Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Yale University 2000
• 

  Previous Appointments & Affiliations

  • James B. Duke Distinguished Professor of Biochemistry, Biochemistry, Basic Science Departments 2015 - 2022
  • Professor of Biochemistry, Biochemistry, Basic Science Departments 2015 - 2022
  • Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2015 - 2021
  • Instructor, Temporary of Biochemistry, Biochemistry, Basic Science Departments 2013 - 2015
• Recognition
• 

  In the News

  • OCT 21, 2020

    Transcription Factors May Inadvertently Lock in DNA Mistakes

  • JAN 22, 2020

    School of Medicine

    Al-Hashimi Receives Prestigious National Academy of Sciences Award in Molecular Biology

  • JUL 18, 2018

    School of Medicine

    Foundation Funds an 'Expedition' to Map Novel Structures in the Human Genome

  • MAY 4, 2018

    Molecular Movies of RNA Guide Drug Discovery

  • JAN 31, 2018

    A Mutational Timer is Built Into the Chemistry of DNA

  • AUG 3, 2016

    The Washington Post

    A weird twist in DNA might explain why it’s such a great blueprint for life

  • JUL 29, 2016

    DNA's Dynamic Nature Well-Suited for Blueprint of Life

  • JUN 7, 2016

    Biochem Grad Student Finalist for International Prize

  • OCT 23, 2015

    The Daily Mail

    Drug made from bananas can kill viruses including hepatitis C and flu

  • MAY 1, 2015

    Duke Announces 2015 Distinguished Professors

  • MAR 13, 2015

    Science a Gogo

    ‘Quantum jitter’ mechanism behind the random mutations that drive evolution and cancer

