NDLI: Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets

Content Provider	PubMed Central
Author	Ma, Buyong Pan, Yongping Zheng, Jie Levine, Arnold J. Nussinov, Ruth
Copyright Year	2007
Abstract	The p53 tetramer recognizes specifically a 20-bp DNA element. Here, we examined symmetries encoded in p53 response elements (p53REs). We analyzed base inversion correlations within the half-site, as well as in the full-site palindrome. We found that p53REs are not only direct repeats of half-sites; rather, two p53 half-sites couple to form a higher order 20 bp palindrome. The palindrome couplings between the half-sites are stronger for the human than for the mouse genome. The full-site palindrome and half-site palindrome are controlled by insertions between the two half-sites. The most notable feature is that the full-site palindrome with coupling between quarter-sites one and four (H14 coupling) dominates the p53REs without insertions. The most frequently observed insertion in human p53REs of 3 bp enhances the half-site palindrome. The statistical frequencies of the coupling between the half-sites in the human genome correlate with grouped experimental p53 affinities with p53REs. Examination of known p53REs indicates the H14 couplings are stronger for positive regulation than for negatively regulated p53REs, with repressors having the lowest H14 couplings. We propose that the palindromic sequence couplings may encode such potential preferred multiple binding modes of the p53 tetramer to DNA.
Related Links	http://dx.doi.org/10.1093/nar/gkm192
Ending Page	3001
Page Count	16
Starting Page	2986
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	9
Volume Number	35
Language	English
Publisher	Oxford University Press
Publisher Date	2007-04-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets

Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements

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