M.HhaI binds tightly to substrates containing mismatches at the target base

Klimasauskas, S., Roberts, R. J. (1995) M.HhaI binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res, 23 (8). pp. 1388-95. ISSN 0305-1048 (Print)

URL: http://www.ncbi.nlm.nih.gov/pubmed/7753630
DOI: 10.1093/nar/23.8.1388

Abstract

The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped completely out of the DNA helix upon binding. We have investigated the effects of replacing the target cytosine by other, mismatched bases, including adenine, guanine, thymine and uracil. We find that M.HhaI binds more tightly to such mismatched substrates and can even transfer a methyl group to uracil if a G:U mismatch is present. Other mismatched substrates in which the orphan guanine is changed exhibit similar behavior. Overall, the affinity of DNA binding correlates inversely with the stability of the target base pair, while the nature of the target base appears irrelevant for complex formation. The presence of a cofactor analog. S-adenosyl-L-homocysteine, greatly enhances the selectivity of the methyltransferase for cytosine at the target site. We propose that the DNA methyltransferases have evolved from mismatch binding proteins and that base flipping was, and still is, a key element in many DNA-enzyme interactions.

Item Type: Paper
Uncontrolled Keywords: 5-Methylcytosine Base Sequence Cytosine/analogs & derivatives/metabolism DNA/ metabolism Dinucleoside Phosphates/metabolism Kinetics Methylation Molecular Sequence Data Nucleic Acid Heteroduplexes/ metabolism Research Support, U.S. Gov't, P.H.S. S-Adenosylhomocysteine/metabolism S-Adenosylmethionine/metabolism Site-Specific DNA Methyltransferase (Cytosine-Specific)/ metabolism Substrate Specificity Uracil/metabolism
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > design
CSHL Authors:
Communities: CSHL labs > Roberts lab
Depositing User: Jessica Koos
Date Deposited: 12 Aug 2014 14:58
Last Modified: 12 Aug 2014 14:58
PMCID: PMC306866
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30609

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