  • MAR 11, 2015

    'Quantum Jitters' Could Form Basis of Evolution, Cancer

  • SEP 5, 2014

    Hashim Al-Hashimi named director for Center for RNA Biology
• Research
• 

  Selected Grants

  • Medical Scientist Training Program awarded by National Institutes of Health 2022 - 2027
  • Cell and Molecular Biology Training Program awarded by National Institutes of Health 2021 - 2026
  • Role of DNA structural dynamics in mutagenesis and oncogenesis awarded by National Institutes of Health 2010 - 2023
  • The Center for HIV RNA Studies (CRNA) awarded by Regents of the University of Michigan 2014 - 2022
  • Deep Topological Sampling of Protein Structures - non-competing renewal for Year 4 awarded by National Institutes of Health 2017 - 2022
  • Harnessing Small Molecules to Probe the Structure and Function of Long Noncoding RNAs awarded by National Institutes of Health 2017 - 2022
  • Medical Scientist Training Program awarded by National Institutes of Health 1997 - 2022
  • Structural studies of post-transcriptionally modified snRNAs and their role in congenital heart disease awarded by National Institutes of Health 2020 - 2022
  • Targeting Regulatory RNA elements in the Zika Virus awarded by National Institutes of Health 2020 - 2022
  • Fundamental Studies of RNA Conformational Thermodynamics awarded by Stanford University 2019 - 2022
  • Targeting an inactive conformation of HIV-1 TAR awarded by National Institutes of Health 2020 - 2022
  • Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
  • PC150506: Small molecule targeting of RNA splice variants driving tumor aggressiveness awarded by United States Army Medical Research Acquisition Activity 2016 - 2020
  • Development and Application of IR-based methods for visualizing Hoogsteen base pairs in the Nucleosome Particle awarded by National Institutes of Health 2017 - 2019
  • Fundamental Studies of RNA Folding Project 1 awarded by Stanford University 2014 - 2019
  • Structure, Function and Targetability of RNA Excited States awarded by National Institutes of Health 2017 - 2018
  • Functions of Carbon-Oxygen Hydrogen Bonding in Biological Methyl Transfer awarded by University of Michigan 2014 - 2018
  • Fundamental Studies of RNA Folding Project 2 awarded by Stanford University 2014 - 2018
  • Fundamental Studies of RNA Folding Project 3 awarded by Stanford University 2014 - 2018
  • Acquisition of a MALDI-TOF Mass Spectrometer System at Duke University awarded by North Carolina Biotechnology Center 2017 - 2018
  • Targeting HIV-1 Regulatory RNA Elements awarded by National Institutes of Health 2005 - 2016
  • Dynamics of Normal and Damaged DNA Under Relaxed and Supercoiled Conditions awarded by National Institutes of Health 2010 - 2015
  • Mechanism of an Acid Activated Chaperone awarded by Regents of the University of Michigan 2014 - 2015
  • Biological Activity of Lead Compounds Targeting HIV-1 TAR RNA awarded by Regents of the University of Michigan 2014
  • Mechanism of an Acid Activated Chaperone awarded by Regents of the University of Michigan 2014
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Ken, Megan L., Rohit Roy, Ainan Geng, Laura R. Ganser, Akanksha Manghrani, Bryan R. Cullen, Ursula Schulze-Gahmen, Daniel Herschlag, and Hashim M. Al-Hashimi. “RNA conformational propensities determine cellular activity.” Nature 617, no. 7962 (May 2023): 835–41. https://doi.org/10.1038/s41586-023-06080-x.
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    • Gu, Stephanie, Eric S. Szymanski, Atul K. Rangadurai, Honglue Shi, Bei Liu, Akanksha Manghrani, and Hashim M. Al-Hashimi. “Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs.” Nat Chem Biol, April 24, 2023. https://doi.org/10.1038/s41589-023-01306-5.
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    • Choi, Seung H., Mathieu N. Flamand, Bei Liu, Huanyu Zhu, Meghan Hu, Melanie Wang, Jonathon Sewell, Christopher L. Holley, Hashim M. Al-Hashimi, and Kate D. Meyer. “RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs.” Cell Rep 40, no. 9 (August 30, 2022): 111293. https://doi.org/10.1016/j.celrep.2022.111293.
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    • Conroy, Daniel W., Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N. Purusottam, Matthew D. Shannon, Hashim M. Al-Hashimi, and Christopher P. Jaroniec. “Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy.” Proc Natl Acad Sci U S A 119, no. 30 (July 26, 2022): e2200681119. https://doi.org/10.1073/pnas.2200681119.
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    • Rangadurai, Atul, Honglue Shi, Yu Xu, Bei Liu, Hala Abou Assi, John D. Boom, Huiqing Zhou, Isaac J. Kimsey, and Hashim M. Al-Hashimi. “Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.” Proc Natl Acad Sci U S A 119, no. 24 (June 14, 2022): e2112496119. https://doi.org/10.1073/pnas.2112496119.
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    • Lai, Lien B., Stella M. Lai, Eric S. Szymanski, Mridu Kapur, Edric K. Choi, Hashim M. Al-Hashimi, Susan L. Ackerman, and Venkat Gopalan. “Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis.” Proc Natl Acad Sci U S A 119, no. 10 (March 8, 2022): e2119529119. https://doi.org/10.1073/pnas.2119529119.
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    • Shi, Honglue, Isaac J. Kimsey, Stephanie Gu, Hsuan-Fu Liu, Uyen Pham, Maria A. Schumacher, and Hashim M. Al-Hashimi. “Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.” Nucleic Acids Res 49, no. 21 (December 2, 2021): 12540–55. https://doi.org/10.1093/nar/gkab936.
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    • Liu, Bei, Honglue Shi, and Hashim M. Al-Hashimi. “Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.” Curr Opin Struct Biol 70 (October 2021): 16–25. https://doi.org/10.1016/j.sbi.2021.02.007.
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    • Liu, Bei, Honglue Shi, Atul Rangadurai, Felix Nussbaumer, Chia-Chieh Chu, Kevin Andreas Erharter, David A. Case, Christoph Kreutz, and Hashim M. Al-Hashimi. “A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions.” Nat Commun 12, no. 1 (August 31, 2021): 5201. https://doi.org/10.1038/s41467-021-25253-8.
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    • Kelly, Megan L., Chia-Chieh Chu, Honglue Shi, Laura R. Ganser, Hal P. Bogerd, Kelly Huynh, Yuze Hou, Bryan R. Cullen, and Hashim M. Al-Hashimi. “Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.” Rna 27, no. 1 (January 2021): 12–26. https://doi.org/10.1261/rna.076257.120.
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    • Liu, B., A. Rangadurai, H. Shi, and H. M. Al-Hashimi. “Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino ¹H CEST.” Magnetic Resonance 2, no. 2 (January 1, 2021): 715–31. https://doi.org/10.5194/mr-2-715-2021.
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    • Abou Assi, Hala, Atul K. Rangadurai, Honglue Shi, Bei Liu, Mary C. Clay, Kevin Erharter, Christoph Kreutz, Christopher L. Holley, and Hashim M. Al-Hashimi. “2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.” Nucleic Acids Res 48, no. 21 (December 2, 2020): 12365–79. https://doi.org/10.1093/nar/gkaa928.
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    • Xu, Yu, Akanksha Manghrani, Bei Liu, Honglue Shi, Uyen Pham, Amy Liu, and Hashim M. Al-Hashimi. “Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.” J Biol Chem 295, no. 47 (November 20, 2020): 15933–47. https://doi.org/10.1074/jbc.RA120.014530.
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    • Shi, Honglue, Atul Rangadurai, Hala Abou Assi, Rohit Roy, David A. Case, Daniel Herschlag, Joseph D. Yesselman, and Hashim M. Al-Hashimi. “Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.” Nat Commun 11, no. 1 (November 2, 2020): 5531. https://doi.org/10.1038/s41467-020-19371-y.
