Recent Publications

2023

  • Megan, Roy, and Ainan et al published a paper entitled “RNA conformational propensities determine cellular activity” in Nature, June 2023.
  • 167. Al-Hashimi H.M. (2023) “Turing, von Neumann, and the computational architecture of biological machines” Proceedings of the National Academy of Sciences of the United States of America 120(25):e2220022120
  • 166. Ken M.L., Roy R., Geng A., Ganser L.R., Manghrani A., Cullen B.R., Schulze-Gahmen U., Herschlag D., Al-Hashimi H.M. (2023) “RNA conformational propensities determine cellular activity” Nature 617(7962):835-841
  • 165. Gu S., Szymanski E.S., Rangadurai A.K., Shi H., Liu B., Manghrani A., Al-Hashimi H.M. (2023) “Dynamic basis for dA• dGTP and dA• d8OGTP misincorporation via Hoogsteen base pairs” Nature Chemical Biology 19:900-910

2022

  • Atul, Honglue, and Yu et al published a paper entitled “Measuring thermodynamic preferences to form non-native conformations in nucleic acids using UV melting” in PNAS, April 2022.
  • 164. Choi S.H., Flamand M.N., Liu B., Zhu H., Hu M., Wang M., Sewell J., Holley C.L., Al-Hashimi H.M., Meyer K.D. (2022) “RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs” Cell Reports 40(9):111293
  • 163. Conroy D.W., Xu Y., Shi H., Gonzalez Salguero N., Purusottam R.N., Shannon M.D., Al-Hashimi H.M., Jaroniec C.P. (2022) “Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy” Proceedings of the National Academy of Sciences of the United States of America 119(30):e2200681119
  • 162. Rangadurai A.*, Shi H.*, Xu Y.*, Liu B., Abou Assi H., Zhou H., Kimsey I.J., Al-Hashimi H.M. (2022) “Measuring thermodynamic preferences to form non-native conformations in nucleic acids using UV melting” Proceedings of the National Academy of Sciences of the United States of America 119(24):e2112496119 *Co-First Authors

2021

  • 161. Shi H., Kimsey I.J., Gu S., Liu H.-F., Pham U., Schumacher M.A., Al-Hashimi H.M. (2021) “Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA” Nucleic Acids Research 49(21):12540-12555
  • 160. Liu B., Shi H., Al-Hashimi H.M. (2021) “Developments in solution state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids” Current Opinion in Structural Biology 70:16-25
  • 159. Liu B., Rangadurai A., Shi H., Al-Hashimi H.M. (2021) “Rapid measurement of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST” Magnetic Resonance 2(2):715-731
  • 158. Liu B., Shi H., Rangadurai A., Nussbaumer F., Chu C-C., Erharter K.A., Case D.A., Kreutz C., Al-Hashimi H.M. (2021) “A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions” Nature Communications 12(1):5201
  • 157. Kelly M., Chu C-C., Shi H., Ganser L.R., Bogerd H.P., Huynh K., Hou Y., Cullen B.R., Al-Hashimi H.M. (2021) “Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays” RNA 27(1):12-26

