Hashim M. Al-Hashimi - Publications

2002-2013 Chemistry and Biophysics University of Michigan, Ann Arbor, Ann Arbor, MI 
 2014- Biochemistry Duke University School of Medicine, Durham, NC, United States 
Structure and dynamics of nucleic acids and ribonucleoproteins using NMR spectroscopy

155 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Shi H, Rangadurai A, Abou Assi H, Roy R, Case DA, Herschlag D, Yesselman JD, Al-Hashimi HM. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nature Communications. 11: 5531. PMID 33139729 DOI: 10.1038/s41467-020-19371-y  1
2020 Abou Assi H, Rangadurai AK, Shi H, Liu B, Clay MC, Erharter K, Kreutz C, Holley CL, Al-Hashimi HM. 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states. Nucleic Acids Research. PMID 33104789 DOI: 10.1093/nar/gkaa928  1
2020 Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. PMID 33087930 DOI: 10.1038/s41586-020-2843-2  1
2020 Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. Rna (New York, N.Y.). PMID 33028652 DOI: 10.1261/rna.076257.120  1
2020 Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R relaxation dispersion. Journal of Biomolecular Nmr. PMID 32789613 DOI: 10.1007/s10858-020-00337-7  1
2020 Li P, Rangadurai A, Al-Hashimi HM, Hammes-Schiffer S. Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. Journal of the American Chemical Society. PMID 32459476 DOI: 10.1021/jacs.0c03774  1
2020 Kladwang W, Topkar V, Liu B, Rangan R, Hodges T, Keane S, Al-Hashimi HM, Das R. Anomalous reverse transcription through chemical modifications in polyadenosine stretches. Biochemistry. PMID 32407625 DOI: 10.1021/acs.biochem.0c00020  1
2020 Ganser LR, Lee J, Rangadurai A, Merriman DK, Kelly ML, Kansal AD, Sathyamoorthy B, Al-Hashimi HM. Publisher Correction: High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nature Structural & Molecular Biology. PMID 32376863 DOI: 10.1038/s41594-020-0434-4  1
2020 Rangadurai A, Shi H, Al-Hashimi HM. Extending the Sensitivity of CEST to Micro-to-Millisecond Dynamics in Nucleic Acids Using High Power Radio-Frequency Fields. Angewandte Chemie (International Ed. in English). PMID 32168407 DOI: 10.1002/anie.202000493  1
2020 Ganser LR, Chu CC, Bogerd HP, Kelly ML, Cullen BR, Al-Hashimi HM. Probing RNA Conformational Equilibria within the Functional Cellular Context. Cell Reports. 30: 2472-2480.e4. PMID 32101729 DOI: 10.1016/j.celrep.2020.02.004  1
2019 Ganser LR, Kelly ML, Patwardhan NN, Hargrove AE, Al-Hashimi HM. Demonstration that small molecules can bind and stabilize low-abundance short-lived RNA excited conformational states. Journal of Molecular Biology. PMID 31863746 DOI: 10.1016/j.jmb.2019.12.009  1
2019 Shi H, Liu B, Nussbaumer F, Rangadurai A, Kreutz C, Al-Hashimi HM. NMR chemical exchange measurements reveal that N6-methyladenosine slows RNA annealing. Journal of the American Chemical Society. PMID 31826614 DOI: 10.1021/jacs.9b10939  1
2019 Chu CC, Liu B, Plangger R, Kreutz C, Al-Hashimi HM. m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB. Plos One. 14: e0224850. PMID 31825959 DOI: 10.1371/journal.pone.0224850  1
2019 Rangadurai A, Kremser J, Shi H, Kreutz C, Al-Hashimi HM. 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. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 308: 106589. PMID 31539864 DOI: 10.1016/j.jmr.2019.106589  1
2019 Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R relaxation dispersion. Progress in Nuclear Magnetic Resonance Spectroscopy. 112: 55-102. PMID 31481159 DOI: 10.1016/j.pnmrs.2019.05.002  1
2019 Stelling AL, Liu AY, Zeng W, Salinas R, Schumacher MA, Al-Hashimi HM. Infrared spectroscopic observation of a G-C+ Hoogsteen base pair in the DNA:TATA box binding protein complex under solution conditions. Angewandte Chemie (International Ed. in English). PMID 31268220 DOI: 10.1002/anie.201902693  1
