Publications

2019

137. 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 In Press.

136. 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 In Press.

2018

135. Travis B., Shaw P., Liu B., Ravindra K., Iliff H., Al-Hashimi H.M., Schumacher M. (2018) “The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA” Nucleic Acids Research 47(4): 2130-2142

134. 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

133. 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

132. 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

131. 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

130. 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

129. 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” J. Biomol. NMR 70(4):229-244

128. 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

127. 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

126. Xu Y., McSally J., Andricioaei I., Al-Hashimi H.M. (2018) “Modulation of Hoogsteen Dynamics on DNA Recognition” Nature Communications 9:1473

125. 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

2017

124. 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. (2017) “The Mechanism of HdeA Unfolding and Chaperone Activation” Journal of Molecular Biology 430(1): 33-40

123. 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

122. 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

121. 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.” MedChemComm 2017(8):1022-1036

120. 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” J. Am. Chem. Soc. 139(12): 4326-4329 JACS Spotlight

119. 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

118. Vaidyanathan P.P., AlSadhan I., Merriman D.K., Al-Hashimi H.M., and Herschlag D. (2017) “Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions.” RNA 23(5):611-618

2016

117. Ganser L., Al-Hashimi H.M. (2016) “The HIV-1 Leader RNA Dimeric Interface Revealed by NMR” Proc. Natl. Acad. Sci. U.S.A. 113(47):13263-13265

116. 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

115. Gracia B., Xue Y., Bisaria N., Herschlag D., Al-Hashimi H.M., and Russell R. (2016) “RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.” Journal of Molecular Biology 428(20): 3972–3985

114. 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

113. 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

112. Xue Y., Gracia B., Herschlag D., Russell R., and Al-Hashimi H.M. (2016) “Visualizing Formation of an RNA Folding Intermediate through a Fast Highly Modular Secondary Structure Switch.” Nature Communications 7:11768

111. 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

2015

110. Mustoe T., Al-Hashimi H.M., Brooks C. (2015) “Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme” Nucleic Acids Research 44(1): 402-412

109. Ren A., Xue Y., Peselis A., Serganov A., Al-Hashimi H.M., and 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

108. 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

107. 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.” J. Am. Chem. Soc. 137(40):12954-12965

106. 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.” Phys. Chem. Chem. Pays. 18(8):5742-5752

105. Yang S. and 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.” J Phys Chem B 119(30):9614-9626.

104. Frank A, Zhang Q, Al-Hashimi HM, and Andricioaei I. (2015) “Slowdown of Interhelical Motions Induces a Glass Transition in RNA.” Biophys J 108(12):2876-2885

103. 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.

102. Mustoe A., 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.” J. Am. Chem. Soc. 137(10):3592-9.

101. 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.

100. Kimsey I.J., Petzold K., Sathyamoorthy B., Stein Z.W., and Al-Hashimi H.M. (2015). “Visualizing Transient Watson-Crick Like Mispairs in DNA and RNA Duplexes.” Nature 519(7543):315-20.

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

2014

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

97. Sathyamoorthy B., Lee J., Kimsey I.J., Ganser L., Al-Hashimi H.M. (2014).  “Development and Application of Aromatic[13C, 1H] SOFAST-HMQC NMR Experiment for Nucleic Acids.”  J. Biomol. 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., and Al-Hashimi H.M. (2014). “Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics.”  Nat Commun 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.”  Proc. Natl. Acad. Sci. U.S.A. 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.”  J Magn Reson 244:18-29.

91. Kimsey I.J. and Al-Hashimi H.M.  (2014).  “Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids.”  Curr Opin in Struct Biol. 24:72-80.

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

89. Eichhorn C.D. and 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.”  Ann Rev Biochem 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.” J. Am. Chem. Soc. 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.”  J Phys Chem 118(10):2615-27.

85. Salmon L., Yang S., and Al-Hashimi H.M.  (2014).  “Advances in the determination of nucleic acid conformational ensembles.”  Ann Rev Phys Chem 65:293-316.

2013

84. Al-Hashimi H.M.  (2013).  “NMR Studies of Nucleic Acid Dynamics.”  J Magn Reson 237:191-204.

83. Lee J., Vogt C.E., McBrairty M., and Al-Hashimi H.M.  (2013).  “Influence of Dimethylsulfoxide on RNA Structure and Ligand Binding.”  Anal Chem 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 Acid Res 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.”  J. Am. Chem. Soc. 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.”  J. Am. Chem. Soc. 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.”  J. Phys. Chem. 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., and 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., and 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., and Banaszak-Holl M.  (2012).  “Intrinsic Dynamics of DNA-Polymer Complexes: A Mechanism for DNA Release.”  Mol. Pharm 9(9):2743-9.

73. Eichhorn C.D., Yang S., and 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. and Al-Hashimi H.M.  (2012).  “Probing Transient Hoogsteen Hydrogen Bonds in Canonical Duplex DNA using NMR Relaxation Dispersion and Single-atom Substitution.”  J. Am. Chem. Soc. 134(8):3667-70.

71. Dethoff E.A., Chugh J., Mustoe A.M. and 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. and 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 Res. 40(3):1345-55 (Featured article).

