Publications

Preprint

Shi H., Kimsey I.J., 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” bioRxiv

Rangadurai A.*, Shi H.*, Xu Y.*, Liu B., Abou Assi H., Zhou H., Kimsey I.J., Al-Hashimi H.M. (2020) “delta-Melt: Nucleic acid conformational penalties from melting experiments” bioRxiv *Co-First Authors

Liu B., Shi H., Rangadurai A., Nussbaumer F., Chu C-C., Erharter K.A., Case D.A., Kreutz C., Al-Hashimi H.M. (2020) “A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions” bioRxiv

2021

158. 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 In Press

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

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):3420-33.

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):3592-9.

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):315-20.

100. Mouzakis K., Dethoff E.A., Al-Hashimi H.M. (2015). “Dynamic motions of the HIV-1 frameshift site RNA.” Biophysical Journal 108(3):644-54.

2014

99. Nikolova E.N., Stull F., Al-Hashimi H.M. (2014). “Guanine to Inosine Substitution Leads to Large Increases in the Population of a Transient G·C Hoogsteen Base Pair.” Biochemistry 53(46):7145–7147.

98. Enrico R., Salmon L., Fragai M., Parigi G., Al-Hashimi H.M.  (2014).  “Insights into Domain-Domain Motions in Proteins and RNA from Solution NMR.”  Accounts of Chemical Research 47(10):3118-26.

97. Sathyamoorthy B., Lee J., Kimsey I.J., Ganser L.R., Al-Hashimi H.M. (2014).  “Development and Application of Aromatic[13C, 1H] SOFAST-HMQC NMR Experiment for Nucleic Acids.”  Journal of Biomolecular NMR 60(2-3):77-83.

96. Ganser L.R., Mustoe A.M., Al-Hashimi H.M.  (2014).  “An RNA tertiary switch by modifying how helices are tethered.”  Genome Biology 15:425.

95. Alvey H.S., Nikolova E.N., Gottardo F.L., Al-Hashimi H.M. (2014). “Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics.”  Nature Communications 4(5):4786.

94. Horowitz S., Adhikari U., Dirk L.M., Del Rizzo P.A., Mehl R.A., Houtz R.L., Al-Hashimi H.M., Scheiner S., Trievel R.C.  (2014).  “Manipulating Unconventional CH-based Hydrogen Bonding in a Methyltransferase via Non-Canonical Amino Acid Mutagenesis.”  ACS Chemical Biology 9(8):1692-7.

93. Lee J., Dethoff E.A., Al-Hashimi H.M.  (2014).  “Invisible RNA State Dynamically Couples Distant Motifs.”  Proceedings of the National Academy of Sciences of the United States of America 111(26):9485-90.

92. Bothe J.R., Stein Z.W., Al-Hashimi H.M.  (2014).  “Evaluating the Uncertainty in Exchange Parameters Determined from Off-Resonance R1rho Relaxation Dispersion for Systems in Fast Exchange.”  Journal of Magnetic Resonance 244:18-29.

91. Kimsey I.J., Al-Hashimi H.M.  (2014).  “Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids.”  Current Opinion in Structural Biology 24:72-80.

90. Yang S., Salmon L., Al-Hashimi H.M.  (2014).  “Measuring the Similarity Between Dynamic Ensembles of Biomolecules.”  Nature Methods 11(5):552-4.

89. Eichhorn C.D., Al-Hashimi H.M.  (2014).  “Structural Dynamics of a Single-Stranded RNA-Helix Junction using NMR.”  RNA 20(6):782-91.

88. Mustoe A.M., Brooks III C.R.L., Al-Hashimi H.M.  (2014).  “Hierarchy of RNA Functional Dynamics.”  Annual Review of Biochemistry 83:441-66.

87. Horowitz S., Dirk L.M., Yesselman J.D., Nimtz J.S., Adhikari U., Mehl R.A., Scheiner S., Houtz R.L., Al-Hashimi H.M., Trievel R.C.  (2013).  “Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.” Journal of the American Chemical Society 135(41):15536-48.