2019 Chu CC, Plangger R, Kreutz C, Al-Hashimi HM. Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site. Nucleic Acids Research. PMID 31199872 DOI: 10.1093/nar/gkz498  1
2019 Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nature Reviews. Molecular Cell Biology. PMID 31182864 DOI: 10.1038/s41580-019-0136-0  1
2019 Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically C- and N-Labeled DNA. Biochemistry. PMID 30950607 DOI: 10.1021/acs.biochem.9b00027  1
2019 Fick RJ, Horowitz S, McDole BG, Clay MC, Mehl RA, Al-Hashimi HM, Scheiner S, Trievel RC. Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Biochemistry. PMID 30810306 DOI: 10.1021/acs.biochem.8b01141  1
2018 Travis B, Shaw PLR, Liu B, Ravindra K, Iliff H, Al-Hashimi HM, Schumacher MA. The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA. Nucleic Acids Research. PMID 30544166 DOI: 10.1093/nar/gky1259  1
2018 Strebitzer E, Rangadurai A, Plangger R, Kremser J, Juen MA, Tollinger M, Al-Hashimi HM, Kreutz C. 5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo U-G Base Pairs. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 30300940 DOI: 10.1002/chem.201805077  1
2018 Rangadurai A, Zhou H, Merriman DK, Meiser N, Liu B, Shi H, Szymanski ES, Al-Hashimi HM. Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? Nucleic Acids Research. PMID 30285154 DOI: 10.1093/nar/gky885  1
2018 Liu B, Merriman DK, Choi SH, Schumacher MA, Plangger R, Kreutz C, Horner SM, Meyer KD, Al-Hashimi HM. A potentially abundant junctional RNA motif stabilized by mA and Mg. Nature Communications. 9: 2761. PMID 30018356 DOI: 10.1038/s41467-018-05243-z  1
2018 Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM. Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. Rna (New York, N.Y.). PMID 30012568 DOI: 10.1261/rna.066258.118  1
2018 Fick RJ, Clay MC, Vander Lee L, Scheiner S, Al-Hashimi HM, Trievel RC. Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates AdoMet Recognition in the Reactivation Domain of Cobalamin-dependent Methionine Synthase. Biochemistry. PMID 29733595 DOI: 10.1021/acs.biochem.8b00375  1
2018 Ganser LR, Lee J, Rangadurai A, Merriman DK, Kelly ML, Kansal AD, Sathyamoorthy B, Al-Hashimi HM. High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nature Structural & Molecular Biology. 25: 425-434. PMID 29728655 DOI: 10.1038/s41594-018-0062-4  1
2018 Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. Journal of Biomolecular Nmr. PMID 29675775 DOI: 10.1007/s10858-018-0177-2  1
2018 Xu Y, McSally J, Andricioaei I, Al-Hashimi HM. Modulation of Hoogsteen dynamics on DNA recognition. Nature Communications. 9: 1473. PMID 29662229 DOI: 10.1038/s41467-018-03516-1  1
2018 Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R. Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Reports. 22: 3240-3250. PMID 29562180 DOI: 10.1016/j.celrep.2018.02.101  1
2018 Kimsey IJ, Szymanski ES, Zahurancik WJ, Shakya A, Xue Y, Chu CC, Sathyamoorthy B, Suo Z, Al-Hashimi HM. Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature. 554: 195-201. PMID 29420478 DOI: 10.1038/nature25487  1
2017 Salmon L, Stull F, Sayle S, Cato C, Akgül Ş, Foit L, Ahlstrom LS, Eisenmesser EZ, Al-Hashimi HM, Bardwell JCA, Horowitz S. The Mechanism of HdeA Unfolding and Chaperone Activation. Journal of Molecular Biology. PMID 29138002 DOI: 10.1016/j.jmb.2017.11.002  1
2017 Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE. Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. Medchemcomm. 8: 1022-1036. PMID 28798862 DOI: 10.1039/C6MD00729E  1
2017 Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Research. PMID 28609788 DOI: 10.1093/nar/gkx525  1
2017 Stelling AL, Xu Y, Zhou H, Choi SH, Clay MC, Merriman DK, Al-Hashimi HM. Robust IR Based Detection of Stable and Fractionally Populated G-C(+) and A-T Hoogsteen Base Pairs in Duplex DNA. Febs Letters. PMID 28524232 DOI: 10.1002/1873-3468.12681  1
2017 Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. Nucleic Acids Research. PMID 28369571 DOI: 10.1093/nar/gkx186  1