2020

  • Ariel, Honglue, and Atul et al published a paper entitled “DNA mismatches reveal conformational penalties in protein-DNA recognition” in Nature, October 2020.
  • 156. Abou Assi A., Rangadurai A., Shi H., Liu B., Clay M., Erharter K.A., Kreutz C., Holley C., Al-Hashimi H.M. (2020) “2′-O-methylation can increase the abundance and lifetime of alternative RNA conformational states” Nucleic Acids Research 48(21):12365-12379
  • 155. Shi H., Rangadurai A., Abou Assi A., Roy R., Case D.A., Herschlag D., Joseph D.Y., Al-Hashimi H.M. (2020) “Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction” Nature Communications 11:5531
  • 154. Xu Y.*, Manghrani A.*, Liu B., Shi H., Pham U., Liu A., Al-Hashimi H.M. (2020) “Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage” Journal of Biological Chemistry 295(47):15933-15947 *Co-First Authors
  • 153. Afek A., Shi H., Rangadurai A., Sahay H., Senitzki A., Xhani S., Fang M., Salinas R., Mielko Z., Pufall M.A., Poon G.M.K., Haran T.E., Schumacher M.A., Al-Hashimi H.M., Gordan R. (2020) “DNA mismatches reveal conformational penalties in protein-DNA recognition” Nature 587(7833):291-296 (News and Views by James Fraser)
  • 152. Rangadurai A., Szymanski E.S., Kimsey I., Shi H., Al-Hashimi H.M. (2020) “Probing conformational transitions towards mutagenic Watson-Crick-like G•T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion” Journal of Biomolecular NMR 74(8-9):457-471
  • 151. Li P., Rangadurai A., Al-Hashimi H.M., Hammes-Schiffer S. (2020) “Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations” Journal of the American Chemical Society 142(25):11183-11191
  • 150. Kladwang W., Topkar V., Liu B., Rangan R., Hodges T., Keane S., Al-Hashimi H.M., Das R. (2020) “Anomalous reverse transcription through chemical modifications in polyadenosine stretches” Biochemistry 59(23):2154-2170
  • 149. Rangadurai A., Shi H., Al-Hashimi H.M. (2020) “Extending the Sensitivity of CEST to Micro-to-Millisecond Dynamics in Nucleic Acids Using High Power Radio-Frequency Fields” Angewandte Chemie International Edition 59(28):11262-11266
  • 148. Ganser L.R.*, Chu C-C.*, Bogerd H.P., Kelly M.L., Cullen B.R., Al-Hashimi H.M. (2020) “Probing RNA conformational equilibria within the functional cellular context” Cell Reports 30(8):2472-2480.e4 *Co-First Authors
  • 147. Ganser L.R., Kelly M.L., Patwardhan N.N., Hargrove A.E., Al-Hashimi H.M. (2020) “Demonstration that small molecules can bind and stabilize low-abundance short-lived RNA excited conformational states” Journal of Molecular Biology 432(4):1297-1304
  • 146. Orlovsky N., Al-Hashimi H.M., Oas T. (2020) “Exposing hidden high-affinity RNA conformational states” Journal of the American Chemical Society 142(2):907-921 (JACS Spotlight)

2019

  • 145. Shi H.*, Liu B.*, Nussbaumer F., Rangadurai A., Kreutz C., Al-Hashimi H.M. (2019) “NMR chemical exchange measurements reveal that N6-methyladenosine slows RNA annealing” Journal of the American Chemical Society 141(51):19988-19993 *Co-First Authors (JACS Spotlight)
  • 144. Chu C-C., Liu B., Plangger R., Kreutz C., Al-Hashimi H.M. (2019) “m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB” PLOS ONE 14(12):e0224850
  • 143. Rangadurai A., Kremser J., Shi H., Kreutz C., Al-Hashimi H.M. (2019) “Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements” Journal of Magnetic Resonance 308:106589
  • 142. Stelling A., Liu A.Y., Zeng W., Salinas R., Schumacher M.A., Al-Hashimi H.M. (2019) “Infrared spectroscopic observation of a G-C+ Hoogsteen base pair in the DNA:TATA box binding protein complex under solution conditions” Angewandte Chemie International Edition 58(35):12010-12013
  • 141. Chu C-C., Plangger, R., Kreutz C., Al-Hashimi H.M. (2019) “Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev binding site” Nucleic Acids Research 47(13):7105-7117
  • 140. Rangadurai A., Szymanski E.S., Kimsey I.J., Shi H., Al-Hashimi H.M. (2019) “Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion” Progress in NMR spectroscopy 112-113:55-102
  • 139. Zhou H., Sathyamoorthy B., Stelling A., Xu Y., Xue Y., Pigli Y., Case D.A., Rice P.A., Al-Hashimi H.M. (2019) “Characterizing Watson-Crick versus Hoogsteen base-pairing in a DNA-protein complex using NMR and site-specifically 13C/15N labeled DNA” Biochemistry 58:1963-1974
  • 138. Fick R.J., Horowitz S., McDole B.G., Clay M.C., Mehl R.A., Al-Hashimi H.M., Scheiner S., Trievel R.C. (2019) “Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1” Biochemistry 58:2152-2159
  • 137. Ganser L.R., Kelly M.L., Herschlag D., Al-Hashimi H.M. (2019) “The roles of structural dynamics in the cellular functions of RNAs” Nature Reviews Molecular Cell Biology 20:474-489
  • 136. Travis B., Shaw P., Liu B., Ravindra K., Iliff H., Al-Hashimi H.M., Schumacher M. (2019) “The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA” Nucleic Acids Research 47(4):2130-2142