86. Mustoe A.M., Al-Hashimi H.M., Brooks III C.R.L.  (2014).  “Coarse Grained Models Reveal Essential Contributions of Topological Constraints to RNA Conformational Free Energy.” The Journal of Physical Chemistry B 118(10):2615-27.

85. Salmon L., Yang S., Al-Hashimi H.M.  (2014).  “Advances in the determination of nucleic acid conformational ensembles.”  Annual Review of Physical Chemistry 65:293-316.

2013

84. Al-Hashimi H.M.  (2013).  “NMR Studies of Nucleic Acid Dynamics.”  Journal of Magnetic Resonance 237:191-204.

83. Lee J., Vogt C.E., McBrairty M., Al-Hashimi H.M.  (2013).  “Influence of Dimethylsulfoxide on RNA Structure and Ligand Binding.”  Analytical Chemistry 85(20):9692-8.

82. Suddala K.C., Rinaldi A.J., Feng J., Mustoe A.M., Eichhorn C.D., Liberman J.A., Wedekind J.E., Al-Hashimi H.M., Brooks III C.R.L., Walter N.G.  (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 Research 41(22):10462-75.

81. Nikolova E.N., Zhou H., Gottardo F.L., Alvey H.S., Kimsey I.J., Al-Hashimi H.M.  (2013).  “A Historical Account of Hoogsteen Base-Pairs in Duplex DNA.”  Biopolymers 99(12):955-68.

80. Nikolova E.N., Goh G.B., Brooks CL, Al-Hashimi H.M.  (2013).  “Characterizing the Protonation State of Cytosine in Transient G•C Hoogsteen Base Pairs in Duplex DNA.”  Journal of the American Chemical Society 135(18):6766-9.

79. Salmon L., Gavin B., Andricioaei I., Al-Hashimi H.M.  (2013).  “A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Inter-helical Motions Revealed.”  Journal of the American Chemical Society 135(14):5457-66.

78. Frank A.T., Horowitz S., Andricioaei I., Al-Hashimi H.M.  (2013).  “Utility of 1H NMR Chemical Shifts in Determining RNA Structure and Dynamics.”  The Journal of Physical Chemistry B 117(7):2045-52.

2012

77. Nikolova E., Bascom G., Andricioaei I., Al-Hashimi H.M.  (2012).  “Probing Sequence-specific DNA Flexibility in A-tracts and Pyrimidine-purine Steps by NMR 13C Relaxation and MD Simulations.”  Biochemistry 51(43):8654-64.

76.  Dethoff L.*, Petzold K.*, Chugh J.*, Casiano-Negroni A., Al-Hashimi H.M.  (2012).  “Visualizing Transient Low-Populated Structures of RNA.”  Nature 491(7426):724-8. *Co-first authors

75. Bothe J., Lowenhaupt K., Al-Hashimi H.M.  (2012).  “Incorporation of CC Steps into Z-DNA: Interplay Between B/Z Junction and Z-DNA Helical Formation.”  Biochemistry 51(34):6871-9.

74. Prevette L. Nikolova E., Al-Hashimi H.M., Banaszak-Holl M.  (2012).  “Intrinsic Dynamics of DNA-Polymer Complexes: A Mechanism for DNA Release.”  Molecular Pharmaceutics 9(9):2743-9.

73. Eichhorn C.D., Yang S., Al-Hashimi H.M.  Characterizing RNA Dynamics using NMR Residual Dipolar Couplings, in Recent Developments in Biomolecular NMR, Royal Society of Chemistry Publishing, Cambridge, 2012.

72. Nikolova E.N., Gottardo F.L., Al-Hashimi H.M.  (2012).  “Probing Transient Hoogsteen Hydrogen Bonds in Canonical Duplex DNA using NMR Relaxation Dispersion and Single-atom Substitution.”  Journal of the American Chemical Society 134(8):3667-70.

71. Dethoff E.A., Chugh J., Mustoe A.M., Al-Hashimi H.M.  (2012).  “Functional Complexity and Regulation through RNA Dynamics.”  Nature 482(7385):322-30.

70. Eichhorn C.D., Feng J., Suddala K.C., Walter N.G., Brooks C.L., Al-Hashimi H.M.  (2012).  “Unraveling the Structural Complexity in a Single Stranded RNA Tail: Implications for Efficient Ligand Binding in the Prequeuosine Riboswitch.”  Nucleic Acids Research 40(3):1345-55 (Featured article).

