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Honglue Shi - Publications

Affiliations: 
Duke University, Durham, NC 
Area:
NMR
Website:
https://www.researchgate.net/profile/Honglue_Shi
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27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Geng A, Ganser L, Roy R, Shi H, Pratihar S, Case DA, Al-Hashimi HM. An RNA excited conformational state at atomic resolution. Nature Communications. 14: 8432. PMID 38114465 DOI: 10.1038/s41467-023-43673-6  0.761
2023 Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. Journal of the American Chemical Society. 145: 22964-22978. PMID 37831584 DOI: 10.1021/jacs.3c04614  0.758
2023 Gu S, Szymanski ES, Rangadurai AK, Shi H, Liu B, Manghrani A, Al-Hashimi HM. Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs. Nature Chemical Biology. PMID 37095237 DOI: 10.1038/s41589-023-01306-5  0.734
2022 Conroy DW, Xu Y, Shi H, Gonzalez Salguero N, Purusottam RN, Shannon MD, Al-Hashimi HM, Jaroniec CP. Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 119: e2200681119. PMID 35857870 DOI: 10.1073/pnas.2200681119  0.681
2022 Rangadurai A, Shi H, Xu Y, Liu B, Abou Assi H, Boom JD, Zhou H, Kimsey IJ, Al-Hashimi HM. Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proceedings of the National Academy of Sciences of the United States of America. 119: e2112496119. PMID 35671421 DOI: 10.1073/pnas.2112496119  0.827
2021 Liu B, Rangadurai A, Shi H, Al-Hashimi HM. Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino H CEST. Magnetic Resonance (Gottingen, Germany). 2: 715-731. PMID 37905209 DOI: 10.5194/mr-2-715-2021  0.795
2021 Shi H, Kimsey IJ, Gu S, Liu HF, Pham U, Schumacher MA, Al-Hashimi HM. Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. Nucleic Acids Research. PMID 34792150 DOI: 10.1093/nar/gkab936  0.795
2021 Liu B, Shi H, Rangadurai A, Nussbaumer F, Chu CC, Erharter KA, Case DA, Kreutz C, Al-Hashimi HM. A quantitative model predicts how mA reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. Nature Communications. 12: 5201. PMID 34465779 DOI: 10.1038/s41467-021-25253-8  0.803
2021 Fick RJ, Liu AY, Nussbaumer F, Kreutz C, Rangadurai A, Xu Y, Sommer RD, Shi H, Scheiner S, Stelling AL. Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy. The Journal of Physical Chemistry. B. PMID 34236202 DOI: 10.1021/acs.jpcb.1c01351  0.74
2021 Liu B, Shi H, Al-Hashimi HM. Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. Current Opinion in Structural Biology. 70: 16-25. PMID 33836446 DOI: 10.1016/j.sbi.2021.02.007  0.634
2020 Shi H, Rangadurai A, Abou Assi H, Roy R, Case DA, Herschlag D, Yesselman JD, Al-Hashimi HM. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nature Communications. 11: 5531. PMID 33139729 DOI: 10.1038/s41467-020-19371-y  0.803
2020 Abou Assi H, Rangadurai AK, Shi H, Liu B, Clay MC, Erharter K, Kreutz C, Holley CL, Al-Hashimi HM. 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states. Nucleic Acids Research. PMID 33104789 DOI: 10.1093/nar/gkaa928  0.815
2020 Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. PMID 33087930 DOI: 10.1038/s41586-020-2843-2  0.78
2020 Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. Rna (New York, N.Y.). PMID 33028652 DOI: 10.1261/rna.076257.120  0.799
2020 Xu Y, Manghrani A, Liu B, Shi H, Pham U, Liu A, Al-Hashimi HM. Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage. The Journal of Biological Chemistry. PMID 32913127 DOI: 10.1074/Jbc.Ra120.014530  0.79
2020 Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R relaxation dispersion. Journal of Biomolecular Nmr. PMID 32789613 DOI: 10.1007/S10858-020-00337-7  0.795
2020 Rangadurai A, Shi H, Al-Hashimi HM. Extending the Sensitivity of CEST to Micro-to-Millisecond Dynamics in Nucleic Acids Using High Power Radio-Frequency Fields. Angewandte Chemie (International Ed. in English). PMID 32168407 DOI: 10.1002/Anie.202000493  0.768
2020 Rangadurai A, Shi H, Al-Hashimi HM. Extending the Sensitivity of CEST to Micro‐to‐Millisecond Dynamics in Nucleic Acids Using High Power Radio‐Frequency Fields Angewandte Chemie. DOI: 10.1002/Ange.202000493  0.753
2019 Shi H, Liu B, Nussbaumer F, Rangadurai A, Kreutz C, Al-Hashimi HM. NMR chemical exchange measurements reveal that N6-methyladenosine slows RNA annealing. Journal of the American Chemical Society. PMID 31826614 DOI: 10.1021/Jacs.9B10939  0.83
2019 Rangadurai A, Kremser J, Shi H, Kreutz C, Al-Hashimi HM. Direct evidence for (G)O6···H-N4(C) hydrogen bonding in transient G(syn)-C and G(syn)-mC Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R relaxation dispersion measurements. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 308: 106589. PMID 31539864 DOI: 10.1016/J.Jmr.2019.106589  0.802
2019 Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R relaxation dispersion. Progress in Nuclear Magnetic Resonance Spectroscopy. 112: 55-102. PMID 31481159 DOI: 10.1016/J.Pnmrs.2019.05.002  0.789
2019 Shi H, Liu B, Rangadurai A, Clay M, Kreutz C, Al-Hashimi H. Visualizing Base Opening in Nucleic Acid Duplexes Biophysical Journal. 116: 359a. DOI: 10.1016/J.Bpj.2018.11.1955  0.747
2019 Kaushik Rangadurai A, Szymanski ES, Shi H, Al-Hashimi HM. Watson-Crick Like Mismatches in Replication Fidelity Biophysical Journal. 116: 359a. DOI: 10.1016/J.Bpj.2018.11.1953  0.782
2018 Rangadurai A, Zhou H, Merriman DK, Meiser N, Liu B, Shi H, Szymanski ES, Al-Hashimi HM. Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? Nucleic Acids Research. PMID 30285154 DOI: 10.1093/Nar/Gky885  0.805
2018 Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM. Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. Rna (New York, N.Y.). PMID 30012568 DOI: 10.1261/Rna.066258.118  0.819
2018 Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. Journal of Biomolecular Nmr. PMID 29675775 DOI: 10.1007/S10858-018-0177-2  0.823
2017 Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM. 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. PMID 28369571 DOI: 10.1093/Nar/Gkx186  0.793
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