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    • Afek, Ariel, Honglue Shi, Atul Rangadurai, Harshit Sahay, Alon Senitzki, Suela Xhani, Mimi Fang, et al. “DNA mismatches reveal conformational penalties in protein-DNA recognition.” Nature 587, no. 7833 (November 2020): 291–96. https://doi.org/10.1038/s41586-020-2843-2.
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    • Rangadurai, Atul, Eric S. Szymanski, Isaac Kimsey, Honglue Shi, and Hashim M. Al-Hashimi. “Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion.” J Biomol Nmr 74, no. 8–9 (September 2020): 457–71. https://doi.org/10.1007/s10858-020-00337-7.
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    • Rangadurai, Atul, Honglue Shi, and Hashim M. Al-Hashimi. “Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields.” Angew Chem Int Ed Engl 59, no. 28 (July 6, 2020): 11262–66. https://doi.org/10.1002/anie.202000493.
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    • Li, Pengfei, Atul Rangadurai, Hashim M. Al-Hashimi, and Sharon Hammes-Schiffer. “Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.” J Am Chem Soc 142, no. 25 (June 24, 2020): 11183–91. https://doi.org/10.1021/jacs.0c03774.
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    • Kladwang, Wipapat, Ved V. Topkar, Bei Liu, Ramya Rangan, Tracy L. Hodges, Sarah C. Keane, Hashim Al-Hashimi, and Rhiju Das. “Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.” Biochemistry 59, no. 23 (June 16, 2020): 2154–70. https://doi.org/10.1021/acs.biochem.0c00020.
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    • Ganser, Laura R., Janghyun Lee, Atul Rangadurai, Dawn K. Merriman, Megan L. Kelly, Aman D. Kansal, Bharathwaj Sathyamoorthy, and Hashim M. Al-Hashimi. “Publisher Correction: High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.” Nat Struct Mol Biol 27, no. 6 (June 2020): 604. https://doi.org/10.1038/s41594-020-0434-4.
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    • Ganser, Laura R., Chia-Chieh Chu, Hal P. Bogerd, Megan L. Kelly, Bryan R. Cullen, and Hashim M. Al-Hashimi. “Probing RNA Conformational Equilibria within the Functional Cellular Context.” Cell Rep 30, no. 8 (February 25, 2020): 2472-2480.e4. https://doi.org/10.1016/j.celrep.2020.02.004.
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    • Ganser, Laura R., Megan L. Kelly, Neeraj N. Patwardhan, Amanda E. Hargrove, and Hashim M. Al-Hashimi. “Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States.” J Mol Biol 432, no. 4 (February 14, 2020): 1297–1304. https://doi.org/10.1016/j.jmb.2019.12.009.
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    • Orlovsky, Nicole I., Hashim M. Al-Hashimi, and Terrence G. Oas. “Exposing Hidden High-Affinity RNA Conformational States.” J Am Chem Soc 142, no. 2 (January 15, 2020): 907–21. https://doi.org/10.1021/jacs.9b10535.
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    • Rangadurai, A., H. Shi, and H. M. Al-Hashimi. “Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields.” Advanced Materials 132, no. 28 (January 1, 2020): 11358–62. https://doi.org/10.1002/ANGE.202000493.
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    • Shi, Honglue, Bei Liu, Felix Nussbaumer, Atul Rangadurai, Christoph Kreutz, and Hashim M. Al-Hashimi. “NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing.” J Am Chem Soc 141, no. 51 (December 26, 2019): 19988–93. https://doi.org/10.1021/jacs.9b10939.
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    • Rangadurai, Atul, Johannes Kremser, Honglue Shi, Christoph Kreutz, and Hashim M. Al-Hashimi. “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.” J Magn Reson 308 (November 2019): 106589. https://doi.org/10.1016/j.jmr.2019.106589.
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    • Stelling, Allison L., Amy Y. Liu, Wenjie Zeng, Raul Salinas, Maria A. Schumacher, and Hashim M. Al-Hashimi. “Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.” Angew Chem Int Ed Engl 58, no. 35 (August 26, 2019): 12010–13. https://doi.org/10.1002/anie.201902693.
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    • Ganser, Laura R., Megan L. Kelly, Daniel Herschlag, and Hashim M. Al-Hashimi. “The roles of structural dynamics in the cellular functions of RNAs.” Nat Rev Mol Cell Biol 20, no. 8 (August 2019): 474–89. https://doi.org/10.1038/s41580-019-0136-0.
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    • Chu, Chia-Chieh, Raphael Plangger, Christoph Kreutz, and Hashim M. Al-Hashimi. “Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site.” Nucleic Acids Res 47, no. 13 (July 26, 2019): 7105–17. https://doi.org/10.1093/nar/gkz498.
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    • Fick, Robert J., Scott Horowitz, Brandon G. McDole, Mary C. Clay, Ryan A. Mehl, Hashim M. Al-Hashimi, Steve Scheiner, and Raymond C. Trievel. “Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.” Biochemistry 58, no. 16 (April 23, 2019): 2152–59. https://doi.org/10.1021/acs.biochem.8b01141.
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    • Zhou, Huiqing, Bharathwaj Sathyamoorthy, Allison Stelling, Yu Xu, Yi Xue, Ying Zhang Pigli, David A. Case, Phoebe A. Rice, and Hashim M. Al-Hashimi. “Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA.” Biochemistry 58, no. 15 (April 16, 2019): 1963–74. https://doi.org/10.1021/acs.biochem.9b00027.
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    • Travis, Brady, Porsha L. R. Shaw, Bei Liu, Krishna Ravindra, Hadley Iliff, Hashim M. Al-Hashimi, and Maria A. Schumacher. “The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA.” Nucleic Acids Res 47, no. 4 (February 28, 2019): 2130–42. https://doi.org/10.1093/nar/gky1259.
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    • Chu, Chia-Chieh, Bei Liu, Raphael Plangger, Christoph Kreutz, and Hashim M. Al-Hashimi. “m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB.” Plos One 14, no. 12 (2019): e0224850. https://doi.org/10.1371/journal.pone.0224850.
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    • Rangadurai, Atul, Eric S. Szymaski, Isaac J. Kimsey, Honglue Shi, and Hashim M. Al-Hashimi. “Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion.” Prog Nucl Magn Reson Spectrosc 112–113 (2019): 55–102. https://doi.org/10.1016/j.pnmrs.2019.05.002.
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    • Strebitzer, Elisabeth, Atul Rangadurai, Raphael Plangger, Johannes Kremser, Michael Andreas Juen, Martin Tollinger, Hashim M. Al-Hashimi, and Christoph Kreutz. “5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo5 U-G Base Pairs.” Chemistry 24, no. 71 (December 17, 2018): 18903–6. https://doi.org/10.1002/chem.201805077.
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    • Rangadurai, Atul, Huiqing Zhou, Dawn K. Merriman, Nathalie Meiser, Bei Liu, Honglue Shi, Eric S. Szymanski, and Hashim M. Al-Hashimi. “Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?” Nucleic Acids Res 46, no. 20 (November 16, 2018): 11099–114. https://doi.org/10.1093/nar/gky885.
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    • Merriman, Dawn K., Jiayi Yuan, Honglue Shi, Ananya Majumdar, Daniel Herschlag, and Hashim M. Al-Hashimi. “Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.” Rna 24, no. 10 (October 2018): 1363–76. https://doi.org/10.1261/rna.066258.118.
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    • Liu, Bei, Dawn K. Merriman, Seung H. Choi, Maria A. Schumacher, Raphael Plangger, Christoph Kreutz, Stacy M. Horner, Kate D. Meyer, and Hashim M. Al-Hashimi. “A potentially abundant junctional RNA motif stabilized by m6A and Mg2.” Nat Commun 9, no. 1 (July 17, 2018): 2761. https://doi.org/10.1038/s41467-018-05243-z.