69. Mustoe A.M., Bailor M.H., Teixeira R., Brooks C.L., Al-Hashimi H.M.  (2012)  “New Insights Into the Fundamental Role of Topological Constraints as a Determinant of Two-Way Junction Conformation.”  Nucleic Acids Research 40(2):892-904.

2011

68. Petzold K., Al-Hashimi H.M.  (2011).  “RNA structure: Adding a second dimension.”  Nature Chemistry 3(12):913-5.

67. Bothe J.R., Nikolova E.N., Eichhorn C.D., Chugh J., Hansen A.L., Al-Hashimi H.M.  (2011).  “Characterizing RNA Dynamics at Atomic Resolution Using Solution State NMR Spectroscopy.”  Nature Methods 8(11):919-31.

66. Suzuki Y., Buer B.C., Al-Hashimi H.M., Marsh E.N.  (2011).  “Using Fluorine NMR to Probe Changes in Structure and Dynamics of Membrane-Active Peptides Interacting with Lipid Bilayers.”  Biochemistry 50(27):5979-87.

65. Bailor M.H., Mustoe A.M., Brooks C.L., Al-Hashimi H.M.  (2011).  “3D Maps of RNA interhelical junctions.”  Nature Protocols 6(10):1536-45 (Featured on cover).

64. Stelzer A.C., Frank A.T., Kratz J.D., Swanson M.D., Gonzalez-Hernandez M.J., Lee J., Andricioaei I., Markovitz D.M., Al-Hashimi H.M.  (2011).  “Discovery of Selective Bioactive Small Molecules by Targeting an RNA Dynamic Ensemble.”  Nature Chemical Biology 7(8):553-9.

63. Bailor M.H., Mustoe A.M., Brooks C.L., Al-Hashimi H.M.  (2011).  “Topological Constraints: Using RNA Secondary Structure to Model 3D Conformation, Folding Pathways, and Dynamic Adaptation.”  Current Opinion in Structural Biology. 21(3):296-305.

62. Horowitz S., Yesselman J.D., Al-Hashimi H.M., Trievel R.C.  (2011).  “Direct evidence for methyl group coordination by CH···O hydrogen bonds in SET domain methyltransferases.”  Journal of Biological Chemistry 286(21):18658-63.

61. Bothe J.R., Lowenhaupt K., Al-Hashimi H.M.  (2011).  “Sequence-Specific B-DNA Flexibility Modulates Z-DNA Formation.”  Journal of the American Chemical Society 133(7):2016-8.

60. Nikolova E.N., Kim E., Wise A.A., O’Brien P.J., Andricioaei I., Al-Hashimi H.M.  (2011).  “Transient Hoogsteen Base-pairs in Canonical Duplex DNA.”  Nature 470(7335):498-502.

2010

59. Dethoff E.A., Al-Hashimi H.M.  (2010).  “A rare example of lock-and-key RNA recognition.”  Journal of Molecular Biology 404(4):553-4.

58. Al-Hashimi H.M.  (2010).  “Exciting Structures.”  Science 329(5997):1295-6.

57. Nikolova E.N., Al-Hashimi H.M.  (2010).  “Thermodynamics of RNA Melting, One Base Pair at a Time.”  RNA 16(9):1687-91.

56. Buer B.C., Chugh J., Al-Hashimi H.M. and Marsh E.N.  (2010).  “Using fluorine NMR to probe the interaction of membrane-active peptides with the lipid bilayer.”  Biochemistry 49(27):5760-5.

55. Stelzer A.C., Kratz J.D., Zhang Q., Al-Hashimi H.M.  (2010).  “RNA Dynamics by Design: Biasing Ensembles Towards the Ligand-Bound State.”  Angewandte Chemie International Edition 49(33):5731-3 (Featured on cover).

54. Bailor M., Sun X., Al-Hashimi H.M.  (2010).  “Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation.”  Science 327(5962):202-6.

