Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.

Biochemistry
Shuangluo XiaWilliam H Konigsberg

Abstract

Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between ...Continue Reading

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Citations

Dec 12, 2012·Journal of the American Chemical Society·Shuangluo XiaWilliam H Konigsberg
Oct 17, 2012·Chemical Research in Toxicology·Michelle L HammAmelia M Weaver
Dec 3, 2013·Nature Structural & Molecular Biology·Matthew HoggErik Johansson
Jan 25, 2014·Protein Science : a Publication of the Protein Society·Shuangluo Xia, William H Konigsberg
Jun 4, 2016·Molecular Cell·Rais A Ganai, Erik Johansson
Apr 12, 2014·Biochemistry·Shuangluo Xia, William H Konigsberg
Apr 14, 2020·Nucleic Acids Research·Myong-Chul KoagSeongmin Lee

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