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    • Fick, Robert J., Mary C. Clay, Lucas Vander Lee, Steve Scheiner, Hashim Al-Hashimi, and Raymond C. Trievel. “Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.” Biochemistry 57, no. 26 (July 3, 2018): 3733–40. https://doi.org/10.1021/acs.biochem.8b00375.
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    • Ganser, Laura R., Janghyun Lee, Atul Rangadurai, Dawn K. Merriman, Megan L. Kelly, Aman D. Kansal, Bharathwaj Sathyamoorthy, and Hashim M. Al-Hashimi. “High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.” Nat Struct Mol Biol 25, no. 5 (May 2018): 425–34. https://doi.org/10.1038/s41594-018-0062-4.
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    • Xu, Yu, James McSally, Ioan Andricioaei, and Hashim M. Al-Hashimi. “Modulation of Hoogsteen dynamics on DNA recognition.” Nat Commun 9, no. 1 (April 16, 2018): 1473. https://doi.org/10.1038/s41467-018-03516-1.
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    • Shi, Honglue, Mary C. Clay, Atul Rangadurai, Bharathwaj Sathyamoorthy, David A. Case, and Hashim M. Al-Hashimi. “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, no. 4 (April 2018): 229–44. https://doi.org/10.1007/s10858-018-0177-2.
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    • Gracia, Brant, Hashim M. Al-Hashimi, Namita Bisaria, Rhiju Das, Daniel Herschlag, and Rick Russell. “Hidden Structural Modules in a Cooperative RNA Folding Transition.” Cell Rep 22, no. 12 (March 20, 2018): 3240–50. https://doi.org/10.1016/j.celrep.2018.02.101.
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    • Kimsey, Isaac J., Eric S. Szymanski, Walter J. Zahurancik, Anisha Shakya, Yi Xue, Chia-Chieh Chu, Bharathwaj Sathyamoorthy, Zucai Suo, and Hashim M. Al-Hashimi. “Dynamic basis for dG•dT misincorporation via tautomerization and ionization.” Nature 554, no. 7691 (February 8, 2018): 195–201. https://doi.org/10.1038/nature25487.
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    • Salmon, Loïc, Frederick Stull, Sabrina Sayle, Claire Cato, Şerife Akgül, Linda Foit, Logan S. Ahlstrom, et al. “The Mechanism of HdeA Unfolding and Chaperone Activation.” J Mol Biol 430, no. 1 (January 5, 2018): 33–40. https://doi.org/10.1016/j.jmb.2017.11.002.
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    • Clay, Mary C., Laura R. Ganser, Dawn K. Merriman, and Hashim M. Al-Hashimi. “Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.” Nucleic Acids Res 45, no. 14 (August 21, 2017): e134. https://doi.org/10.1093/nar/gkx525.
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    • Stelling, Allison L., Yu Xu, Huiqing Zhou, Seung H. Choi, Mary C. Clay, Dawn K. Merriman, and Hashim M. Al-Hashimi. “Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA.” Febs Lett 591, no. 12 (June 2017): 1770–84. https://doi.org/10.1002/1873-3468.12681.
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    • Sathyamoorthy, Bharathwaj, Honglue Shi, Huiqing Zhou, Yi Xue, Atul Rangadurai, Dawn K. Merriman, and Hashim M. Al-Hashimi. “Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.” Nucleic Acids Res 45, no. 9 (May 19, 2017): 5586–5601. https://doi.org/10.1093/nar/gkx186.
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    • Vaidyanathan, Pavanapuresan P., Ishraq AlSadhan, Dawn K. Merriman, Hashim M. Al-Hashimi, and Daniel Herschlag. “Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions.” Rna 23, no. 5 (May 2017): 611–18. https://doi.org/10.1261/rna.060053.116.
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    • Patwardhan, Neeraj N., Laura R. Ganser, Gary J. Kapral, Christopher S. Eubanks, Janghyun Lee, Bharathwaj Sathyamoorthy, Hashim M. Al-Hashimi, and Amanda E. Hargrove. “Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR.” Medchemcomm 8, no. 5 (May 1, 2017): 1022–36. https://doi.org/10.1039/C6MD00729E.
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    • Szymanski, Eric S., Isaac J. Kimsey, and Hashim M. Al-Hashimi. “Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs.” J Am Chem Soc 139, no. 12 (March 29, 2017): 4326–29. https://doi.org/10.1021/jacs.7b01156.
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    • Ganser, Laura R., and Hashim M. Al-Hashimi. “HIV-1 leader RNA dimeric interface revealed by NMR.” Proc Natl Acad Sci U S A 113, no. 47 (November 22, 2016): 13263–65. https://doi.org/10.1073/pnas.1615789113.
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    • Shakya, Anisha, Hashim M. Al-Hashimi, and Mark M. Banaszak Holl. “Three RNA Microenvironments Detected in Fluxional Gene Delivery Polyplex Nanoassemblies.” Acs Macro Lett 5, no. 10 (October 18, 2016): 1104–8. https://doi.org/10.1021/acsmacrolett.6b00668.
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    • Gracia, Brant, Yi Xue, Namita Bisaria, Daniel Herschlag, Hashim M. Al-Hashimi, and Rick Russell. “RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.” J Mol Biol 428, no. 20 (October 9, 2016): 3972–85. https://doi.org/10.1016/j.jmb.2016.07.013.
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    • Zhou, Huiqing, Isaac J. Kimsey, Evgenia N. Nikolova, Bharathwaj Sathyamoorthy, Gianmarc Grazioli, James McSally, Tianyu Bai, et al. “m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.” Nat Struct Mol Biol 23, no. 9 (September 2016): 803–10. https://doi.org/10.1038/nsmb.3270.
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    • Merriman, Dawn K., Yi Xue, Shan Yang, Isaac J. Kimsey, Anisha Shakya, Mary Clay, and Hashim M. Al-Hashimi. “Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.” Biochemistry 55, no. 32 (August 16, 2016): 4445–56. https://doi.org/10.1021/acs.biochem.6b00285.
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    • Xue, Yi, Brant Gracia, Daniel Herschlag, Rick Russell, and Hashim M. Al-Hashimi. “Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.” Nat Commun 7 (June 13, 2016): ncomms11768. https://doi.org/10.1038/ncomms11768.
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    • Andrałojć, Witold, Enrico Ravera, Loïc Salmon, Giacomo Parigi, Hashim M. Al-Hashimi, and Claudio Luchinat. “Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.” Phys Chem Chem Phys 18, no. 8 (February 17, 2016): 5743–52. https://doi.org/10.1039/c5cp03993b.
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    • Shakya, Anisha, Casey A. Dougherty, Yi Xue, Hashim M. Al-Hashimi, and Mark M. Banaszak Holl. “Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release.” Biomacromolecules 17, no. 1 (January 11, 2016): 154–64. https://doi.org/10.1021/acs.biomac.5b01280.
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    • Mustoe, Anthony M., Hashim M. Al-Hashimi, and Charles L. Brooks. “Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.” Nucleic Acids Res 44, no. 1 (January 8, 2016): 402–12. https://doi.org/10.1093/nar/gkv1055.
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    • Ren, Aiming, Yi Xue, Alla Peselis, Alexander Serganov, Hashim M. Al-Hashimi, and Dinshaw J. Patel. “Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.” Cell Rep 13, no. 9 (December 1, 2015): 1800–1813. https://doi.org/10.1016/j.celrep.2015.10.062.
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    • Swanson, Michael D., Daniel M. Boudreaux, Loïc Salmon, Jeetender Chugh, Harry C. Winter, Jennifer L. Meagher, Sabine André, et al. “Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity.” Cell 163, no. 3 (October 22, 2015): 746–58. https://doi.org/10.1016/j.cell.2015.09.056.
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    • Salmon, Loïc, George M. Giambaşu, Evgenia N. Nikolova, Katja Petzold, Akash Bhattacharya, David A. Case, and Hashim M. Al-Hashimi. “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, no. 40 (October 14, 2015): 12954–65. https://doi.org/10.1021/jacs.5b07229.
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    • Yang, Shan, and Hashim M. Al-Hashimi. “Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.” J Phys Chem B 119, no. 30 (July 30, 2015): 9614–26. https://doi.org/10.1021/acs.jpcb.5b03859.
