Publications by authors named "Hashim Al-Hashimi"

100Publications

2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.

Nucleic Acids Res 2020 Oct 26. Epub 2020 Oct 26.

Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.

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http://dx.doi.org/10.1093/nar/gkaa928DOI Listing
October 2020

Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.

J Biol Chem 2020 Nov 10;295(47):15933-15947. Epub 2020 Sep 10.

Department of Chemistry, Duke University, Durham, North Carolina, USA

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http://dx.doi.org/10.1074/jbc.RA120.014530DOI Listing
November 2020

Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R relaxation dispersion.

J Biomol NMR 2020 Sep 12;74(8-9):457-471. Epub 2020 Aug 12.

Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1007/s10858-020-00337-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508749PMC
September 2020

Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

J Am Chem Soc 2020 Jun 11;142(25):11183-11191. Epub 2020 Jun 11.

Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States.

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http://dx.doi.org/10.1021/jacs.0c03774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7354846PMC
June 2020

Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.

Biochemistry 2020 Jun 1;59(23):2154-2170. Epub 2020 Jun 1.

Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.biochem.0c00020DOI Listing
June 2020

Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields.

Angew Chem Int Ed Engl 2020 07 11;59(28):11262-11266. Epub 2020 May 11.

Department of Biochemistry, Duke University, 229, Nanaline Duke Building, 307 Research Drive, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1002/anie.202000493DOI Listing
July 2020

Probing RNA Conformational Equilibria within the Functional Cellular Context.

Cell Rep 2020 02;30(8):2472-2480.e4

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.02.004DOI Listing
February 2020

Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States.

J Mol Biol 2020 02 18;432(4):1297-1304. Epub 2019 Dec 18.

Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054137PMC
February 2020

NMR Chemical Exchange Measurements Reveal That -Methyladenosine Slows RNA Annealing.

J Am Chem Soc 2019 12 16;141(51):19988-19993. Epub 2019 Dec 16.

Department of Chemistry , Duke University , Durham , North Carolina 27710 , United States.

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http://dx.doi.org/10.1021/jacs.9b10939DOI Listing
December 2019

m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB.

PLoS One 2019 11;14(12):e0224850. Epub 2019 Dec 11.

Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224850PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6905585PMC
March 2020

Exposing Hidden High-Affinity RNA Conformational States.

J Am Chem Soc 2020 01 31;142(2):907-921. Epub 2019 Dec 31.

Department of Biochemistry , Duke University Medical Center , Durham , North Carolina 27710 , United States.

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http://dx.doi.org/10.1021/jacs.9b10535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380322PMC
January 2020

Direct evidence for (G)O6···H-N4(C) hydrogen bonding in transient G(syn)-C and G(syn)-mC Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R relaxation dispersion measurements.

J Magn Reson 2019 11 5;308:106589. Epub 2019 Sep 5.

Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmr.2019.106589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933314PMC
November 2019

Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R relaxation dispersion.

Prog Nucl Magn Reson Spectrosc 2019 Jun - Aug;112-113:55-102. Epub 2019 May 11.

Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pnmrs.2019.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727989PMC
June 2020

Infrared Spectroscopic Observation of a G-C Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.

Angew Chem Int Ed Engl 2019 08 25;58(35):12010-12013. Epub 2019 Jul 25.

Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1002/anie.201902693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719543PMC
August 2019

Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site.

Nucleic Acids Res 2019 07;47(13):7105-7117

Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.

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http://dx.doi.org/10.1093/nar/gkz498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6649712PMC
July 2019

The roles of structural dynamics in the cellular functions of RNAs.

Nat Rev Mol Cell Biol 2019 08;20(8):474-489

Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.

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http://dx.doi.org/10.1038/s41580-019-0136-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656661PMC
August 2019

Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.

Biochemistry 2019 04 8;58(16):2152-2159. Epub 2019 Apr 8.

Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.

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http://dx.doi.org/10.1021/acs.biochem.8b01141DOI Listing
April 2019

5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo U-G Base Pairs.

Chemistry 2018 Dec 20;24(71):18903-18906. Epub 2018 Nov 20.

Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.

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http://doi.wiley.com/10.1002/chem.201805077
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http://dx.doi.org/10.1002/chem.201805077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348377PMC
December 2018

A potentially abundant junctional RNA motif stabilized by mA and Mg.

Nat Commun 2018 07 17;9(1):2761. Epub 2018 Jul 17.

Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1038/s41467-018-05243-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050335PMC
July 2018

Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.

Biochemistry 2018 07 21;57(26):3733-3740. Epub 2018 May 21.

Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.

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http://dx.doi.org/10.1021/acs.biochem.8b00375DOI Listing
July 2018

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.

