8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme

8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme Full article

Journal

PLoS ONE
ISSN: 1932-6203

Output data

Year: 2016, Volume: 11, Number: 10, Article number : e0164424, Pages count : 15 DOI: 10.1371/journal.pone.0164424

Authors

Hoppins Joanna J. ¹ , Gruber David R. ¹ , Miears Heather L ¹ , Kiryutin Alexey S. ^2,3 , Kasymov Rustem D. ^4,5 , Petrova Darya V. ^3,4 , Endutkin Anton V. ^3,4 , Popov Alexander V. ⁴ , Yurkovskaya Alexandra V. ^2,3 , Fedechkin Stanislav O. ^1,6 , Brockerman Jacob A. ^1,7 , Zharkov Dmitry O. ^3,4 , Smirnov Serge L. ¹

Affiliations

1	Chemistry Department, Western Washington University, Bellingham, WA, United States of America
2	SB RAS International Tomography Center, Novosibirsk, Russia
3	Novosibirsk State University, Novosibirsk, Russia
4	SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
5	Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
6	University of California Santa Cruz, Program in Biomedical Science and Engineering, Santa Cruz, CA, United States of America
7	Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada

8-oxoguanine is one of the most abundant and impactful oxidative DNA lesions. However, the reasons underlying its effects, especially those not directly explained by the altered base pairing ability, are poorly understood. We report the effect of the lesion on the action of <italic>Eco</italic>RI, a widely used restriction endonuclease. Introduction of 8-oxoguanine inside, or adjacent to, the GAATTC recognition site embedded within the Drew—Dickerson dodecamer sequence notably reduced the <italic>Eco</italic>RI activity. Solution NMR revealed that 8-oxoguanine in the DNA duplex causes substantial alterations in the sugar—phosphate backbone conformation, inducing a BI→BII transition. Moreover, molecular dynamics of the complex suggested that 8-oxoguanine, although does not disrupt the sequence-specific contacts formed by the enzyme with DNA, shifts the distribution of BI/BII backbone conformers. Based on our data, we propose that the disruption of enzymatic cleavage can be linked with the altered backbone conformation and dynamics in the free oxidized DNA substrate and, possibly, at the protein—DNA interface.

Hoppins J.J. , Gruber D.R. , Miears H.L. , Kiryutin A.S. , Kasymov R.D. , Petrova D.V. , Endutkin A.V. , Popov A.V. , Yurkovskaya A.V. , Fedechkin S.O. , Brockerman J.A. , Zharkov D.O. , Smirnov S.L.
8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme
PLoS ONE. 2016. V.11. N10. e0164424 :1-15. DOI: 10.1371/journal.pone.0164424

Submitted:	Aug 5, 2016
Accepted:	Sep 23, 2016
Published online:	Oct 17, 2016

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