2018

  • 135. Strebitzer E.*, Rangadurai A.*, Plangger R., Kremser J., Juen M.A., Tollinger M., Al-Hashimi H.M., Kreutz C. (2018) “The 5-oxyacetic acid modification destabilizes double helical stem structures and favors anionic Watson-Crick like cmo5U-G base pairs” Chemistry 24(71):18903-18906 *Co-First Authors
  • 134. Rangadurai A., Zhou H., Merriman D.K., Meiser N., Liu B., Shi H., Szymanski E.S., Al-Hashimi H.M. (2018) “Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?” Nucleic Acids Research 46(20):11099-11114
  • 133. Merriman D.K., Yuan J., Shi H., Majumdar A., Herschlag D., Al-Hashimi H.M. (2018) “Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics” RNA 24(10):1363-1376
  • 132. Fick R., Clay M.C., Vander Lee L., Scheiner S., Al-Hashimi H.M., Trievel R. (2018) “Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates AdoMet Recognition in the Reactivation Domain of Cobalamin-dependent Methionine Synthase” Biochemistry 57(26):3733-3740
  • 131. Liu B., Merriman D.K., Choi S.H., Schumacher M.A., Plangger R., Kreutz C., Horner S.M., Meyer K.D., Al-Hashimi H.M. (2018) “A potentially abundant junctional RNA motif stabilized by m6A and Mg2+” Nature Communications 9:2761
  • 130. Shi H., Clay M.C., Rangadurai A., Sathyamoorthy B., Case D.A., Al-Hashimi H.M. (2018) “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 70(4):229-244
  • 129. Gracia B., Al-Hashimi H.M., Bisaria N., Das R., Herschlag D., Russell R. (2018) “Hidden Structural Modules in a Cooperative RNA Folding Transition” Cell Reports 22(12):3240-3250
  • 128. Ganser L.R., Lee J., Rangadurai A., Merriman D.K., Kelly M.L., Kansal A.D., Sathyamoorthy B., Al-Hashimi H.M. (2018) “High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble” Nature Structural and Molecular Biology 25, 425-434
  • 127. Xu Y., McSally J., Andricioaei I., Al-Hashimi H.M. (2018) “Modulation of Hoogsteen Dynamics on DNA Recognition” Nature Communications 9:1473
  • 126. Kimsey I.J.*, Szymanski E.S.*, Zahurancik W.J., Shakya A., Xue Y., Chu C-C., Sathyamoorthy B., Suo Z., Al-Hashimi H.M. (2018) “Dynamic Basis for dG•dT misincorporation via tautomerization and ionization” Nature 554(7691):195-201 *Co-First Authors (News and Views by Myron Goodman)
  • 125. Salmon L., Stull F., Sayle S., Cato C., Akgul S., Foit L., Ahlstrom L.S., Eisenmesser E.Z., Al-Hashimi H.M., Bardwell J.C.A., Horowitz S. (2018) “The Mechanism of HdeA Unfolding and Chaperone Activation” Journal of Molecular Biology 430(1):33-40

2017

  • 124. Clay M.C., Ganser L.R., Merriman D.K., Al-Hashimi H.M. (2017) “Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics” Nucleic Acids Research 45(14):e134
  • 123. Stelling A., Xu Y., Zhou H., Choi S.; Clay M.C., Merriman D.K., Al-Hashimi H.M. (2017) “Robust IR Based Detection of Stable and Fractionally Populated G-C+ and A-T Hoogsteen Base Pairs in Duplex DNA” FEBS Letters 591(12):1770-1784
  • 122. Patwardhan N.N., Ganser L.R., Kapral G.J., Eubanks C.S., Lee J., Sathyamoorthy B., Al-Hashimi H.M., Hargrove A.E. (2017) “Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR” Medicinal Chemistry Communications 2017(8):1022-1036
  • 121. Szymanski E.S., Kimsey I.J., Al-Hashimi H.M. (2017) “Direct NMR Evidence that Transient Tautomeric and Anionic States in dG•dT Form Watson-Crick like Base Pairs” Journal of the American Chemical Society 139(12):4326-4329 (JACS Spotlight)
  • 120. Sathyamoorthy B., Shi H., Zhou H., Xue Y., Rangadurai A., Merriman D.K., Al-Hashimi H.M. (2017) “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 45(9):5586-5601
  • 119. Vaidyanathan P.P., AlSadhan I., Merriman D.K., Al-Hashimi H.M., Herschlag D. (2017) “Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions” RNA 23(5):611-618