2017 Szymanski ES, Kimsey IJ, Al-Hashimi HM. Direct NMR Evidence that Transient Tautomeric and Anionic States in dG•dT Form Watson-Crick like Base Pairs. Journal of the American Chemical Society. PMID 28290687 DOI: 10.1021/jacs.7b01156  1
2017 Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi H, Herschlag D. Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions. Rna (New York, N.Y.). PMID 28138061 DOI: 10.1261/rna.060053.116  1
2016 Ganser LR, Al-Hashimi HM. HIV-1 leader RNA dimeric interface revealed by NMR. Proceedings of the National Academy of Sciences of the United States of America. PMID 27837023 DOI: 10.1073/pnas.1615789113  1
2016 Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nature Structural & Molecular Biology. PMID 27478929 DOI: 10.1038/nsmb.3270  1
2016 Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. Journal of Molecular Biology. PMID 27452365 DOI: 10.1016/j.jmb.2016.07.013  1
2016 Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nature Communications. 7: ncomms11768. PMID 27292179 DOI: 10.1038/ncomms11768  1
2016 Merriman DK, Xue Y, Yang S, Kimsey IJ, Shakya A, Clay MC, Al-Hashimi HM. Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes Over a Broad Range of Timescales. Biochemistry. PMID 27232530 DOI: 10.1021/acs.biochem.6b00285  1
2015 Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Reports. 13: 1800-1813. PMID 26655897 DOI: 10.1016/j.celrep.2015.10.062  1
2015 Shakya A, Dougherty CA, Xue Y, Al-Hashimi HM, Banaszak Holl MM. Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release. Biomacromolecules. PMID 26595195 DOI: 10.1021/acs.biomac.5b01280  1
2015 Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, ... ... Al-Hashimi HM, et al. Engineering a Therapeutic Lectin by Uncoupling Mitogenicity from Antiviral Activity. Cell. 163: 746-58. PMID 26496612 DOI: 10.1016/j.cell.2015.09.056  1
2015 Mustoe AM, Al-Hashimi HM, Brooks CL. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Research. PMID 26481360 DOI: 10.1093/nar/gkv1055  1
2015 Andrałojć W, Ravera E, Salmon L, Parigi G, Al-Hashimi HM, Luchinat C. Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. PMID 26360616 DOI: 10.1039/c5cp03993b  1
2015 Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. Journal of the American Chemical Society. PMID 26306428 DOI: 10.1021/jacs.5b07229  1
2015 Yang S, Al-Hashimi HM. Unveiling Inherent Degeneracies in Determining Population-weighted Ensembles of Inter-domain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. The Journal of Physical Chemistry. B. PMID 26131693 DOI: 10.1021/acs.jpcb.5b03859  1
2015 Kimsey IJ, Zhou H, Alvey H, Al-Hashimi HM. 120 Role of dynamic base pair polymorphism in the central dogma of molecular biology. Journal of Biomolecular Structure & Dynamics. 33: 75-6. PMID 26103330 DOI: 10.1080/07391102.2015.1032753  1
2015 Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophysical Journal. 108: 2876-85. PMID 26083927 DOI: 10.1016/j.bpj.2015.04.041  1
2015 Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM. Characterizing RNA Excited States Using NMR Relaxation Dispersion. Methods in Enzymology. 558: 39-73. PMID 26068737 DOI: 10.1016/bs.mie.2015.02.002  1
2015 Allain FH, Al-Hashimi HM. Editorial overview: Nucleic acids and their protein complexes: Progress in nucleic acid structural biology: new technologies and discoveries. Current Opinion in Structural Biology. 30: vii-viii. PMID 25882905 DOI: 10.1016/j.sbi.2015.03.006  1
2015 Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Research. 43: 3420-33. PMID 25813047 DOI: 10.1093/nar/gkv241  1
2015 Kimsey IJ, Petzold K, Sathyamoorthy B, Stein ZW, Al-Hashimi HM. Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. Nature. 519: 315-20. PMID 25762137 DOI: 10.1038/nature14227  1
2015 Mustoe AM, Liu X, Lin PJ, Al-Hashimi HM, Fierke CA, Brooks CL. Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding. Journal of the American Chemical Society. 137: 3592-9. PMID 25705930 DOI: 10.1021/ja5130308  1
