A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA

被引：78

作者：

Bishop, Eric P. ^{[1
]}

Rohs, Remo ^{[3
]}

Parker, Stephen C. J. ^{[4
]}

West, Sean M. ^{[5
,6
]}

Liu, Peng ^{[5
,6
]}

Mann, Richard S. ^{[6
]}

Honig, Barry ^{[5
,6
,7
]}

Tullius, Thomas D. ^{[1
,2
]}

机构：

[1] Boston Univ, Program Bioinformat, Boston, MA 02215 USA

[2] Boston Univ, Dept Chem, Boston, MA 02215 USA

[3] Univ So Calif, Mol & Computat Biol Program, Dept Biol Sci, Los Angeles, CA 90089 USA

[4] NHGRI, NIH, Rockville, MD 20852 USA

[5] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA

[6] Columbia Univ, Dept Biochem & Mol Biophys, New York, NY 10032 USA

[7] Columbia Univ, Howard Hughes Med Inst, New York, NY 10032 USA

来源：

ACS CHEMICAL BIOLOGY | 2011年 / 6卷 / 12期

基金：

美国国家卫生研究院;

关键词：

G-C-G; B-DNA; MONOVALENT CATIONS; NUCLEOSOME ORGANIZATION; BINDING-SITES; DODECAMER; GENOME; RECOGNITION; RESOLUTION; CONSTRUCTION;

D O I：

10.1021/cb200155t

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

DNA shape variation and the associated variation in minor groove electrostatic, potential are widely exploited by proteins for DNA recognition. Here we show that the hydroxyl radical cleavage pattern is a quantitative measure of DNA backbone solvent accessibility, minor groove width, and minor groove electrostatic potential, at single nucleotide resolution. We introduce maps of DNA shape and electrostatic potential as tools for understanding how proteins recognize binding sites in a genome. These maps reveal periodic structural signals in yeast and Drosophila genomic DNA sequences that are associated with positioned nucleosomes.

引用

页码：1314 / 1320

页数：7

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