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Items: 1 to 50 of 151


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

Ganser LR, Kelly ML, Patwardhan NN, Hargrove AE, Al-Hashimi HM.

J Mol Biol. 2019 Dec 18. pii: S0022-2836(19)30709-0. doi: 10.1016/j.jmb.2019.12.009. [Epub ahead of print]


NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing.

Shi H, Liu B, Nussbaumer F, Rangadurai A, Kreutz C, Al-Hashimi HM.

J Am Chem Soc. 2019 Dec 26;141(51):19988-19993. doi: 10.1021/jacs.9b10939. Epub 2019 Dec 16.


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

Chu CC, Liu B, Plangger R, Kreutz C, Al-Hashimi HM.

PLoS One. 2019 Dec 11;14(12):e0224850. doi: 10.1371/journal.pone.0224850. eCollection 2019.


Exposing Hidden High-Affinity RNA Conformational States.

Orlovsky NI, Al-Hashimi HM, Oas TG.

J Am Chem Soc. 2020 Jan 15;142(2):907-921. doi: 10.1021/jacs.9b10535. Epub 2019 Dec 31.


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 R relaxation dispersion measurements.

Rangadurai A, Kremser J, Shi H, Kreutz C, Al-Hashimi HM.

J Magn Reson. 2019 Nov;308:106589. doi: 10.1016/j.jmr.2019.106589. Epub 2019 Sep 5.


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

Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM.

Prog Nucl Magn Reson Spectrosc. 2019 Jun - Aug;112-113:55-102. doi: 10.1016/j.pnmrs.2019.05.002. Epub 2019 May 11. Review.


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

Stelling AL, Liu AY, Zeng W, Salinas R, Schumacher MA, Al-Hashimi HM.

Angew Chem Int Ed Engl. 2019 Aug 26;58(35):12010-12013. doi: 10.1002/anie.201902693. Epub 2019 Jul 25.


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

Chu CC, Plangger R, Kreutz C, Al-Hashimi HM.

Nucleic Acids Res. 2019 Jul 26;47(13):7105-7117. doi: 10.1093/nar/gkz498.


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

Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM.

Nat Rev Mol Cell Biol. 2019 Aug;20(8):474-489. doi: 10.1038/s41580-019-0136-0. Review.


Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA.

Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM.

Biochemistry. 2019 Apr 16;58(15):1963-1974. doi: 10.1021/acs.biochem.9b00027. Epub 2019 Apr 5.


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

Fick RJ, Horowitz S, McDole BG, Clay MC, Mehl RA, Al-Hashimi HM, Scheiner S, Trievel RC.

Biochemistry. 2019 Apr 23;58(16):2152-2159. doi: 10.1021/acs.biochem.8b01141. Epub 2019 Apr 8.


The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA.

Travis B, Shaw PLR, Liu B, Ravindra K, Iliff H, Al-Hashimi HM, Schumacher MA.

Nucleic Acids Res. 2019 Feb 28;47(4):2130-2142. doi: 10.1093/nar/gky1259.


5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo5 U-G Base Pairs.

Strebitzer E, Rangadurai A, Plangger R, Kremser J, Juen MA, Tollinger M, Al-Hashimi HM, Kreutz C.

Chemistry. 2018 Dec 17;24(71):18903-18906. doi: 10.1002/chem.201805077. Epub 2018 Nov 20.


Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?

Rangadurai A, Zhou H, Merriman DK, Meiser N, Liu B, Shi H, Szymanski ES, Al-Hashimi HM.

Nucleic Acids Res. 2018 Nov 16;46(20):11099-11114. doi: 10.1093/nar/gky885.


A potentially abundant junctional RNA motif stabilized by m6A and Mg2.

Liu B, Merriman DK, Choi SH, Schumacher MA, Plangger R, Kreutz C, Horner SM, Meyer KD, Al-Hashimi HM.

Nat Commun. 2018 Jul 17;9(1):2761. doi: 10.1038/s41467-018-05243-z.


Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.

Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM.

RNA. 2018 Oct;24(10):1363-1376. doi: 10.1261/rna.066258.118. Epub 2018 Jul 16.


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

Ganser LR, Lee J, Rangadurai A, Merriman DK, Kelly ML, Kansal AD, Sathyamoorthy B, Al-Hashimi HM.

Nat Struct Mol Biol. 2018 May;25(5):425-434. doi: 10.1038/s41594-018-0062-4. Epub 2018 May 4.


Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.

Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM.

J Biomol NMR. 2018 Apr;70(4):229-244. doi: 10.1007/s10858-018-0177-2. Epub 2018 Apr 19.


Modulation of Hoogsteen dynamics on DNA recognition.

Xu Y, McSally J, Andricioaei I, Al-Hashimi HM.

Nat Commun. 2018 Apr 16;9(1):1473. doi: 10.1038/s41467-018-03516-1.


Hidden Structural Modules in a Cooperative RNA Folding Transition.

Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R.

Cell Rep. 2018 Mar 20;22(12):3240-3250. doi: 10.1016/j.celrep.2018.02.101.


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

Kimsey IJ, Szymanski ES, Zahurancik WJ, Shakya A, Xue Y, Chu CC, Sathyamoorthy B, Suo Z, Al-Hashimi HM.

Nature. 2018 Feb 8;554(7691):195-201. doi: 10.1038/nature25487. Epub 2018 Jan 31.


The Mechanism of HdeA Unfolding and Chaperone Activation.

Salmon L, Stull F, Sayle S, Cato C, Akgül Ş, Foit L, Ahlstrom LS, Eisenmesser EZ, Al-Hashimi HM, Bardwell JCA, Horowitz S.