2015 Mouzakis KD, Dethoff EA, Tonelli M, Al-Hashimi H, Butcher SE. Dynamic motions of the HIV-1 frameshift site RNA. Biophysical Journal. 108: 644-54. PMID 25650931 DOI: 10.1016/j.bpj.2014.12.006  1
2014 Nikolova EN, Stull F, Al-Hashimi HM. Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair. Biochemistry. 53: 7145-7. PMID 25339065 DOI: 10.1021/bi5011909  1
2014 Ganser LR, Mustoe AM, Al-Hashimi HM. An RNA tertiary switch by modifying how helices are tethered. Genome Biology. 15: 425. PMID 25315677 DOI: 10.1186/s13059-014-0425-z  1
2014 Mustoe AM, Brooks CL, Al-Hashimi HM. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. Nucleic Acids Research. 42: 11792-804. PMID 25217593 DOI: 10.1093/nar/gku807  1
2014 Alvey HS, Gottardo FL, Nikolova EN, Al-Hashimi HM. Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. Nature Communications. 5: 4786. PMID 25185517 DOI: 10.1038/ncomms5786  1
2014 Lee J, Dethoff EA, Al-Hashimi HM. Invisible RNA state dynamically couples distant motifs. Proceedings of the National Academy of Sciences of the United States of America. 111: 9485-90. PMID 24979799 DOI: 10.1073/pnas.1407969111  1
2014 Horowitz S, Adhikari U, Dirk LM, Del Rizzo PA, Mehl RA, Houtz RL, Al-Hashimi HM, Scheiner S, Trievel RC. Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis. Acs Chemical Biology. 9: 1692-7. PMID 24914947 DOI: 10.1021/cb5001185  1
2014 Bothe JR, Stein ZW, Al-Hashimi HM. Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 244: 18-29. PMID 24819426 DOI: 10.1016/j.jmr.2014.04.010  1
2014 Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. Journal of Molecular Biology. 426: 3201-13. PMID 24813122 DOI: 10.1016/j.jmb.2014.04.029  1
2014 Eichhorn CD, Al-Hashimi HM. Structural dynamics of a single-stranded RNA-helix junction using NMR. Rna (New York, N.Y.). 20: 782-91. PMID 24742933 DOI: 10.1261/rna.043711.113  1
2014 Kimsey I, Al-Hashimi HM. Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids. Current Opinion in Structural Biology. 24: 72-80. PMID 24721455 DOI: 10.1016/j.sbi.2013.12.003  1
2014 Yang S, Salmon L, Al-Hashimi HM. Measuring similarity between dynamic ensembles of biomolecules. Nature Methods. 11: 552-4. PMID 24705474 DOI: 10.1038/nmeth.2921  1
2014 Mustoe AM, Brooks CL, Al-Hashimi HM. Hierarchy of RNA functional dynamics. Annual Review of Biochemistry. 83: 441-66. PMID 24606137 DOI: 10.1146/annurev-biochem-060713-035524  1
2014 Mustoe AM, Al-Hashimi HM, Brooks CL. Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. The Journal of Physical Chemistry. B. 118: 2615-27. PMID 24547945 DOI: 10.1021/jp411478x  1
2014 Salmon L, Yang S, Al-Hashimi HM. Advances in the determination of nucleic acid conformational ensembles. Annual Review of Physical Chemistry. 65: 293-316. PMID 24364917 DOI: 10.1146/annurev-physchem-040412-110059  1
2014 Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi H, Luchinat C. Insights into domain-domain motions in proteins and RNA from solution NMR Accounts of Chemical Research. 47: 3118-3126. DOI: 10.1021/ar5002318  1
2014 Sathyamoorthy B, Lee J, Kimsey I, Ganser LR, Al-Hashimi H. Development and application of aromatic [13C, 1H] SOFAST-HMQC NMR experiment for nucleic acids Journal of Biomolecular Nmr. DOI: 10.1007/s10858-014-9856-9  1
2013 Al-Hashimi HM. NMR studies of nucleic acid dynamics. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 237: 191-204. PMID 24149218 DOI: 10.1016/j.jmr.2013.08.014  1
2013 Horowitz S, Dirk LM, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. Journal of the American Chemical Society. 135: 15536-48. PMID 24093804 DOI: 10.1021/ja407140k  1
2013 Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL, Walter NG. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Research. 41: 10462-75. PMID 24003028 DOI: 10.1093/nar/gkt798  1