53. Koutmou K.S., Casiano-Negroni A., Getz M.M., Pazicni S., Penner-Hahn J.E., Al-Hashimi H.M., Fierke C.A.  (2010).  “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(6):2479-84.

52. Musselman C., Zhang Q., Al-Hashimi H.M., Andricioaei I.  (2010).  “Referencing strategy for the direct comparison of NMR and MD motional parameters in RNA.”  The Journal of Physical Chemistry B 114(2):929-39.

51. Dethoff E.A., Hansen A.L., Zhang Q., Al-Hashimi H.M.  (2010).  “Variable Helix Elongation as a Tool to Modulate RNA Alignment and Motional Couplings.”  Journal of Magnetic Resonance 202(1):117-21.

2009

50. Buer B.C., de la Salud-Bea R., Al-Hashimi H.M., Marsh E.N.  (2009).  “Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects.”  Biochemistry 48(45):10810-7.

49. Zhang Q., Al-Hashimi H.M.  (2009).  “Domain-elongation NMR Spectroscopy Yields New Insights into RNA Dynamics and Adaptive Recognition.”  RNA 15(11):1941-8. (Invited article accompanying The RNA Society/Scarnge Award for best research in RNA by a graduate student).

48. Al-Hashimi H.M.  (2009).  “Structural Biology: Aerial View of the HIV Genome.”  Nature 460(7256):696-698.

47. Nikolova E.N., Al-Hashimi H.M.  (2009).  “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(1-2):9-16.

46. Stelzer A.C., Frank A.T., Bailor M.H., Andricioaei I., Al-Hashimi H.M.  (2009).  “Constructing Atomic-Resolution RNA Structural Ensembles Using MD and Motionally Decoupled NMR RDCs.”  Methods 49(2):167-73.

45. Buhrlage S.L., Bates C.A., Rowe S.P., Minter A.R., Brennan B.B., Majmudar C.Y., Wemmer D.E., Al-Hashimi H.M., Mapp A.K.  (2009).  “Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors.”  ACS Chemical Biology 4(5):335-44.

44. Stelzer A.C., Frazee R.W., Van Huis C., Cleary J., Glick G.D., Al-Hashimi H.M. (2010).  “NMR Studies of an Immunomodulatory Benzodiazepine Binding to its Molecular Target on the Mitochondrial F(1)F(0)-ATPase.”  Biopolymers 93(1):85-92.

43. Fisher C.K., Al-Hashimi H.M.  (2009).  “Approximate Reconstruction of Continuous Domain Motional Paths by Multi-alignment Residual Dipolar Couplings.”  The Journal of Physical Chemistry B 113(18):6173-6.

42. Frank A.T., Stelzer A., Al-Hashimi H.M., Andricioaei I.  (2009).  “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(11):3670-9.

41. Hansen A.L., Nikolova E.N., Casiano-Negroni A., Al-Hashimi H.M.  (2009).  “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(11):3818-9.

2008

40. Fisher C.K., Zhang Q., Stelzer A., Al-Hashimi H.M.  (2008).  “Ultra-high spatial resolution characterization of domain motions by multi-alignment and multi-reference RDC NMR.”  The Journal of Physical Chemistry B 112(51):16815-22.

39. Dethoff E.A., Hansen A.L., Musselman C., Watt E.D., Andricioaei I., Al-Hashimi H.M.  (2008).  “Characterizing Complex Dynamics in the TAR Apical Loop and Motional Correlations with the Bulge by NMR, MD and Mutagenesis.”  Biophysical Journal 95(8):3906-15.

38. Al-Hashimi H.M., Walter N.G.  (2008).  “RNA Dynamics: It is about time.”  Current Opinion in Structural Biology 18(3):321-9.

37. Zhang Q., Al-Hashimi H.M.  (2008).  “Extending the NMR Spatial Resolution Limit in RNA by Motional Couplings.”  Nature Methods 5(3):243-5.

2007

36. Zhang Q., Stelzer A., Fisher C.K., Al-Hashimi H.M.  (2007).  “Visualizing Spatially Correlated Dynamics that Directs RNA Conformational Transitions.”  Nature 450:1263-7 (highlighted in Nature, 450:1171-2 2007).