2016

  • 118. Ganser L.R., Al-Hashimi H.M. (2016) “The HIV-1 Leader RNA Dimeric Interface Revealed by NMR” Proceedings of the National Academy of Sciences of the United States of America 113(47):13263-13265
  • 117. Shakya A., Al-Hashimi H.M., Holl M.B. (2016) “Three RNA Microenvironments Detected in Fluxional Gene Delivery Polyplex Nano-assemblies” ACS Macro Letters 5(10):1104-1108
  • 116. Gracia B., Xue Y., Bisaria N., Herschlag D., Al-Hashimi H.M., Russell R. (2016) “RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly” Journal of Molecular Biology 428(20):3972-3985
  • 115. Zhou H., Kimsey I.J., Nikolova E.N., Sathyamoorthy B., Grazioli G., Sally J.M., Bai T., Wunderlich C.H., Kreutz C., Andricioaei I., Al-Hashimi H.M. (2016) “m1A and m1G Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs” Nature Structural and Molecular Biology 23:803-810
  • 114. Merriman D.K., Xue Y., Yang S., Kimsey I.J., Shakya A., Clay M.C., Al-Hashimi H.M. (2016) “Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes Over a Broad Range of Timescales” Biochemistry 55(32):4445-4456
  • 113. Xue Y., Gracia B., Herschlag D., Russell R., Al-Hashimi H.M. (2016) “Visualizing Formation of an RNA Folding Intermediate through a Fast Highly Modular Secondary Structure Switch” Nature Communications 7:11768
  • 112. Shakya A.; Dougherty C.; Xue Y.; Al-Hashimi H.M.; Holl M.B. (2016) “Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release” Biomacromolecules 17(1):154-164
  • 111. Mustoe A.M., Al-Hashimi H.M., Brooks C. (2016) “Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme” Nucleic Acids Research 44(1):402-412

2015

  • 110. Ren A.*, Xue Y.*, Peselis A., Serganov A., Al-Hashimi H.M., Patel D.J. (2015) “Structural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by the Gln-riboswitch” Cell Reports 13(9):1800-1813 *Co-First Authors
  • 109. Swanson M.,Boudreaux D., Salmon L., Chugh J., Winter H., Meagher J., Andre S., Murphy P., Roy R., King S., Kaplan M., Goldstein I., Tarbet E.B., Hurst B., Smee D., de al Fuente C., Hoffmann H.H., Xue Y., Rice C., Schols D., Garcia J.V., Stuckey., Gabius H.H., Al-Hashimi H.M., Markovitz, D. (2015) “Engineering A Therapeutic Lectin: Uncoupling Mitogenicity from Antiviral Activity” Cell 163(3):746-758
  • 108. Salmon L., Giambasu G., Nikolova E.N., Petzold K., Bhattacharya A., Case D., Al-Hashimi H.M. (2015) “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 137(40):12954-12965
  • 107. Andralojc W., Ravera E., Salmon L., Parigi G., Al-Hashimi H.M., Luchiant C. (2016) “Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations” Physical Chemistry Chemical Physics 18(8):5742-5752
  • 106. Yang S., Al-Hashimi H.M. (2015) “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 119(30):9614-9626
  • 105. Frank A, Zhang Q, Al-Hashimi HM, Andricioaei I. (2015) “Slowdown of Interhelical Motions Induces a Glass Transition in RNA” Biophysical Journal 108(12):2876-2885
  • 104. Zhou H., Hintze B., Kimsey I.J. Sathyamoorthy B., Yang S., Richardson J., Al-Hashimi H.M. (2015) “New Insights into Hoogsteen Base Pairs in DNA Duplexes from a Structure-based Survey” Nucleic Acids Research 43(7):3420-3433
  • 103. Mustoe A.M., Liu X., Lin P., Al-Hashimi H.M., Fierke C., Brooks C. (2015) “A non-canonical secondary structure stabilizes mitochondrial tRNASer(UCN) by reducing the entropic cost of tertiary folding” Journal of the American Chemical Society 137(10):3592-3599
  • 102. Xue Y., Kellogg D., Kimsey I.J., Sathyamoorthy B., Stein Z., McBrairty M., Al-Hashimi H.M. (2015) “Characterizing RNA Excited States using NMR Relaxation Dispersion” Methods in Enzymology 558:39-73
  • 101. Kimsey I.J., Petzold K., Sathyamoorthy B., Stein Z.W., Al-Hashimi H.M. (2015) “Visualizing Transient Watson-Crick Like Mispairs in DNA and RNA Duplexes” Nature 519(7543):315-320
  • 100. Mouzakis K., Dethoff E.A., Al-Hashimi H.M. (2015) “Dynamic motions of the HIV-1 frameshift site RNA” Biophysical Journal 108(3):644-654