2013 Lee J, Vogt CE, McBrairty M, Al-Hashimi HM. Influence of dimethylsulfoxide on RNA structure and ligand binding. Analytical Chemistry. 85: 9692-8. PMID 23987474 DOI: 10.1021/ac402038t  1
2013 Nikolova EN, Zhou H, Gottardo FL, Alvey HS, Kimsey IJ, Al-Hashimi HM. A historical account of hoogsteen base-pairs in duplex DNA. Biopolymers. 99: 955-68. PMID 23818176 DOI: 10.1002/bip.22334  1
2013 Nikolova EN, Goh GB, Brooks CL, Al-Hashimi HM. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. Journal of the American Chemical Society. 135: 6766-9. PMID 23506098 DOI: 10.1021/ja400994e  1
2013 Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. Journal of the American Chemical Society. 135: 5457-66. PMID 23473378 DOI: 10.1021/ja400920w  1
2013 Frank AT, Horowitz S, Andricioaei I, Al-Hashimi HM. Utility of 1H NMR chemical shifts in determining RNA structure and dynamics. The Journal of Physical Chemistry. B. 117: 2045-52. PMID 23320790 DOI: 10.1021/jp310863c  1
2012 Dethoff EA, Petzold K, Chugh J, Casiano-Negroni A, Al-Hashimi HM. Visualizing transient low-populated structures of RNA. Nature. 491: 724-8. PMID 23041928 DOI: 10.1038/nature11498  1
2012 Nikolova EN, Bascom GD, Andricioaei I, Al-Hashimi HM. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. Biochemistry. 51: 8654-64. PMID 23035755 DOI: 10.1021/bi3009517  1
2012 Bothe JR, Lowenhaupt K, Al-Hashimi HM. Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation. Biochemistry. 51: 6871-9. PMID 22873788 DOI: 10.1021/bi300785b  1
2012 Prevette LE, Nikolova EN, Al-Hashimi HM, Banaszak Holl MM. Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release. Molecular Pharmaceutics. 9: 2743-9. PMID 22823140 DOI: 10.1021/mp3002864  1
2012 Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM. Functional complexity and regulation through RNA dynamics. Nature. 482: 322-30. PMID 22337051 DOI: 10.1038/nature10885  1
2012 Nikolova EN, Gottardo FL, Al-Hashimi HM. Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution. Journal of the American Chemical Society. 134: 3667-70. PMID 22309937 DOI: 10.1021/ja2117816  1
2012 Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL, Al-Hashimi HM. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Research. 40: 1345-55. PMID 22009676 DOI: 10.1093/nar/gkr833  1
2012 Mustoe AM, Bailor MH, Teixeira RM, Brooks CL, Al-Hashimi HM. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Research. 40: 892-904. PMID 21937512 DOI: 10.1093/nar/gkr751  1
2012 Eichhorn CD, Yang S, Al-Hashimi HM. Characterising RNA dynamics using NMR residual dipolar couplings Rsc Biomolecular Sciences. 184-215.  1
2011 Petzold K, Al-Hashimi HM. RNA structure: Adding a second dimension. Nature Chemistry. 3: 913-5. PMID 22109268 DOI: 10.1038/nchem.1209  1
2011 Bothe JR, Nikolova EN, Eichhorn CD, Chugh J, Hansen AL, Al-Hashimi HM. Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nature Methods. 8: 919-31. PMID 22036746 DOI: 10.1038/nmeth.1735  1
2011 Bailor MH, Mustoe AM, Brooks CL, Al-Hashimi HM. 3D maps of RNA interhelical junctions. Nature Protocols. 6: 1536-45. PMID 21959236 DOI: 10.1038/nprot.2011.385  1
2011 Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nature Chemical Biology. 7: 553-9. PMID 21706033 DOI: 10.1038/nchembio.596  1
2011 Suzuki Y, Buer BC, Al-Hashimi HM, Marsh EN. Using fluorine nuclear magnetic resonance to probe changes in the structure and dynamics of membrane-active peptides interacting with lipid bilayers. Biochemistry. 50: 5979-87. PMID 21644540 DOI: 10.1021/bi200639c  1
2011 Bailor MH, Mustoe AM, Brooks CL, Al-Hashimi HM. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Current Opinion in Structural Biology. 21: 296-305. PMID 21497083 DOI: 10.1016/j.sbi.2011.03.009  1
2011 Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC. Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. The Journal of Biological Chemistry. 286: 18658-63. PMID 21454678 DOI: 10.1074/jbc.M111.232876  1