J Mol Biol. 2018 Jan 5;430(1):33-40. doi: 10.1016/j.jmb.2017.11.002. Epub 2017 Nov 11.


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

Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE.

Medchemcomm. 2017 May 1;8(5):1022-1036. doi: 10.1039/C6MD00729E. Epub 2017 Mar 15.


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

Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM.

Nucleic Acids Res. 2017 Aug 21;45(14):e134. doi: 10.1093/nar/gkx525.


Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA.

Stelling AL, Xu Y, Zhou H, Choi SH, Clay MC, Merriman DK, Al-Hashimi HM.

FEBS Lett. 2017 Jun;591(12):1770-1784. doi: 10.1002/1873-3468.12681. Epub 2017 Jun 19.


Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM.

Nucleic Acids Res. 2017 May 19;45(9):5586-5601. doi: 10.1093/nar/gkx186.


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

Szymanski ES, Kimsey IJ, Al-Hashimi HM.

J Am Chem Soc. 2017 Mar 29;139(12):4326-4329. doi: 10.1021/jacs.7b01156. Epub 2017 Mar 20.


Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions.

Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi HM, Herschlag D.

RNA. 2017 May;23(5):611-618. doi: 10.1261/rna.060053.116. Epub 2017 Jan 30.


HIV-1 leader RNA dimeric interface revealed by NMR.

Ganser LR, Al-Hashimi HM.

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):13263-13265. Epub 2016 Nov 11. No abstract available.


m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.

Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM.

Nat Struct Mol Biol. 2016 Sep;23(9):803-10. doi: 10.1038/nsmb.3270. Epub 2016 Aug 1.


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

Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R.

J Mol Biol. 2016 Oct 9;428(20):3972-3985. doi: 10.1016/j.jmb.2016.07.013. Epub 2016 Jul 22.


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

Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM.

Nat Commun. 2016 Jun 13;7:ncomms11768. doi: 10.1038/ncomms11768.


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

Merriman DK, Xue Y, Yang S, Kimsey IJ, Shakya A, Clay M, Al-Hashimi HM.

Biochemistry. 2016 Aug 16;55(32):4445-56. doi: 10.1021/acs.biochem.6b00285. Epub 2016 Aug 4.


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

Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ.

Cell Rep. 2015 Dec 1;13(9):1800-13. doi: 10.1016/j.celrep.2015.10.062. Epub 2015 Nov 19.


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

Shakya A, Dougherty CA, Xue Y, Al-Hashimi HM, Banaszak Holl MM.

Biomacromolecules. 2016 Jan 11;17(1):154-64. doi: 10.1021/acs.biomac.5b01280. Epub 2015 Dec 11.


Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity.

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, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM.

Cell. 2015 Oct 22;163(3):746-58. doi: 10.1016/j.cell.2015.09.056. Epub 2015 Oct 22.


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

Mustoe AM, Al-Hashimi HM, Brooks CL 3rd.

Nucleic Acids Res. 2016 Jan 8;44(1):402-12. doi: 10.1093/nar/gkv1055. Epub 2015 Oct 19.


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

Andrałojć W, Ravera E, Salmon L, Parigi G, Al-Hashimi HM, Luchinat C.

Phys Chem Chem Phys. 2016 Feb 17;18(8):5743-52. doi: 10.1039/c5cp03993b.


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

Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM.

J Am Chem Soc. 2015 Oct 14;137(40):12954-65. doi: 10.1021/jacs.5b07229. Epub 2015 Sep 29.


Slowdown of Interhelical Motions Induces a Glass Transition in RNA.

Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I.

Biophys J. 2015 Jun 16;108(12):2876-85. doi: 10.1016/j.bpj.2015.04.041.


Characterizing RNA Excited States Using NMR Relaxation Dispersion.

Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM.

Methods Enzymol. 2015;558:39-73. doi: 10.1016/bs.mie.2015.02.002. Epub 2015 Mar 25.


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

Allain FH, Al-Hashimi HM.

Curr Opin Struct Biol. 2015 Feb;30:vii-viii. doi: 10.1016/ Epub 2015 Apr 13. No abstract available.


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

Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM.

Nucleic Acids Res. 2015 Apr 20;43(7):3420-33. doi: 10.1093/nar/gkv241. Epub 2015 Mar 26. Review.


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

Kimsey IJ, Petzold K, Sathyamoorthy B, Stein ZW, Al-Hashimi HM.

Nature. 2015 Mar 19;519(7543):315-20. doi: 10.1038/nature14227. Epub 2015 Mar 11.


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

Mustoe AM, Liu X, Lin PJ, Al-Hashimi HM, Fierke CA, Brooks CL 3rd.

J Am Chem Soc. 2015 Mar 18;137(10):3592-9. doi: 10.1021/ja5130308. Epub 2015 Mar 9.


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

Nikolova EN, Stull F, Al-Hashimi HM.

Biochemistry. 2014 Nov 25;53(46):7145-7. doi: 10.1021/bi5011909. Epub 2014 Nov 10.


An RNA tertiary switch by modifying how helices are tethered.

Ganser LR, Mustoe AM, Al-Hashimi HM.

Genome Biol. 2014 Jul 30;15(7):425. doi: 10.1186/s13059-014-0425-z.


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

Mustoe AM, Brooks CL 3rd, Al-Hashimi HM.

Nucleic Acids Res. 2014 Oct;42(18):11792-804. doi: 10.1093/nar/gku807. Epub 2014 Sep 12.


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

Alvey HS, Gottardo FL, Nikolova EN, Al-Hashimi HM.

Nat Commun. 2014 Sep 4;5:4786. doi: 10.1038/ncomms5786.

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