Nat Struct Mol Biol 2018 05 4;25(5):425-434. Epub 2018 May 4.

Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.

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http://dx.doi.org/10.1038/s41594-018-0062-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5942591PMC
May 2018

Modulation of Hoogsteen dynamics on DNA recognition.

Nat Commun 2018 04 16;9(1):1473. Epub 2018 Apr 16.

Department of Chemistry, Duke University, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1038/s41467-018-03516-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902632PMC
April 2018

Hidden Structural Modules in a Cooperative RNA Folding Transition.

Cell Rep 2018 03;22(12):3240-3250

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.02.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894117PMC
March 2018

Dynamic basis for dG•dT misincorporation via tautomerization and ionization.

Nature 2018 02 31;554(7691):195-201. Epub 2018 Jan 31.

Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1038/nature25487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808992PMC
February 2018

The Mechanism of HdeA Unfolding and Chaperone Activation.

J Mol Biol 2018 01 11;430(1):33-40. Epub 2017 Nov 11.

Department of Chemistry & Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2017.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738273PMC
January 2018

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR.

Medchemcomm 2017 May 15;8(5):1022-1036. Epub 2017 Mar 15.

Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.

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http://dx.doi.org/10.1039/C6MD00729EDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546750PMC
May 2017

Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.

Nucleic Acids Res 2017 Aug;45(14):e134

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.1093/nar/gkx525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737546PMC
August 2017

Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs.

J Am Chem Soc 2017 03 20;139(12):4326-4329. Epub 2017 Mar 20.

Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.

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http://dx.doi.org/10.1021/jacs.7b01156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581979PMC
March 2017

HIV-1 leader RNA dimeric interface revealed by NMR.

Proc Natl Acad Sci U S A 2016 11 11;113(47):13263-13265. Epub 2016 Nov 11.

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710;

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http://dx.doi.org/10.1073/pnas.1615789113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127310PMC
November 2016

RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.

J Mol Biol 2016 10 22;428(20):3972-3985. Epub 2016 Jul 22.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048535PMC
http://dx.doi.org/10.1016/j.jmb.2016.07.013DOI Listing
October 2016

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.

Nat Commun 2016 06 13;7:ncomms11768. Epub 2016 Jun 13.

Department of Biochemistry, Duke Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1038/ncomms11768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909931PMC
June 2016

Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.

Biochemistry 2016 08 4;55(32):4445-56. Epub 2016 Aug 4.

Department of Chemistry, Duke University , Durham, North Carolina 27708, United States.

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http://dx.doi.org/10.1021/acs.biochem.6b00285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302190PMC
August 2016

Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.

Cell Rep 2015 Dec 19;13(9):1800-13. Epub 2015 Nov 19.

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.10.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690532PMC
December 2015

Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release.

Biomacromolecules 2016 Jan 11;17(1):154-64. Epub 2015 Dec 11.

Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5070374PMC
http://dx.doi.org/10.1021/acs.biomac.5b01280DOI Listing
January 2016

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.

Nucleic Acids Res 2016 Jan 19;44(1):402-12. Epub 2015 Oct 19.

Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA

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http://dx.doi.org/10.1093/nar/gkv1055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705646PMC
January 2016

Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.

Phys Chem Chem Phys 2016 Feb;18(8):5743-52

Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.

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http://dx.doi.org/10.1039/c5cp03993bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589165PMC
February 2016

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

J Am Chem Soc 2015 Oct 29;137(40):12954-65. Epub 2015 Sep 29.

Department of Biochemistry and Chemistry, Duke University School of Medicine , Durham, North Carolina 27710, United States.

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http://dx.doi.org/10.1021/jacs.5b07229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748170PMC
October 2015

Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.

J Phys Chem B 2015 Jul 17;119(30):9614-26. Epub 2015 Jul 17.

‡Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27705, United States.

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http://dx.doi.org/10.1021/acs.jpcb.5b03859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748182PMC
July 2015

Slowdown of Interhelical Motions Induces a Glass Transition in RNA.

Biophys J 2015 Jun;108(12):2876-85

Department of Chemistry, University of California at Irvine, Irvine, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.04.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472199PMC
June 2015

Characterizing RNA Excited States Using NMR Relaxation Dispersion.

Methods Enzymol 2015 25;558:39-73. Epub 2015 Mar 25.

Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA; Department of Chemistry, Duke University, Durham, North Carolina, USA. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2015.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756924PMC
March 2016

Editorial overview: Nucleic acids and their protein complexes: Progress in nucleic acid structural biology: new technologies and discoveries.

Curr Opin Struct Biol 2015 Feb 13;30:vii-viii. Epub 2015 Apr 13.

Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2015.03.006DOI Listing
February 2015

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.

