Stelling AL, Xu Y, Zhou H, Choi SH, Clay MC, Merriman DK, Al-Hashimi HM. Robust IR-based detection of stable and fractionally populated G-C
+ and A-T Hoogsteen base pairs in duplex DNA.
FEBS Lett 2017;
591:1770-1784. [PMID:
28524232 PMCID:
PMC5584567 DOI:
10.1002/1873-3468.12681]
[Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/28/2017] [Accepted: 05/06/2017] [Indexed: 11/11/2022]
Abstract
Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.
Collapse