2011 Bothe JR, Lowenhaupt K, Al-Hashimi HM. Sequence-specific B-DNA flexibility modulates Z-DNA formation. Journal of the American Chemical Society. 133: 2016-8. PMID 21275369 DOI: 10.1021/ja1073068  1
2011 Nikolova EN, Kim E, Wise AA, O'Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature. 470: 498-502. PMID 21270796 DOI: 10.1038/nature09775  1
2010 Dethoff EA, Al-Hashimi HM. A rare example of lock-and-key RNA recognition. Journal of Molecular Biology. 404: 553-4. PMID 20951707 DOI: 10.1016/j.jmb.2010.10.014  1
2010 Al-Hashimi HM. Biochemistry. Exciting structures. Science (New York, N.Y.). 329: 1295-6. PMID 20829475 DOI: 10.1126/science.1195571  1
2010 Nikolova EN, Al-Hashimi HM. Thermodynamics of RNA melting, one base pair at a time. Rna (New York, N.Y.). 16: 1687-91. PMID 20660079 DOI: 10.1261/rna.2235010  1
2010 Stelzer AC, Kratz JD, Zhang Q, Al-Hashimi HM. RNA dynamics by design: biasing ensembles towards the ligand-bound state. Angewandte Chemie (International Ed. in English). 49: 5731-3. PMID 20583015 DOI: 10.1002/anie.201000814  1
2010 Buer BC, Chugh J, Al-Hashimi HM, Marsh EN. Using fluorine nuclear magnetic resonance to probe the interaction of membrane-active peptides with the lipid bilayer. Biochemistry. 49: 5760-5. PMID 20527804 DOI: 10.1021/bi100605e  1
2010 Koutmou KS, Casiano-Negroni A, Getz MM, Pazicni S, Andrews AJ, Penner-Hahn JE, Al-Hashimi HM, Fierke CA. NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P. Proceedings of the National Academy of Sciences of the United States of America. 107: 2479-84. PMID 20133747 DOI: 10.1073/pnas.0906319107  0.76
2010 Bailor MH, Sun X, Al-Hashimi HM. Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science (New York, N.Y.). 327: 202-6. PMID 20056889 DOI: 10.1126/science.1181085  1
2010 Musselman C, Zhang Q, Al-Hashimi H, Andricioaei I. Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA. The Journal of Physical Chemistry. B. 114: 929-39. PMID 20039757 DOI: 10.1021/jp905286h  1
2010 Dethoff EA, Hansen AL, Zhang Q, Al-Hashimi HM. Variable helix elongation as a tool to modulate RNA alignment and motional couplings. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 202: 117-21. PMID 19854083 DOI: 10.1016/j.jmr.2009.09.022  1
2010 Stelzer AC, Frazee RW, Van Huis C, Cleary J, Opipari AW, Glick GD, Al-Hashimi HM. NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F(1)F(0)-ATPase. Biopolymers. 93: 85-92. PMID 19768783 DOI: 10.1002/bip.21306  1
2009 Zhang Q, Al-Hashimi HM. Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition. Rna (New York, N.Y.). 15: 1941-8. PMID 19776156 DOI: 10.1261/rna.1806909  1
2009 Stelzer AC, Frank AT, Bailor MH, Andricioaei I, Al-Hashimi HM. Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs. Methods (San Diego, Calif.). 49: 167-73. PMID 19699798 DOI: 10.1016/j.ymeth.2009.08.006  1
2009 Al-Hashimi HM. Structural biology: Aerial view of the HIV genome. Nature. 460: 696-8. PMID 19661906 DOI: 10.1038/460696a  1
2009 Nikolova EN, Al-Hashimi HM. Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR. Journal of Biomolecular Nmr. 45: 9-16. PMID 19636798 DOI: 10.1007/s10858-009-9350-y  1
2009 Frank AT, Stelzer AC, Al-Hashimi HM, Andricioaei I. Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Research. 37: 3670-9. PMID 19369218 DOI: 10.1093/nar/gkp156  1
2009 Fisher CK, Al-Hashimi HM. Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings. The Journal of Physical Chemistry. B. 113: 6173-6. PMID 19358547 DOI: 10.1021/jp900411z  1
2009 Buhrlage SJ, Bates CA, Rowe SP, Minter AR, Brennan BB, Majmudar CY, Wemmer DE, Al-Hashimi H, Mapp AK. Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors. Acs Chemical Biology. 4: 335-44. PMID 19348463 DOI: 10.1021/cb900028j  1
2009 Hansen AL, Nikolova EN, Casiano-Negroni A, Al-Hashimi HM. Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy. Journal of the American Chemical Society. 131: 3818-9. PMID 19243182 DOI: 10.1021/ja8091399  1
