Robust IR‐based detection of stable and fractionally populated G‐C+ and A‐T Hoogsteen base pairs in duplex DNA

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...

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Bibliographic Details
Published in:FEBS letters 2017-06, Vol.591 (12), p.1770-1784
Main Authors: Stelling, Allison L., Xu, Yu, Zhou, Huiqing, Choi, Seung H., Clay, Mary C., Merriman, Dawn K., Al‐Hashimi, Hashim M.
Format: Article
Language:English
Subjects:
Adenine - analogs & derivatives
Adenine - chemistry
Adenine - metabolism
Anti-Bacterial Agents - chemistry
Anti-Bacterial Agents - metabolism
Anti-Bacterial Agents - pharmacology
Base Pairing - drug effects
Binding Sites
Chromosomal Instability - drug effects
Circular Dichroism
DNA
DNA - chemistry
DNA - metabolism
Echinomycin - chemistry
Echinomycin - metabolism
Echinomycin - pharmacology
Feasibility Studies
Guanine - analogs & derivatives
Guanine - chemistry
Guanine - metabolism
Hoogsteen
Hydrogen Bonding - drug effects
Hydrogen-Ion Concentration
infrared
m1A
m1G
Models, Molecular
NMR
Nuclear Magnetic Resonance, Biomolecular
Nucleic Acid Conformation - drug effects
Spectrophotometry
Spectrophotometry, Infrared
Spectroscopy, Fourier Transform Infrared
Stereoisomerism
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Summary: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.
ISSN:0014-5793
1873-3468
DOI:10.1002/1873-3468.12681