35. Hansen A., Al-Hashimi H.M.  (2007).  “Dynamics of large elongated RNA by NMR carbon relaxation.”  Journal of the American Chemical Society 129(51):16072-82.

34. Bailor M., Musselman C., Hansen A., Gulati K., Patel D.J., Al-Hashimi H.M.  (2007).  “Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.”  Nature Protocols 2(6):1536-46 (Featured on cover).

33. Musselman C., Al-Hashimi H.M., Andricioaei I.  (2007).  “iRED Analysis of TAR RNA Reveals Motional Coupling, Long-Range Correlations, and a Dynamical Hinge.”  Biophysical Journal 93(2):411-22.

32. Casiano-Negroni A., Sun X., Al-Hashimi H.M.  (2007).  “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(22):6525-35.

31. Sun X., Zhang Q., Al-Hashimi H.M.  (2007).  “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(5):1698-713.

30. Getz M., Andrews A.J., Fierke C.A., Al-Hashimi H.M.  (2007).  “Structural Plasticity and Mg2+ Binding Properties of RNase P P4 from Combined Analysis of NMR Residual Dipolar Couplings and Motionally Decoupled Spin Relaxation.”  RNA 13(2):251-66.

29. Al-Hashimi H.M.  (2007).  “Beyond Static structures of RNA by NMR: Folding, re-folding and dynamics at atomic resolution.” Biopolymers 86(5-6):345-7.

28. Getz M., Sun X., Casiano-Negroni A., Zhang Q., Al-Hashimi H.M.  (2007).  “NMR Studies of RNA Structural Plasticity and Dynamics using Residual Dipolar Couplings.” Biopolymers 86(5-6):384-402.

2006

27. Musselman C., Pitt S.W., Gulati K., Foster L.L., Andricioaei I., Al-Hashimi H.M.  (2006).  “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(4):235-49.

26. Zhang Q., Sun X., Watt E.W., Al-Hashimi H.M.  (2006).  “Resolving the Motional Modes that Code for RNA Adaptation.”  Science 311(5761):653-6 (highlighted in Trends Biochem. Sci. 311:421-4.

25. Hansen A., Al-Hashimi H.M.  (2006).  “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 179(2):299-307.

24. Lee H., Lee K., Al-Hashimi H.M., Marsh E.N.G.  (2006).  “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(1):337-43.

2005

23. Al-Hashimi H.M.  (2005).  “Dynamics-Based Amplification of RNA Function and its Characterization By Using NMR Spectroscopy.”  ChemBioChem 6(9):1506-19 (featured on the cover).

22. Pitt S.W., Zhang Q., Patel D.J., Al-Hashimi H.M.  (2005).  “Electrostatic interactions dictate the ligand-induced arrest of RNA global motions.”  Angewandte Chemie International Edition 44(22):3412-5.

2004

21. Pitt S.W., Majumdar A., Patel D.J., Al-Hashimi H.M.  (2004).  “Argininamide Binding Arrests Global Motions in HIV-1 TAR RNA: Comparison with Mg2+ induced Conformational Stabilization.”  Journal of Molecular Biology 338(1):7-16.

2003

20. Tolman J.R., Al-Hashimi H.M.  (2003).  “Probing biomolecule structural dynamics using residual dipolar couplings.”  Annual Reports on NMR Spectroscopy 51:105-166.

19. Al-Hashimi H.M., Gorin A.  (2003).  “Application of NMR residual dipolar couplings in studies of RNA: Towards high throughput investigations.”  Application on Genome and Proteome 2(1):3-16.

18. Zhang Q., Throolin R., Pitt S.W., Serganov A., Al-Hashimi H.M.  (2003).  “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(35):10530-1.

17. Al-Hashimi H.M., Pitt S.W., Majumdar A., Xu W., Patel D.J.  (2003).  “Mg2+ induced changes in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings.”  Journal of Molecular Biology 329(5):867-73.