2008 Fisher CK, Zhang Q, Stelzer A, Al-Hashimi HM. Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR. The Journal of Physical Chemistry. B. 112: 16815-22. PMID 19367865 DOI: 10.1021/jp806188j  1
2008 Dethoff EA, Hansen AL, Musselman C, Watt ED, Andricioaei I, Al-Hashimi HM. Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophysical Journal. 95: 3906-15. PMID 18621815 DOI: 10.1529/biophysj.108.140285  1
2008 Al-Hashimi HM, Walter NG. RNA dynamics: it is about time. Current Opinion in Structural Biology. 18: 321-9. PMID 18547802 DOI: 10.1016/j.sbi.2008.04.004  1
2008 Zhang Q, Al-Hashimi HM. Extending the NMR spatial resolution limit for RNA by motional couplings. Nature Methods. 5: 243-5. PMID 18246076 DOI: 10.1038/nmeth.1180  1
2007 Zhang Q, Stelzer AC, Fisher CK, Al-Hashimi HM. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature. 450: 1263-7. PMID 18097416 DOI: 10.1038/nature06389  1
2007 Hansen AL, Al-Hashimi HM. Dynamics of large elongated RNA by NMR carbon relaxation. Journal of the American Chemical Society. 129: 16072-82. PMID 18047338 DOI: 10.1021/ja0757982  1
2007 Al-Hashimi HM. Beyond static structures of RNA by NMR: folding, refolding, and dynamics at atomic resolution. Biopolymers. 86: 345-7. PMID 17597469 DOI: 10.1002/bip.20754  1
2007 Getz M, Sun X, Casiano-Negroni A, Zhang Q, Al-Hashimi HM. NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers. 86: 384-402. PMID 17594140 DOI: 10.1002/bip.20765  1
2007 Bailor MH, Musselman C, Hansen AL, Gulati K, Patel DJ, Al-Hashimi HM. Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nature Protocols. 2: 1536-46. PMID 17571061 DOI: 10.1038/nprot.2007.221  1
2007 Casiano-Negroni A, Sun X, Al-Hashimi HM. Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition. Biochemistry. 46: 6525-35. PMID 17488097 DOI: 10.1021/bi700335n  1
2007 Musselman C, Al-Hashimi HM, Andricioaei I. iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge. Biophysical Journal. 93: 411-22. PMID 17449677 DOI: 10.1529/biophysj.107.104620  1
2007 Sun X, Zhang Q, Al-Hashimi HM. Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition. Nucleic Acids Research. 35: 1698-713. PMID 17311812 DOI: 10.1093/nar/gkm020  1
2007 Getz MM, Andrews AJ, Fierke CA, Al-Hashimi HM. Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation. Rna (New York, N.Y.). 13: 251-66. PMID 17194721 DOI: 10.1261/rna.264207  1
2006 Musselman C, Pitt SW, Gulati K, Foster LL, Andricioaei I, Al-Hashimi HM. Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. Journal of Biomolecular Nmr. 36: 235-49. PMID 17077936 DOI: 10.1007/s10858-006-9087-9  1
2006 Zhang Q, Sun X, Watt ED, Al-Hashimi HM. Resolving the motional modes that code for RNA adaptation. Science (New York, N.Y.). 311: 653-6. PMID 16456078 DOI: 10.1126/science.1119488  1
2006 Hansen AL, Al-Hashimi HM. Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 179: 299-307. PMID 16431143 DOI: 10.1016/j.jmr.2005.12.012  1
2006 Lee HY, Lee KH, Al-Hashimi HM, Marsh EN. Modulating protein structure with fluorous amino acids: increased stability and native-like structure conferred on a 4-helix bundle protein by hexafluoroleucine. Journal of the American Chemical Society. 128: 337-43. PMID 16390163 DOI: 10.1021/ja0563410  1
2005 Al-Hashimi HM. Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy. Chembiochem : a European Journal of Chemical Biology. 6: 1506-19. PMID 16138302 DOI: 10.1002/cbic.200500002  1
2005 Pitt SW, Zhang Q, Patel DJ, Al-Hashimi HM. Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility. Angewandte Chemie (International Ed. in English). 44: 3412-5. PMID 15861447 DOI: 10.1002/anie.200500075  1
2004 Pitt SW, Majumdar A, Serganov A, Patel DJ, Al-Hashimi HM. Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization. Journal of Molecular Biology. 338: 7-16. PMID 15050819 DOI: 10.1016/j.jmb.2004.02.031  1