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    • Frank, Aaron T., Qi Zhang, Hashim M. Al-Hashimi, and Ioan Andricioaei. “Slowdown of Interhelical Motions Induces a Glass Transition in RNA.” Biophys J 108, no. 12 (June 16, 2015): 2876–85. https://doi.org/10.1016/j.bpj.2015.04.041.
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    • Zhou, Huiqing, Bradley J. Hintze, Isaac J. Kimsey, Bharathwaj Sathyamoorthy, Shan Yang, Jane S. Richardson, and Hashim M. Al-Hashimi. “New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.” Nucleic Acids Res 43, no. 7 (April 20, 2015): 3420–33. https://doi.org/10.1093/nar/gkv241.
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    • Kimsey, Isaac J., Katja Petzold, Bharathwaj Sathyamoorthy, Zachary W. Stein, and Hashim M. Al-Hashimi. “Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.” Nature 519, no. 7543 (March 19, 2015): 315–20. https://doi.org/10.1038/nature14227.
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    • Mustoe, Anthony M., Xin Liu, Paul J. Lin, Hashim M. Al-Hashimi, Carol A. Fierke, and Charles L. Brooks. “Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.” J Am Chem Soc 137, no. 10 (March 18, 2015): 3592–99. https://doi.org/10.1021/ja5130308.
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    • Mouzakis, Kathryn D., Elizabeth A. Dethoff, Marco Tonelli, Hashim Al-Hashimi, and Samuel E. Butcher. “Dynamic motions of the HIV-1 frameshift site RNA.” Biophys J 108, no. 3 (February 3, 2015): 644–54. https://doi.org/10.1016/j.bpj.2014.12.006.
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    • Allain, Frédéric H-T, and Hashim M. Al-Hashimi. “Editorial overview: Nucleic acids and their protein complexes: Progress in nucleic acid structural biology: new technologies and discoveries.” Curr Opin Struct Biol 30 (February 2015): vii–viii. https://doi.org/10.1016/j.sbi.2015.03.006.
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    • Xue, Yi, Dawn Kellogg, Isaac J. Kimsey, Bharathwaj Sathyamoorthy, Zachary W. Stein, Mitchell McBrairty, and Hashim M. Al-Hashimi. “Characterizing RNA Excited States Using NMR Relaxation Dispersion.” Methods Enzymol 558 (2015): 39–73. https://doi.org/10.1016/bs.mie.2015.02.002.
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    • Nikolova, Evgenia N., Frederick Stull, and Hashim M. Al-Hashimi. “Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair.” Biochemistry 53, no. 46 (November 25, 2014): 7145–47. https://doi.org/10.1021/bi5011909.
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    • Sathyamoorthy, Bharathwaj, Janghyun Lee, Isaac Kimsey, Laura R. Ganser, and Hashim Al-Hashimi. “Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids.” J Biomol Nmr 60, no. 2–3 (November 2014): 77–83. https://doi.org/10.1007/s10858-014-9856-9.
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    • Ravera, Enrico, Loïc Salmon, Marco Fragai, Giacomo Parigi, Hashim Al-Hashimi, and Claudio Luchinat. “Insights into domain-domain motions in proteins and RNA from solution NMR.” Acc Chem Res 47, no. 10 (October 21, 2014): 3118–26. https://doi.org/10.1021/ar5002318.
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    • Mustoe, Anthony M., Charles L. Brooks, and Hashim M. Al-Hashimi. “Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.” Nucleic Acids Res 42, no. 18 (October 2014): 11792–804. https://doi.org/10.1093/nar/gku807.
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    • Zeng, Xiancheng, Jeetender Chugh, Anette Casiano-Negroni, Hashim M. Al-Hashimi, and Charles L. Brooks. “Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.” J Mol Biol 426, no. 19 (September 23, 2014): 3201–13. https://doi.org/10.1016/j.jmb.2014.04.029.
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    • Alvey, Heidi S., Federico L. Gottardo, Evgenia N. Nikolova, and Hashim M. Al-Hashimi. “Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.” Nat Commun 5 (September 4, 2014): 4786. https://doi.org/10.1038/ncomms5786.
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    • Horowitz, Scott, Upendra Adhikari, Lynnette M. A. Dirk, Paul A. Del Rizzo, Ryan A. Mehl, Robert L. Houtz, Hashim M. Al-Hashimi, Steve Scheiner, and Raymond C. Trievel. “Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis.” Acs Chem Biol 9, no. 8 (August 15, 2014): 1692–97. https://doi.org/10.1021/cb5001185.
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    • Ganser, Laura R., Anthony M. Mustoe, and Hashim M. Al-Hashimi. “An RNA tertiary switch by modifying how helices are tethered.” Genome Biol 15, no. 7 (July 30, 2014): 425. https://doi.org/10.1186/s13059-014-0425-z.
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    • Lee, Janghyun, Elizabeth A. Dethoff, and Hashim M. Al-Hashimi. “Invisible RNA state dynamically couples distant motifs.” Proc Natl Acad Sci U S A 111, no. 26 (July 1, 2014): 9485–90. https://doi.org/10.1073/pnas.1407969111.
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    • Bothe, Jameson R., Zachary W. Stein, and Hashim M. Al-Hashimi. “Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange.” J Magn Reson 244 (July 2014): 18–29. https://doi.org/10.1016/j.jmr.2014.04.010.
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    • Eichhorn, Catherine D., and Hashim M. Al-Hashimi. “Structural dynamics of a single-stranded RNA-helix junction using NMR.” Rna 20, no. 6 (June 2014): 782–91. https://doi.org/10.1261/rna.043711.113.
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    • Yang, Shan, Loïc Salmon, and Hashim M. Al-Hashimi. “Measuring similarity between dynamic ensembles of biomolecules.” Nat Methods 11, no. 5 (May 2014): 552–54. https://doi.org/10.1038/nmeth.2921.
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    • Mustoe, Anthony M., Hashim M. Al-Hashimi, and Charles L. Brooks. “Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.” J Phys Chem B 118, no. 10 (March 13, 2014): 2615–27. https://doi.org/10.1021/jp411478x.
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    • Kimsey, Isaac, and Hashim M. Al-Hashimi. “Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids.” Curr Opin Struct Biol 24 (February 2014): 72–80. https://doi.org/10.1016/j.sbi.2013.12.003.
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    • Mustoe, Anthony M., Charles L. Brooks, and Hashim M. Al-Hashimi. “Hierarchy of RNA functional dynamics.” Annu Rev Biochem 83 (2014): 441–66. https://doi.org/10.1146/annurev-biochem-060713-035524.
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    • Salmon, Loïc, Shan Yang, and Hashim M. Al-Hashimi. “Advances in the determination of nucleic acid conformational ensembles.” Annu Rev Phys Chem 65 (2014): 293–316. https://doi.org/10.1146/annurev-physchem-040412-110059.
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    • Al-Hashimi, Hashim M. “NMR studies of nucleic acid dynamics.” J Magn Reson 237 (December 2013): 191–204. https://doi.org/10.1016/j.jmr.2013.08.014.
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    • Nikolova, Evgenia N., Huiqing Zhou, Federico L. Gottardo, Heidi S. Alvey, Isaac J. Kimsey, and Hashim M. Al-Hashimi. “A historical account of Hoogsteen base-pairs in duplex DNA.” Biopolymers 99, no. 12 (December 2013): 955–68. https://doi.org/10.1002/bip.22334.
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    • Suddala, Krishna C., Arlie J. Rinaldi, Jun Feng, Anthony M. Mustoe, Catherine D. Eichhorn, Joseph A. Liberman, Joseph E. Wedekind, Hashim M. Al-Hashimi, Charles L. Brooks, and Nils G. Walter. “Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.” Nucleic Acids Res 41, no. 22 (December 2013): 10462–75. https://doi.org/10.1093/nar/gkt798.