2002

16. Heffelfinger G.S., Martino A., Gorin A., Xu Y., Rintoul M.D., Geist A., Al-Hashimi H.M., Davidson G.S., Faulon J.L., Frink L.J., Haaland D.M., Hart W.E., Jakobsson E., Lane T., Li M., Locascio P., Olken F., Olman V., Palenik B., Plimpton S.J., Roe D.C., Samatova N.F., Shah M., Shoshoni A., Strauss C.E., Thomas E.V., Timlin J.A., Xu D.  (2002).  “Carbon sequestration in synechococcus sp.: from molecular machines to hierarchical modeling.”  OMICS 6(4):305-30.

15. Al-Hashimi H.M., Patel D.J.  (2002).  “Residual dipolar couplings: synergy between NMR and structural genomics.”  Journal of Biomolecular NMR 22(1):1-8.

14. Al-Hashimi H.M., Gorin A., Majumdar A., Gosser Y., Patel D.J.  (2002).  “Towards structural genomics of RNA: Rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings.”  Journal of Molecular Biology 318(3):637-49.

13. Al-Hashimi H.M., Gosser Y., Gorin A., Hu W., Majumdar A., Patel D.J.  (2002).  “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(2):95-102 (featured on cover).

2001

12. Al-Hashimi H.M., Majumdar A., Gorin A., Kettani A., Skripkin E., Patel D.J.  (2001).  “Field and phage induced dipolar couplings in a homodimeric DNA duplex: 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(4):633-640.

11. Al-Hashimi H.M., Gorin A., Majumdar A., Patel D.J.  (2001).  “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(13):3179-80.

10. Al-Hashimi H.M., Tolman J.R., Majumdar A., Gorin A., Patel D.J.  (2001).  “Determining stoichiometery in homomultimeric nucleic acid complexes using magnetic field induced residual dipolar couplings.”  Journal of the American Chemical Society 123(24):5806-7.

9. Tolman J.R., Al-Hashimi H.M., Kay L.E., Prestegard J.H.  (2001).  “Structural and Dynamic Analysis of Residual Dipolar Coupling Data for Proteins.”  Journal of the American Chemical Society 123(7):1416-24.

8. Tian, F., Al-Hashimi H.M., Craighead J.L., Prestegard J.H.  (2001).  “Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.”  Journal of the American Chemical Society 123(3):485-92.

7. Prestegard J.H., Al-Hashimi H.M., Tolman J.R.  (2001).  “NMR structures of biomolecules using field oriented media and residual dipolar couplings.”  Quarterly Reviews of Biophysics 33(4):371-424.

2000

6. Al-Hashimi H.M., Valafar H., Zartler R., Terrell M., Prestegard J.H.  (2000).  “Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.”  Journal of Magnetic Resonance 143(2):402-6.

5. Fowler C.A, Tian F., Al-Hashimi H.M., Prestegard J.H.  (2000).  “Rapid determination of protein folds using residual dipolar couplings.”  Journal of Molecular Biology 304(3):447-460.

4. Al-Hashimi H.M., Bolon P.J., Prestegard J.H.  (2000).  “Molecular symmetry as an aid to geometry determination in ligand protein complexes.”  Journal of Magnetic Resonance 142(1):153-158.

1999

3. Bolon P.J., Al-Hashimi H.M., Prestegard J.H.  (1999).  “Residual dipolar coupling derived orientational constraints on ligand geometry in a 53 kDa protein-ligand complex.”  Journal of Molecular Biology 293(1):107-15 (Highlighted in Chemical & Engineering News).

2. Prestegard J.H., Bolon P.J., Al-Hashimi H.M., Losonczi J., Fischer M.W.F. 1999. Field induced order in biomolecular solutions: A new source of NMR structural data, In: Proceedings of the Physical Phenomena at High Magnetic Fields-III (Z. Fisk, L.W.Gorkov, R. Schrieffer, eds.), pp. 419-420. World Scientific Publishing Co. Singapore.

1998

1. Prestegard J.H., Tolman J.R., Al-Hashimi H.M., Andrec M. Protein structure and dynamics from field induced residual dipolar couplings, in Modern Techniques in Protein NMR, pp. 311-355, Plenum, New York, 1998.

U.S. and International Patent Applications

1. “High-Throughput Ensemble-Based Docking Against Flexible Biomolecular Targets” Hashim M. Al-Hashimi, Andrew Stelzer, Ioan Andricioaei, Aaron Frank, USSN 61/194,291.