期刊
NUCLEIC ACIDS RESEARCH
卷 41, 期 13, 页码 6750-6760出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt357
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资金
- National Institutes of Health (NIH) [GM038509]
- Italian Institute of Technology
- Alfred P. Sloan Research Fellowship
- Department of Energy [E-FC02-02ER63421, DE-AC02-06CH11357]
- National Center for Research Resources [5P41RR015301-10]
- National Institutes of General Medical Sciences [8 P41 GM103403-10]
The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes.
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