="_blank"〉PubMed〈/a〉
    Keywords: Genome, Viral/*genetics ; HIV-1/chemistry/*genetics/ultrastructure ; Human Immunodeficiency Virus Proteins/chemistry/genetics ; *Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; RNA, Viral/*chemistry/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-03-13
    Description: Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG*dT and rG*rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10(-3) to 10(-5)) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547696/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547696/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kimsey, Isaac J -- Petzold, Katja -- Sathyamoorthy, Bharathwaj -- Stein, Zachary W -- Al-Hashimi, Hashim M -- R01 GM089846/GM/NIGMS NIH HHS/ -- R01GM089846/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Mar 19;519(7543):315-20. doi: 10.1038/nature14227. Epub 2015 Mar 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27710, USA. ; Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. ; Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25762137" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; Base Sequence ; DNA/*chemistry ; DNA Fingerprinting ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Mutation/genetics ; Nucleic Acid Heteroduplexes/*chemistry ; Probability ; RNA/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Biochemistry. Exciting structures (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-09-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Al-Hashimi, Hashim M -- R01 AI066975-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1295-6. doi: 10.1126/science.1195571.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA. hashimi@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829475" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/*chemistry ; Computational Biology ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Topology links RNA secondary structure with global conformation, dynamics, and adaptation (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-09
    Description: Thermodynamic rules that link RNA sequences to secondary structure are well established, but the link between secondary structure and three-dimensional global conformation remains poorly understood. We constructed comprehensive three-dimensional maps depicting the orientation of A-form helices across RNA junctions in the Protein Data Bank and rationalized our findings with modeling and nuclear magnetic resonance spectroscopy. We show that the secondary structures of junctions encode readily computable topological constraints that accurately predict the three-dimensional orientation of helices across all two-way junctions. Our results suggest that RNA global conformation is largely defined by topological constraints encoded at the secondary structural level and that tertiary contacts and intermolecular interactions serve to stabilize specific conformers within the topologically allowed ensemble.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bailor, Maximillian H -- Sun, Xiaoyan -- Al-Hashimi, Hashim M -- R01 AI066975-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 8;327(5962):202-6. doi: 10.1126/science.1181085.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20056889" target="_blank"〉PubMed〈/a〉
    Keywords: Anisotropy ; Base Pairing ; Base Sequence ; Biochemical Phenomena ; Databases, Nucleic Acid ; *HIV Long Terminal Repeat ; Hiv-1 ; Kanamycin/chemistry/metabolism ; Ligands ; Models, Molecular ; Neomycin/chemistry/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; *Nucleic Acid Conformation ; RNA/*chemistry/metabolism ; RNA, Viral/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Visualizing transient low-populated structures of RNA (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-10-09
    Description: The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captured by structure characterization techniques. Here we report the nuclear magnetic resonance visualization of RNA transitions towards 'invisible' excited states (ESs), which exist in too little abundance (2-13%) and for too short a duration (45-250 mus) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix-junction-helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signalling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590852/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590852/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dethoff, Elizabeth A -- Petzold, Katja -- Chugh, Jeetender -- Casiano-Negroni, Anette -- Al-Hashimi, Hashim M -- R01 AI066975/AI/NIAID NIH HHS/ -- England -- Nature. 2012 Nov 29;491(7426):724-8. doi: 10.1038/nature11498. Epub 2012 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23041928" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; HIV Long Terminal Repeat/*genetics ; HIV-1/*genetics ; Nuclear Magnetic Resonance, Biomolecular ; *Nucleic Acid Conformation ; RNA, Viral/*chemistry/genetics ; Ribosomes/chemistry/metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Transient Hoogsteen base pairs in canonical duplex DNA (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-01-29
    Description: Sequence-directed variations in the canonical DNA double helix structure that retain Watson-Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson-Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A*T and G*C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson-Crick base-pairing. The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074620/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074620/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nikolova, Evgenia N -- Kim, Eunae -- Wise, Abigail A -- O'Brien, Patrick J -- Andricioaei, Ioan -- Al-Hashimi, Hashim M -- R01 GM089846/GM/NIGMS NIH HHS/ -- R01 GM089846-01A1/GM/NIGMS NIH HHS/ -- R01GM089846/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 Feb 24;470(7335):498-502. doi: 10.1038/nature09775. Epub 2011 Jan 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21270796" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; Base Sequence ; DNA/*chemistry/metabolism ; Genetic Code ; Hydrogen Bonding ; Kinetics ; Magnetic Resonance Spectroscopy ; Molecular Dynamics Simulation ; Quantum Theory ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Functional complexity and regulation through RNA dynamics (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-02-18
    Description: Changes to the conformation of coding and non-coding RNAs form the basis of elements of genetic regulation and provide an important source of complexity, which drives many of the fundamental processes of life. Although the structure of RNA is highly flexible, the underlying dynamics of RNA are robust and are limited to transitions between the few conformations that preserve favourable base-pairing and stacking interactions. The mechanisms by which cellular processes harness the intrinsic dynamic behaviour of RNA and use it within functionally productive pathways are complex. The versatile functions and ease by which it is integrated into a wide variety of genetic circuits and biochemical pathways suggests there is a general and fundamental role for RNA dynamics in cellular processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320162/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320162/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dethoff, Elizabeth A -- Chugh, Jeetender -- Mustoe, Anthony M -- Al-Hashimi, Hashim M -- R01 AI066975/AI/NIAID NIH HHS/ -- R01 AI066975-07/AI/NIAID NIH HHS/ -- R01 GM089846/GM/NIGMS NIH HHS/ -- R01 GM089846-03/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Feb 15;482(7385):322-30. doi: 10.1038/nature10885.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22337051" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Models, Molecular ; Molecular Chaperones/metabolism ; Nucleic Acid Conformation ; RNA/*chemistry/genetics/*metabolism ; RNA Helicases/metabolism ; RNA, Untranslated/chemistry/genetics/metabolism ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Resolving the motional modes that code for RNA adaptation (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-04
    Description: Using a domain elongation strategy, we decoupled internal motions in RNA from overall rotational diffusion. This allowed us to site-specifically resolve a manifold of motional modes in two regulatory RNAs from HIV-1 with the use of nuclear magnetic resonance spin relaxation methods. Base and sugar librations vary on a picosecond time scale and occur within helical domains that move collectively at diffusion-limited nanosecond time scales. Pivot points are short, functionally important, and highly mobile internal loops. These spontaneous changes in RNA conformation correlate quantitatively with those that follow adaptive recognition of diverse targets. Thus, ligands may stabilize existing RNA conformations rather than inducing new ones.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Qi -- Sun, Xiaoyan -- Watt, Eric D -- Al-Hashimi, Hashim M -- R01 AI066975-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2006 Feb 3;311(5761):653-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16456078" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/analogs & derivatives/metabolism ; Base Pairing ; Guanine/chemistry ; *HIV Long Terminal Repeat ; HIV-1/*genetics ; Nuclear Magnetic Resonance, Biomolecular ; *Nucleic Acid Conformation ; RNA, Double-Stranded/chemistry/genetics ; RNA, Viral/*chemistry/metabolism ; Rotation ; Uridine/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P (2010)
    National Academy of Sciences
    Details
    Publication Date: 2010-01-25
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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