New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey
Huiqing Zhou,Bradley J. Hintze,Isaac J. Kimsey,Bharathwaj Sathyamoorthy,Shan Yang,Jane S. Richardson,Hashim M. Al-Hashimi +6 more
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TLDR
The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5′-purine.Abstract:
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA.read more
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m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Huiqing Zhou,Isaac J. Kimsey,Evgenia N. Nikolova,Bharathwaj Sathyamoorthy,Gianmarc Grazioli,James McSally,Tianyu Bai,Christoph H. Wunderlich,Christoph Kreutz,Ioan Andricioaei,Hashim M. Al-Hashimi +10 more
TL;DR: It is shown that G-C+ and A-U Hoogsteen base pairs are strongly disfavored in A-RNA, providing a mechanism for disrupting RNA structure through post-transcriptional modifications.
Journal ArticleDOI
DNA mismatches reveal conformational penalties in protein-DNA recognition.
Ariel Afek,Honglue Shi,Atul Rangadurai,Harshit Sahay,Alon Senitzki,Suela Xhani,Mimi Fang,Mimi Fang,Raul E. Salinas,Zachery Mielko,Miles A. Pufall,Miles A. Pufall,Gregory M.K. Poon,Tali E. Haran,Maria A. Schumacher,Hashim M. Al-Hashimi,Raluca Gordân +16 more
TL;DR: Determination of high-resolution X-ray structures, combined with nuclear magnetic resonance measurements and structural analyses, showed that many of the DNA mismatches that increase binding induce distortions that are similar to those induced by protein binding—thus prepaying some of the energetic cost incurred from deforming the DNA.
Journal ArticleDOI
Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.
Bharathwaj Sathyamoorthy,Honglue Shi,Huiqing Zhou,Yi Xue,Atul Rangadurai,Dawn K. Merriman,Hashim M. Al-Hashimi +6 more
TL;DR: Atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes are provided as well as structural and dynamic signatures that could play roles in m1A recognition and repair are identified.
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How DNA polymerases catalyse replication and repair with contrasting fidelity
TL;DR: This Review highlights how large differences in the fidelity of DNA replication arise from subtle structural differences between individual DNA polymerases, which enable polymerases to perform diverse functions that are important to nature as well as technology.
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Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction
Honglue Shi,Atul Rangadurai,Hala Abou Assi,Rohit Roy,David A. Case,Daniel Herschlag,Joseph D. Yesselman,Hashim M. Al-Hashimi +7 more
TL;DR: This work dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformation library and provided an atomistic ensemble model for HIV-1 TAR.
References
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The Protein Data Bank
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Xiang-Jun Lu,Wilma K. Olson +1 more
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