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    • Horowitz, Scott, Lynnette M. A. Dirk, Joseph D. Yesselman, Jennifer S. Nimtz, Upendra Adhikari, Ryan A. Mehl, Steve Scheiner, Robert L. Houtz, Hashim M. Al-Hashimi, and Raymond C. Trievel. “Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.” J Am Chem Soc 135, no. 41 (October 16, 2013): 15536–48. https://doi.org/10.1021/ja407140k.
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    • Lee, Janghyun, Catherine E. Vogt, Mitchell McBrairty, and Hashim M. Al-Hashimi. “Influence of dimethylsulfoxide on RNA structure and ligand binding.” Anal Chem 85, no. 20 (October 15, 2013): 9692–98. https://doi.org/10.1021/ac402038t.
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    • Nikolova, Evgenia N., Garrett B. Goh, Charles L. Brooks, and Hashim M. Al-Hashimi. “Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.” J Am Chem Soc 135, no. 18 (May 8, 2013): 6766–69. https://doi.org/10.1021/ja400994e.
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    • Salmon, Loïc, Gavin Bascom, Ioan Andricioaei, and Hashim M. Al-Hashimi. “A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.” J Am Chem Soc 135, no. 14 (April 10, 2013): 5457–66. https://doi.org/10.1021/ja400920w.
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    • Frank, Aaron T., Scott Horowitz, Ioan Andricioaei, and Hashim M. Al-Hashimi. “Utility of 1H NMR chemical shifts in determining RNA structure and dynamics.” J Phys Chem B 117, no. 7 (February 21, 2013): 2045–52. https://doi.org/10.1021/jp310863c.
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    • Dethoff, Elizabeth A., Katja Petzold, Jeetender Chugh, Anette Casiano-Negroni, and Hashim M. Al-Hashimi. “Visualizing transient low-populated structures of RNA.” Nature 491, no. 7426 (November 29, 2012): 724–28. https://doi.org/10.1038/nature11498.
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    • Nikolova, Evgenia N., Gavin D. Bascom, Ioan Andricioaei, and Hashim M. Al-Hashimi. “Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.” Biochemistry 51, no. 43 (October 30, 2012): 8654–64. https://doi.org/10.1021/bi3009517.
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    • Prevette, Lisa E., Evgenia N. Nikolova, Hashim M. Al-Hashimi, and Mark M. Banaszak Holl. “Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release.” Mol Pharm 9, no. 9 (September 4, 2012): 2743–49. https://doi.org/10.1021/mp3002864.
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    • Bothe, Jameson R., Ky Lowenhaupt, and Hashim M. Al-Hashimi. “Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation.” Biochemistry 51, no. 34 (August 28, 2012): 6871–79. https://doi.org/10.1021/bi300785b.
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    • Nikolova, Evgenia N., Federico L. Gottardo, and Hashim M. Al-Hashimi. “Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution.” J Am Chem Soc 134, no. 8 (February 29, 2012): 3667–70. https://doi.org/10.1021/ja2117816.
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    • Dethoff, Elizabeth A., Jeetender Chugh, Anthony M. Mustoe, and Hashim M. Al-Hashimi. “Functional complexity and regulation through RNA dynamics.” Nature 482, no. 7385 (February 15, 2012): 322–30. https://doi.org/10.1038/nature10885.
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    • Eichhorn, Catherine D., Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks, and Hashim M. Al-Hashimi. “Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.” Nucleic Acids Res 40, no. 3 (February 2012): 1345–55. https://doi.org/10.1093/nar/gkr833.
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    • Mustoe, Anthony M., Maximillian H. Bailor, Robert M. Teixeira, Charles L. Brooks, and Hashim M. Al-Hashimi. “New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.” Nucleic Acids Res 40, no. 2 (January 2012): 892–904. https://doi.org/10.1093/nar/gkr751.
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    • Eichhorn, C. D., S. Yang, and H. M. Al-Hashimi. “Characterising RNA dynamics using NMR residual dipolar couplings.” Rsc Biomolecular Sciences, 2012, 184–215.
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    • Petzold, Katja, and Hashim M. Al-Hashimi. “RNA structure: Adding a second dimension.” Nat Chem 3, no. 12 (November 23, 2011): 913–15. https://doi.org/10.1038/nchem.1209.
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    • Bothe, Jameson R., Evgenia N. Nikolova, Catherine D. Eichhorn, Jeetender Chugh, Alexandar L. Hansen, and Hashim M. Al-Hashimi. “Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.” Nat Methods 8, no. 11 (October 28, 2011): 919–31. https://doi.org/10.1038/nmeth.1735.
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    • Bailor, Maximillian H., Anthony M. Mustoe, Charles L. Brooks, and Hashim M. Al-Hashimi. “3D maps of RNA interhelical junctions.” Nat Protoc 6, no. 10 (September 15, 2011): 1536–45. https://doi.org/10.1038/nprot.2011.385.
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    • Suzuki, Yuta, Benjamin C. Buer, Hashim M. Al-Hashimi, and E Neil G. Marsh. “Using fluorine nuclear magnetic resonance to probe changes in the structure and dynamics of membrane-active peptides interacting with lipid bilayers.” Biochemistry 50, no. 27 (July 12, 2011): 5979–87. https://doi.org/10.1021/bi200639c.
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    • Stelzer, Andrew C., Aaron T. Frank, Jeremy D. Kratz, Michael D. Swanson, Marta J. Gonzalez-Hernandez, Janghyun Lee, Ioan Andricioaei, David M. Markovitz, and Hashim M. Al-Hashimi. “Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble.” Nat Chem Biol 7, no. 8 (June 26, 2011): 553–59. https://doi.org/10.1038/nchembio.596.
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    • Bailor, Maximillian H., Anthony M. Mustoe, Charles L. Brooks, and Hashim M. Al-Hashimi. “Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.” Curr Opin Struct Biol 21, no. 3 (June 2011): 296–305. https://doi.org/10.1016/j.sbi.2011.03.009.
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    • Horowitz, Scott, Joseph D. Yesselman, Hashim M. Al-Hashimi, and Raymond C. Trievel. “Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9.” J Biol Chem 286, no. 21 (May 27, 2011): 18658–63. https://doi.org/10.1074/jbc.M111.232876.
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    • Nikolova, Evgenia N., Eunae Kim, Abigail A. Wise, Patrick J. O’Brien, Ioan Andricioaei, and Hashim M. Al-Hashimi. “Transient Hoogsteen base pairs in canonical duplex DNA.” Nature 470, no. 7335 (February 24, 2011): 498–502. https://doi.org/10.1038/nature09775.
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    • Bothe, Jameson R., Ky Lowenhaupt, and Hashim M. Al-Hashimi. “Sequence-specific B-DNA flexibility modulates Z-DNA formation.” J Am Chem Soc 133, no. 7 (February 23, 2011): 2016–18. https://doi.org/10.1021/ja1073068.
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    • Dethoff, Elizabeth A., and Hashim M. Al-Hashimi. “A rare example of lock-and-key RNA recognition.” J Mol Biol 404, no. 4 (December 10, 2010): 553–54. https://doi.org/10.1016/j.jmb.2010.10.014.
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    • Al-Hashimi, Hashim M. “Biochemistry. Exciting structures.” Science 329, no. 5997 (September 10, 2010): 1295–96. https://doi.org/10.1126/science.1195571.
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    • Nikolova, Evgenia N., and Hashim M. Al-Hashimi. “Thermodynamics of RNA melting, one base pair at a time.” Rna 16, no. 9 (September 2010): 1687–91. https://doi.org/10.1261/rna.2235010.
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    • Stelzer, Andrew C., Jeremy D. Kratz, Qi Zhang, and Hashim M. Al-Hashimi. “RNA dynamics by design: biasing ensembles towards the ligand-bound state.” Angew Chem Int Ed Engl 49, no. 33 (August 2, 2010): 5731–33. https://doi.org/10.1002/anie.201000814.
