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

England

2015-11-01T13:54:22Z

2015-04-20

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.

http://www.ncbi.nlm.nih.gov/pubmed/25813047

gkv241

1362-4962

https://hdl.handle.net/10161/10806

eng

Oxford University Press (OUP)

Nucleic Acids Res

10.1093/nar/gkv241

Base Pairing

Crystallography, X-Ray

DNA

Nucleic Acid Conformation

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

Journal article

Richardson, JS|0000-0002-3311-2944

http://www.ncbi.nlm.nih.gov/pubmed/25813047

3420

3433

7

Basic Science Departments

Biochemistry

Chemistry

Duke

School of Medicine

Trinity College of Arts & Sciences

Published

43