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

2011

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

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

66. Suzuki Y., Buer B.C., Al-Hashimi H.M. and 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., and Al-Hashimi H.M.  (2011).  “3D Maps of RNA interhelical junctions.”  Nat. Protoc. 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., and Al-Hashimi H.M.  (2011).  “Discovery of Selective Bioactive Small Molecules by Targeting an RNA Dynamic Ensemble.”  Nat. Chem. Biol. 7(8):553-9.

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

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

61. Bothe J.R., Lowenhaupt K., and Al-Hashimi H.M.  (2011).  “Sequence-Specific B-DNA Flexibility Modulates Z-DNA Formation.”  J. Am. Chem. Soc. 133(7):2016-8.

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

2010

59. Dethoff E.A. and Al-Hashimi H.M.  (2010).  “A rare example of lock-and-key RNA recognition.”  J. Mol. Biol. 404(4):553-4.

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

57. Nikolova E.N. and 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., and Al-Hashimi H.M.  (2010).  “RNA Dynamics by Design: Biasing Ensembles Towards the Ligand-Bound State.”  Angew. Chem. Int. Ed. 49(33):5731-3 (Featured on cover).

54. Bailor M., Sun X., and 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., and Fierke C.A.  (2010).  “NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.”  Proc. Natl. Acad. Sci. U.S.A. 107(6):2479-84.

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

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

2009

50. Buer B.C., de la Salud-Bea R., Al-Hashimi H.M., and 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. and 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. and 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.”  J. Biomol. NMR 45(1-2):9-16.

46. Stelzer A.C., Frank A.T., Bailor M.H., Andricioaei I., and 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., and Mapp A.K.  (2009).  “Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors.”  ACS Chem. Biol. 4(5):335-44.

44. Stelzer A.C., Frazee R.W., Van Huis C., Cleary J., Glick G.D., and 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. and Al-Hashimi H.M.  (2009).  “Approximate Reconstruction of Continuous Domain Motional Paths by Multi-alignment Residual Dipolar Couplings.”  J. Phys. Chem. B. 113(18):6173-6.

42. Frank A.T., Stelzer A., Al-Hashimi H.M., and 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 Res. 37(11):3670-9.

41. Hansen A.L., Nikolova E.N., Casiano-Negroni A., and 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.”  J. Am. Chem. Soc. 131(11):3818-9.

40. Fisher C.K., Zhang Q., Stelzer A., and Al-Hashimi H.M.  (2009).  “Ultra-high spatial resolution characterization of domain motions by multi-alignment and multi-reference RDC NMR.”  J. Phys. Chem. B. 112(51):16815-22.

2008

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

38. Al-Hashimi H.M. and Walter N.G.  (2008).  “RNA Dynamics: It is about time.”  Curr. Opin. Struct. Biol. 18(3):321-9.

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

2007

36. Zhang Q., Stelzer A., Fisher C.K., and 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., and Al-Hashimi H.M.  (2007).  “Dynamics of large elongated RNA by NMR carbon relaxation.”  J. Am. Chem. Soc. 129(51):16072-82.

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

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

32. Casiano-Negroni A., Sun X., and 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., and 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 Res. 35(5):1698-713.

30. Getz M., Andrews A.J., Fierke C.A., and 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., and 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., and 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.”  J. Biomol. NMR 36(4):235-49.

26. Zhang Q., Sun X., Watt E.W., and 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. and 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.”  J. Magn. Reson. 179(2):299-307.

24. Lee H., Lee K., Al-Hashimi H.M., and 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.”  J. Am. Chem. Soc. 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., and Al-Hashimi H.M.  (2005).  “Electrostatic interactions dictate the ligand-induced arrest of RNA global motions.”  Angew. Chem. Int. Ed. 44(22):3412-5.

2004

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

2003

20. Tolman J.R. and Al-Hashimi H.M.  (2003).  “Probing biomolecule structural dynamics using residual dipolar couplings.”  Ann. Rep. NMR Spect. 51:105-166.

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

18. Zhang Q., Throolin R., Pitt S.W., Serganov A., and 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.”  J. Am. Chem. Soc. 125(35):10530-1.

17. Al-Hashimi H.M., Pitt S.W., Majumdar A., Xu W., and Patel D.J.  (2003).  “Mg2+ induced changes in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings.”  J. Mol. Biol. 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., and Xu D.  (2002).  “Carbon sequestration in synechococcus sp.: from molecular machines to hierarchical modeling.”  OMICS 6(4):305-30.

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

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

13. Al-Hashimi H.M., Gosser Y., Gorin A., Hu W., Majumdar A., and 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.”  J. Mol. Biol. 315(2):95-102 (featured on cover).

2001

12. Al-Hashimi H.M., Majumdar A., Gorin A., Kettani A., Skripkin E., and 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.”  J. Am. Chem. Soc. 123(4):633-640.

11. Al-Hashimi H.M., Gorin A., Majumdar A., and 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.”  J. Am. Chem. Soc. 123(13):3179-80.

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

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

8. Tian, F., Al-Hashimi H.M., Craighead J.L., and Prestegard J.H.  (2001).  “Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.”  J. Am. Chem. Soc. 123(3):485-92.

2000

7. Prestegard J.H., Al-Hashimi H.M., and Tolman J.R.  (2000).  “NMR structures of biomolecules using field oriented media and residual dipolar couplings.”  Q. Rev. Biophys. 33(4):371-424.

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

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

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

1999

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

2. Prestegard J.H., Bolon P.J., Al-Hashimi H.M., Losonczi J., and 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., and 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, and Aaron Frank, USSN 61/194,291.