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    • Buer, Benjamin C., Jeetender Chugh, Hashim M. Al-Hashimi, and E Neil G. Marsh. “Using fluorine nuclear magnetic resonance to probe the interaction of membrane-active peptides with the lipid bilayer.” Biochemistry 49, no. 27 (July 13, 2010): 5760–65. https://doi.org/10.1021/bi100605e.
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    • Koutmou, Kristin S., Anette Casiano-Negroni, Melissa M. Getz, Samuel Pazicni, Andrew J. Andrews, James E. Penner-Hahn, Hashim M. Al-Hashimi, and Carol A. Fierke. “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, no. 6 (February 9, 2010): 2479–84. https://doi.org/10.1073/pnas.0906319107.
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    • Musselman, Catherine, Qi Zhang, Hashim Al-Hashimi, and Ioan Andricioaei. “Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.” J Phys Chem B 114, no. 2 (January 21, 2010): 929–39. https://doi.org/10.1021/jp905286h.
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    • Bailor, Maximillian H., Xiaoyan Sun, and Hashim M. Al-Hashimi. “Topology links RNA secondary structure with global conformation, dynamics, and adaptation.” Science 327, no. 5962 (January 8, 2010): 202–6. https://doi.org/10.1126/science.1181085.
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    • Dethoff, Elizabeth A., Alexandar L. Hansen, Qi Zhang, and Hashim M. Al-Hashimi. “Variable helix elongation as a tool to modulate RNA alignment and motional couplings.” J Magn Reson 202, no. 1 (January 2010): 117–21. https://doi.org/10.1016/j.jmr.2009.09.022.
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    • Stelzer, Andrew C., Richard W. Frazee, Chad Van Huis, Joanne Cleary, Anthony W. Opipari, Gary D. Glick, and Hashim M. Al-Hashimi. “NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F(1)F(0)-ATPase.” Biopolymers 93, no. 1 (January 2010): 85–92. https://doi.org/10.1002/bip.21306.
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    • Buer, Benjamin C., Roberto de la Salud-Bea, Hashim M. Al Hashimi, and E Neil G. Marsh. “Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects.” Biochemistry 48, no. 45 (November 17, 2009): 10810–17. https://doi.org/10.1021/bi901481k.
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    • Zhang, Qi, and Hashim M. Al-Hashimi. “Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.” Rna 15, no. 11 (November 2009): 1941–48. https://doi.org/10.1261/rna.1806909.
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    • Stelzer, Andrew C., Aaron T. Frank, Maximillian H. Bailor, Ioan Andricioaei, and Hashim M. Al-Hashimi. “Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.” Methods 49, no. 2 (October 2009): 167–73. https://doi.org/10.1016/j.ymeth.2009.08.006.
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    • Nikolova, Evgenia N., and Hashim M. Al-Hashimi. “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, no. 1–2 (September 2009): 9–16. https://doi.org/10.1007/s10858-009-9350-y.
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    • Al-Hashimi, Hashim M. “Structural biology: Aerial view of the HIV genome.” Nature 460, no. 7256 (August 6, 2009): 696–98. https://doi.org/10.1038/460696a.
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    • Frank, Aaron T., Andrew C. Stelzer, Hashim M. Al-Hashimi, and Ioan Andricioaei. “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, no. 11 (June 2009): 3670–79. https://doi.org/10.1093/nar/gkp156.
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    • Buhrlage, Sara J., Caleb A. Bates, Steven P. Rowe, Aaron R. Minter, Brian B. Brennan, Chinmay Y. Majmudar, David E. Wemmer, Hashim Al-Hashimi, and Anna K. Mapp. “Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors.” Acs Chem Biol 4, no. 5 (May 15, 2009): 335–44. https://doi.org/10.1021/cb900028j.
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    • Fisher, Charles K., and Hashim M. Al-Hashimi. “Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.” J Phys Chem B 113, no. 18 (May 7, 2009): 6173–76. https://doi.org/10.1021/jp900411z.
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    • Hansen, Alexandar L., Evgenia N. Nikolova, Anette Casiano-Negroni, and Hashim M. Al-Hashimi. “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, no. 11 (March 25, 2009): 3818–19. https://doi.org/10.1021/ja8091399.
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    • Fisher, Charles K., Qi Zhang, Andrew Stelzer, and Hashim M. Al-Hashimi. “Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR.” J Phys Chem B 112, no. 51 (December 25, 2008): 16815–22. https://doi.org/10.1021/jp806188j.
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    • Dethoff, Elizabeth A., Alexandar L. Hansen, Catherine Musselman, Eric D. Watt, Ioan Andricioaei, and Hashim M. Al-Hashimi. “Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.” Biophys J 95, no. 8 (October 2008): 3906–15. https://doi.org/10.1529/biophysj.108.140285.
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    • Al-Hashimi, Hashim M., and Nils G. Walter. “RNA dynamics: it is about time.” Curr Opin Struct Biol 18, no. 3 (June 2008): 321–29. https://doi.org/10.1016/j.sbi.2008.04.004.
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    • Zhang, Qi, and Hashim M. Al-Hashimi. “Extending the NMR spatial resolution limit for RNA by motional couplings.” Nat Methods 5, no. 3 (March 2008): 243–45. https://doi.org/10.1038/nmeth.1180.
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    • Hansen, Alexandar L., and Hashim M. Al-Hashimi. “Dynamics of large elongated RNA by NMR carbon relaxation.” J Am Chem Soc 129, no. 51 (December 26, 2007): 16072–82. https://doi.org/10.1021/ja0757982.
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    • Zhang, Qi, Andrew C. Stelzer, Charles K. Fisher, and Hashim M. Al-Hashimi. “Visualizing spatially correlated dynamics that directs RNA conformational transitions.” Nature 450, no. 7173 (December 20, 2007): 1263–67. https://doi.org/10.1038/nature06389.
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    • Al-Hashimi, Hashim M. “Beyond static structures of RNA by NMR: folding, refolding, and dynamics at atomic resolution.” Biopolymers 86, no. 5–6 (August 5, 2007): 345–47. https://doi.org/10.1002/bip.20754.
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    • Getz, Melissa, Xiaoyan Sun, Anette Casiano-Negroni, Qi Zhang, and Hashim M. Al-Hashimi. “NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.” Biopolymers 86, no. 5–6 (August 5, 2007): 384–402. https://doi.org/10.1002/bip.20765.
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    • Musselman, Catherine, Hashim M. Al-Hashimi, and Ioan Andricioaei. “iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.” Biophys J 93, no. 2 (July 15, 2007): 411–22. https://doi.org/10.1529/biophysj.107.104620.
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    • Casiano-Negroni, Anette, Xiaoyan Sun, and Hashim M. Al-Hashimi. “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, no. 22 (June 5, 2007): 6525–35. https://doi.org/10.1021/bi700335n.
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    • Getz, Melissa M., Andy J. Andrews, Carol A. Fierke, and Hashim M. Al-Hashimi. “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, no. 2 (February 2007): 251–66. https://doi.org/10.1261/rna.264207.
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    • Bailor, Maximillian H., Catherine Musselman, Alexandar L. Hansen, Kush Gulati, Dinshaw J. Patel, and Hashim M. Al-Hashimi. “Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.” Nat Protoc 2, no. 6 (2007): 1536–46. https://doi.org/10.1038/nprot.2007.221.