Nucleic Acids Res 2015 Apr 26;43(7):3420-33. Epub 2015 Mar 26.

Department of Biochemistry, Duke University, Durham, NC 27710, USA Department of Chemistry, Duke University, Durham, NC 27708, USA

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http://dx.doi.org/10.1093/nar/gkv241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402545PMC
April 2015

Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.

Nature 2015 Mar 11;519(7543):315-20. Epub 2015 Mar 11.

Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1038/nature14227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547696PMC
March 2015

Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

J Am Chem Soc 2015 Mar 9;137(10):3592-9. Epub 2015 Mar 9.

∥Departments of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.

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http://dx.doi.org/10.1021/ja5130308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399864PMC
March 2015

Dynamic motions of the HIV-1 frameshift site RNA.

Biophys J 2015 Feb;108(3):644-54

Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00063495140474
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http://dx.doi.org/10.1016/j.bpj.2014.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317556PMC
February 2015

Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair.

Biochemistry 2014 Nov 10;53(46):7145-7. Epub 2014 Nov 10.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States.

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http://dx.doi.org/10.1021/bi5011909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245982PMC
November 2014

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.

Nucleic Acids Res 2014 Oct 12;42(18):11792-804. Epub 2014 Sep 12.

Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, USA

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http://dx.doi.org/10.1093/nar/gku807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191394PMC
October 2014

Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids.

J Biomol NMR 2014 Nov 4;60(2-3):77-83. Epub 2014 Sep 4.

Department of Biochemistry, Duke University, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1007/s10858-014-9856-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4324173PMC
November 2014

Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.

Nat Commun 2014 Sep 4;5:4786. Epub 2014 Sep 4.

Department of Biochemistry and Chemistry, Duke University School of Medicine, 307 Research Dr, Nanaline H. Duke Building, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1038/ncomms5786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537320PMC
September 2014

Insights into domain-domain motions in proteins and RNA from solution NMR.

Acc Chem Res 2014 Oct 22;47(10):3118-26. Epub 2014 Aug 22.

CERM, University of Florence , Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.

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http://dx.doi.org/10.1021/ar5002318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4204921PMC
October 2014

Invisible RNA state dynamically couples distant motifs.

Proc Natl Acad Sci U S A 2014 Jul 16;111(26):9485-90. Epub 2014 Jun 16.

Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710

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http://dx.doi.org/10.1073/pnas.1407969111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084437PMC
July 2014

Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange.

J Magn Reson 2014 Jul 20;244:18-29. Epub 2014 Apr 20.

Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jmr.2014.04.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222517PMC
July 2014

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

J Mol Biol 2014 Sep 9;426(19):3201-3213. Epub 2014 May 9.

Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.04.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150856PMC
September 2014

Structural dynamics of a single-stranded RNA-helix junction using NMR.

RNA 2014 Jun 17;20(6):782-91. Epub 2014 Apr 17.

Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1261/rna.043711.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024633PMC
June 2014

Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids.

Curr Opin Struct Biol 2014 Feb 9;24:72-80. Epub 2014 Jan 9.

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, United States. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2013.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048017PMC
February 2014

Measuring similarity between dynamic ensembles of biomolecules.

Nat Methods 2014 May 6;11(5):552-4. Epub 2014 Apr 6.

Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina, USA.

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http://dx.doi.org/10.1038/nmeth.2921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041546PMC
May 2014

Hierarchy of RNA functional dynamics.

Annu Rev Biochem 2014 5;83:441-66. Epub 2014 Mar 5.

Departments of 1Biophysics and.

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http://dx.doi.org/10.1146/annurev-biochem-060713-035524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048628PMC
January 2015

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.

J Phys Chem B 2014 Mar 3;118(10):2615-27. Epub 2014 Mar 3.

Departments of Biophysics and ‡Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States.

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http://pubs.acs.org/doi/10.1021/jp411478x
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http://dx.doi.org/10.1021/jp411478xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983386PMC
March 2014

Advances in the determination of nucleic acid conformational ensembles.

Annu Rev Phys Chem 2014 16;65:293-316. Epub 2013 Dec 16.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109; email:

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http://dx.doi.org/10.1146/annurev-physchem-040412-110059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748180PMC
April 2015

NMR studies of nucleic acid dynamics.

J Magn Reson 2013 Dec 3;237:191-204. Epub 2013 Sep 3.

Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmr.2013.08.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984477PMC
December 2013

Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

J Am Chem Soc 2013 Oct 7;135(41):15536-48. Epub 2013 Oct 7.

Howard Hughes Medical Institute , Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/ja407140kDOI Listing
October 2013

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.

Nucleic Acids Res 2013 Dec 3;41(22):10462-75. Epub 2013 Sep 3.

Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkt798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905878PMC
December 2013

Influence of dimethylsulfoxide on RNA structure and ligand binding.

Anal Chem 2013 Oct 25;85(20):9692-8. Epub 2013 Sep 25.

Department of Chemistry and Biophysics, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/ac402038tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855037PMC
October 2013

A historical account of Hoogsteen base-pairs in duplex DNA.

Biopolymers 2013 Dec;99(12):955-68

Department of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109-1055; Integrative Structural & Computational Biology Department, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037.

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http://dx.doi.org/10.1002/bip.22334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844552PMC
December 2013

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

J Am Chem Soc 2013 May 29;135(18):6766-9. Epub 2013 Apr 29.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/ja400994eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713198PMC
May 2013

A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

J Am Chem Soc 2013 Apr 28;135(14):5457-66. Epub 2013 Mar 28.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1021/ja400920wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676943PMC
April 2013

Utility of 1H NMR chemical shifts in determining RNA structure and dynamics.

J Phys Chem B 2013 Feb 7;117(7):2045-52. Epub 2013 Feb 7.

Department of Chemistry, University of California Irvine 1102 Natural Sciences 2, Irvine, California 92697, USA.

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http://dx.doi.org/10.1021/jp310863cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676946PMC
February 2013

Visualizing transient low-populated structures of RNA.

Nature 2012 Nov 7;491(7426):724-8. Epub 2012 Oct 7.

Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA.

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http://www.nature.com/articles/nature11498
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590852PMC
November 2012

Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.

Biochemistry 2012 Oct 18;51(43):8654-64. Epub 2012 Oct 18.

Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1021/bi3009517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676944PMC
October 2012

Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation.

Biochemistry 2012 Aug 17;51(34):6871-9. Epub 2012 Aug 17.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1021/bi300785bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676945PMC
August 2012

Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release.

Mol Pharm 2012 Sep 20;9(9):2743-9. Epub 2012 Aug 20.

Department of Chemistry, University of Michigan, 911 North University Avenue, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/mp3002864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436429PMC
September 2012

Functional complexity and regulation through RNA dynamics.

Nature 2012 Feb 15;482(7385):322-30. Epub 2012 Feb 15.

Department of Chemistry and Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA.

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http://www.nature.com/articles/nature10885
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320162PMC
February 2012

Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution.

J Am Chem Soc 2012 Feb 16;134(8):3667-70. Epub 2012 Feb 16.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1021/ja2117816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791138PMC
February 2012

RNA structure: Adding a second dimension.

Nat Chem 2011 Nov 23;3(12):913-5. Epub 2011 Nov 23.

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http://dx.doi.org/10.1038/nchem.1209DOI Listing
November 2011

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.

Nat Methods 2011 Oct 28;8(11):919-31. Epub 2011 Oct 28.

Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1038/nmeth.1735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320163PMC
October 2011

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.

Nucleic Acids Res 2012 Feb 18;40(3):1345-55. Epub 2011 Oct 18.

Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/nar/gkr833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273816PMC
February 2012

3D maps of RNA interhelical junctions.

Nat Protoc 2011 Sep 15;6(10):1536-45. Epub 2011 Sep 15.

Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1038/nprot.2011.385DOI Listing
September 2011

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.

Nucleic Acids Res 2012 Jan 21;40(2):892-904. Epub 2011 Sep 21.

Departments of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.

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http://dx.doi.org/10.1093/nar/gkr751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258142PMC
January 2012

Using fluorine nuclear magnetic resonance to probe changes in the structure and dynamics of membrane-active peptides interacting with lipid bilayers.

Biochemistry 2011 Jul 15;50(27):5979-87. Epub 2011 Jun 15.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1021/bi200639cDOI Listing
July 2011

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.

Curr Opin Struct Biol 2011 Jun 14;21(3):296-305. Epub 2011 Apr 14.

Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, United States.

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http://dx.doi.org/10.1016/j.sbi.2011.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319143PMC
June 2011

Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9.

J Biol Chem 2011 May 18;286(21):18658-63. Epub 2011 Mar 18.

Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1074/jbc.M111.232876DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099682PMC
May 2011

Sequence-specific B-DNA flexibility modulates Z-DNA formation.

J Am Chem Soc 2011 Feb 28;133(7):2016-8. Epub 2011 Jan 28.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/ja1073068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319140PMC
February 2011

Transient Hoogsteen base pairs in canonical duplex DNA.

Nature 2011 Feb 26;470(7335):498-502. Epub 2011 Jan 26.

Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA.

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http://www.nature.com/articles/nature09775
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http://dx.doi.org/10.1038/nature09775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074620PMC
February 2011