2003 Zhang Q, Throolin R, Pitt SW, Serganov A, Al-Hashimi HM. Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment. Journal of the American Chemical Society. 125: 10530-1. PMID 12940730 DOI: 10.1021/ja0363056  1
2003 Al-Hashimi HM, Pitt SW, Majumdar A, Xu W, Patel DJ. Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings. Journal of Molecular Biology. 329: 867-73. PMID 12798678 DOI: 10.1016/S0022-2836(03)00517-5  1
2003 TOLMAN JR, AL-HASHIMI HM. NMR Studies of Biomolecular Dynamics and Structural Plasticity Using Residual Dipolar Couplings Annual Reports On Nmr Spectroscopy. 51: 105-166. DOI: 10.1016/S0066-4103(03)51003-1  1
2002 Heffelfinger GS, Martino A, Gorin A, Xu Y, Rintoul MD, Geist A, Al-Hashimi HM, Davidson GS, Faulon JL, Frink LJ, Haaland DM, Hart WE, Jakobsson E, Lane T, Li M, et al. Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling. Omics : a Journal of Integrative Biology. 6: 305-30. PMID 12626091 DOI: 10.1089/153623102321112746  1
2002 Al-Hashimi HM, Gorin A, Majumdar A, Gosser Y, Patel DJ. Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. Journal of Molecular Biology. 318: 637-49. PMID 12054812 DOI: 10.1016/S0022-2836(02)00160-2  1
2002 Al-Hashimi HM, Patel DJ. Residual dipolar couplings: synergy between NMR and structural genomics. Journal of Biomolecular Nmr. 22: 1-8. PMID 11885976 DOI: 10.1023/A:1013801714041  1
2002 Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. Journal of Molecular Biology. 315: 95-102. PMID 11779230 DOI: 10.1006/jmbi.2001.5235  1
2001 Al-Hashimi HM, Gorin A, Majumdar A, Patel DJ. Alignment of the HTLV-I Rex peptide bound to its target RNA aptamer from magnetic field-induced residual dipolar couplings and intermolecular hydrogen bonds. Journal of the American Chemical Society. 123: 3179-80. PMID 11457047 DOI: 10.1021/ja004133w  1
2001 Tolman JR, Al-Hashimi HM, Kay LE, Prestegard JH. Structural and dynamic analysis of residual dipolar coupling data for proteins. Journal of the American Chemical Society. 123: 1416-24. PMID 11456715 DOI: 10.1021/ja002500y  1
2001 Al-Hashimi HM, Majumdar A, Gorin A, Kettani A, Skripkin E, Patel DJ. Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation. Journal of the American Chemical Society. 123: 633-40. PMID 11456575 DOI: 10.1021/ja003379y  1
2001 Tian F, Al-Hashimi HM, Craighead JL, Prestegard JH. Conformational analysis of a flexible oligosaccharide using residual dipolar couplings. Journal of the American Chemical Society. 123: 485-92. PMID 11456551 DOI: 10.1021/ja002900l  1
2001 Al-Hashimi HM, Tolman JR, Majumdar A, Gorin A, Patel DJ. Determining stoichiometry in homomultimeric nucleic acid complexes using magnetic field induced residual dipolar couplings. Journal of the American Chemical Society. 123: 5806-7. PMID 11403617 DOI: 10.1021/ja0105865  1
2000 Prestegard JH, al-Hashimi HM, Tolman JR. NMR structures of biomolecules using field oriented media and residual dipolar couplings. Quarterly Reviews of Biophysics. 33: 371-424. PMID 11233409 DOI: 10.1017/S0033583500003656  1
2000 Fowler CA, Tian F, Al-Hashimi HM, Prestegard JH. Rapid determination of protein folds using residual dipolar couplings. Journal of Molecular Biology. 304: 447-60. PMID 11090286 DOI: 10.1006/jmbi.2000.4199  1
2000 Al-Hashimi HM, Valafar H, Terrell M, Zartler ER, Eidsness MK, Prestegard JH. Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 143: 402-6. PMID 10729267 DOI: 10.1006/jmre.2000.2049  1
2000 Al-Hashimi HM, Bolon PJ, Prestegard JH. Molecular symmetry as an aid to geometry determination in ligand protein complexes. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 142: 153-8. PMID 10617446 DOI: 10.1006/jmre.1999.1937  1
1999 Bolon PJ, Al-Hashimi HM, Prestegard JH. Residual dipolar coupling derived orientational constraints on ligand geometry in a 53 kDa protein-ligand complex. Journal of Molecular Biology. 293: 107-15. PMID 10512719 DOI: 10.1006/jmbi.1999.3133  1
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