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

FEBS Letters
Allison L StellingHashim M Al-Hashimi

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.

References

Nov 1, 1976·Biochimica Et Biophysica Acta·T O'ConnorW M Scovell
Dec 1, 1992·Journal of Biomolecular Structure & Dynamics·A AkhebatE Taillandier
Jan 1, 1990·The International Journal of Biochemistry·M GhomiE Taillandier
May 1, 1989·Quarterly Reviews of Biophysics·X L Gao, D J Patel
May 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·D E GilbertJ Feigon
Jun 1, 1987·Journal of Biomolecular Structure & Dynamics·P B Keller, K A Hartman
Dec 1, 1986·Journal of Biomolecular Structure & Dynamics·A H WangA Rich
Jun 1, 1988·Journal of Biomolecular Structure & Dynamics·P B KellerK A Hartman
Sep 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·U C SinghP A Kollman
Jul 25, 1984·Nucleic Acids Research·J M BenevidesG J Thomas
Sep 14, 1984·Science·A H WangA Rich
Jul 29, 1980·Biochimica Et Biophysica Acta·J L Strobel, W M Scovell
Nov 14, 1995·Biochemistry·C DagneauxE Taillandier
Aug 14, 1995·FEBS Letters·H A Tajmir-RiahiM Naoui
Apr 28, 1995·Journal of Molecular Biology·T MiuraG J Thomas
Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Jan 1, 1996·Chemistry & Biology·C EscudéC Hélène
Mar 7, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nicola G A AbresciaJuan A Subirana
Sep 18, 2002·Nucleic Acids Research·Christoph KrafftGeorge J Thomas
Dec 6, 2002·Nucleic Acids Research·Jun AishimaCynthia Wolberger
Jul 25, 2003·Biophysical Chemistry·Martina BanyayAstrid Gräslund

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Citations

Oct 31, 2019·Nucleic Acids Research·Jocelyne VreedeDavid W H Swenson
Oct 5, 2018·Nucleic Acids Research·Atul RangaduraiHashim M Al-Hashimi
Mar 3, 2020·The Journal of Chemical Physics·Yaoyukun Jiang, Lu Wang
Apr 18, 2018·Nature Communications·Yu XuHashim M Al-Hashimi
Jul 9, 2021·The Journal of Physical Chemistry. B·Robert J FickAllison L Stelling
Dec 25, 2019·The Journal of Physical Chemistry. B·Brennan AshwoodAndrei Tokmakoff

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