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    • Sun, Xiaoyan, Qi Zhang, and Hashim M. Al-Hashimi. “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, no. 5 (2007): 1698–1713. https://doi.org/10.1093/nar/gkm020.
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    • Musselman, Catherine, Stephen W. Pitt, Kush Gulati, Lesley L. Foster, Ioan Andricioaei, and Hashim M. Al-Hashimi. “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, no. 4 (December 2006): 235–49. https://doi.org/10.1007/s10858-006-9087-9.
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    • Hansen, Alexandar L., and Hashim M. Al-Hashimi. “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, no. 2 (April 2006): 299–307. https://doi.org/10.1016/j.jmr.2005.12.012.
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    • Zhang, Qi, Xiaoyan Sun, Eric D. Watt, and Hashim M. Al-Hashimi. “Resolving the motional modes that code for RNA adaptation.” Science 311, no. 5761 (February 3, 2006): 653–56. https://doi.org/10.1126/science.1119488.
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    • Lee, Hyang-Yeol, Kyung-Hoon Lee, Hashim M. Al-Hashimi, and E Neil G. Marsh. “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, no. 1 (January 11, 2006): 337–43. https://doi.org/10.1021/ja0563410.
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    • Al-Hashimi, Hashim M. “Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy.” Chembiochem 6, no. 9 (September 2005): 1506–19. https://doi.org/10.1002/cbic.200500002.
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    • Pitt, Stephen W., Qi Zhang, Dinshaw J. Patel, and Hashim M. Al-Hashimi. “Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility.” Angew Chem Int Ed Engl 44, no. 22 (May 30, 2005): 3412–15. https://doi.org/10.1002/anie.200500075.
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    • Pitt, Stephen W., Ananya Majumdar, Alexander Serganov, Dinshaw J. Patel, and Hashim M. Al-Hashimi. “Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization.” J Mol Biol 338, no. 1 (April 16, 2004): 7–16. https://doi.org/10.1016/j.jmb.2004.02.031.
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    • Zhang, Qi, Rachel Throolin, Stephen W. Pitt, Alexander Serganov, and Hashim M. Al-Hashimi. “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, no. 35 (September 3, 2003): 10530–31. https://doi.org/10.1021/ja0363056.
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    • Al-Hashimi, Hashim M., Stephen W. Pitt, Ananya Majumdar, Weijun Xu, and Dinshaw J. Patel. “Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings.” J Mol Biol 329, no. 5 (June 20, 2003): 867–73. https://doi.org/10.1016/s0022-2836(03)00517-5.
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    • TOLMAN, J. R., and H. M. AL-HASHIMI. “NMR Studies of Biomolecular Dynamics and Structural Plasticity Using Residual Dipolar Couplings.” Annual Reports on Nmr Spectroscopy 51 (2003): 105–66. https://doi.org/10.1016/S0066-4103(03)51003-1.
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    • Al-Hashimi, Hashim M., Andrey Gorin, Ananya Majumdar, Yuying Gosser, and Dinshaw J. Patel. “Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings.” J Mol Biol 318, no. 3 (May 3, 2002): 637–49. https://doi.org/10.1016/S0022-2836(02)00160-2.
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    • Al-Hashimi, Hashim M., Yuying Gosser, Andrey Gorin, Weidong Hu, Ananya Majumdar, and Dinshaw J. Patel. “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, no. 2 (January 11, 2002): 95–102. https://doi.org/10.1006/jmbi.2001.5235.
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    • Heffelfinger, Grant S., Anthony Martino, Andrey Gorin, Ying Xu, Mark D. Rintoul, Al Geist, Hashim M. Al-Hashimi, et al. “Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.” Omics 6, no. 4 (2002): 305–30. https://doi.org/10.1089/153623102321112746.
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    • Al-Hashimi, Hashim M., and Dinshaw J. Patel. “Residual dipolar couplings: synergy between NMR and structural genomics.” J Biomol Nmr 22, no. 1 (January 2002): 1–8. https://doi.org/10.1023/a:1013801714041.
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    • Al-Hashimi, H. M., J. R. Tolman, A. Majumdar, A. Gorin, and D. J. Patel. “Determining stoichiometry in homomultimeric nucleic acid complexes using magnetic field induced residual dipolar couplings.” J Am Chem Soc 123, no. 24 (June 20, 2001): 5806–7. https://doi.org/10.1021/ja0105865.
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    • Al-Hashimi, H. M., A. Gorin, A. Majumdar, and D. J. Patel. “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, no. 13 (April 4, 2001): 3179–80. https://doi.org/10.1021/ja004133w.
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    • Tolman, J. R., H. M. Al-Hashimi, L. E. Kay, and J. H. Prestegard. “Structural and dynamic analysis of residual dipolar coupling data for proteins.” J Am Chem Soc 123, no. 7 (February 21, 2001): 1416–24. https://doi.org/10.1021/ja002500y.
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    • Al-Hashimi, H. M., A. Majumdar, A. Gorin, A. Kettani, E. Skripkin, and D. J. Patel. “Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.” J Am Chem Soc 123, no. 4 (January 31, 2001): 633–40. https://doi.org/10.1021/ja003379y.
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    • Tian, F., H. M. Al-Hashimi, J. L. Craighead, and J. H. Prestegard. “Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.” J Am Chem Soc 123, no. 3 (January 24, 2001): 485–92. https://doi.org/10.1021/ja002900l.
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    • Fowler, C. A., F. Tian, H. M. Al-Hashimi, and J. H. Prestegard. “Rapid determination of protein folds using residual dipolar couplings.” J Mol Biol 304, no. 3 (December 1, 2000): 447–60. https://doi.org/10.1006/jmbi.2000.4199.
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    • Prestegard, J. H., H. M. al-Hashimi, and J. R. Tolman. “NMR structures of biomolecules using field oriented media and residual dipolar couplings.” Q Rev Biophys 33, no. 4 (November 2000): 371–424. https://doi.org/10.1017/s0033583500003656.
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    • Al-Hashimi, H. M., H. Valafar, M. Terrell, E. R. Zartler, M. K. Eidsness, and J. H. Prestegard. “Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.” J Magn Reson 143, no. 2 (April 2000): 402–6. https://doi.org/10.1006/jmre.2000.2049.
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    • Al-Hashimi, H. M., P. J. Bolon, and J. H. Prestegard. “Molecular symmetry as an aid to geometry determination in ligand protein complexes.” J Magn Reson 142, no. 1 (January 2000): 153–58. https://doi.org/10.1006/jmre.1999.1937.
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    • Bolon, P. J., H. M. Al-Hashimi, and J. H. Prestegard. “Residual dipolar coupling derived orientational constraints on ligand geometry in a 53 kDa protein-ligand complex.” J Mol Biol 293, no. 1 (October 15, 1999): 107–15. https://doi.org/10.1006/jmbi.1999.3133.
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  • Conference Papers

    • Goh, Garrett B., Evgenia N. Nikolova, Hashim Al-Hashimi, and Charles L. Brooks. “Elucidating transient protonated GC(+) Hoogstein base pairs in canonical DNA duplexes.” In Abstracts of Papers of the American Chemical Society, Vol. 245, 2013.
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• Teaching & Mentoring
• 

  Recent Courses

  • BIOCHEM 393: Research Independent Study 2022
  • BIOCHEM 593: Research Independent Study 2022
  • BIOCHEM 695: Understanding NMR Spectroscopy 2022
  • BIOCHEM 393: Research Independent Study 2021
  • BIOCHEM 593: Research Independent Study 2021
  • BIOCHEM 700: Graduate Training Internship 2021
  • PHARM 493: Research Independent Study 2021

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