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Identification and analysis of a template‐primer (ds‐DNA) binding cleft in E. coli DNA polymerase I: An electrostatic potential contour pattern of the modeled structure
Author(s) -
Yadav Prem N. S.,
Modek Mukund J.,
Yadav Janardan S.
Publication year - 1994
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.300070308
Subject(s) - klenow fragment , dna polymerase , dna , primer (cosmetics) , base pair , dna polymerase i , polymerase , chemistry , duplex (building) , polymerase chain reaction , biophysics , microbiology and biotechnology , crystallography , biology , biochemistry , reverse transcriptase , gene , exonuclease , organic chemistry
In the modeled structure of the Klenow fragment of E. coli DNA polymerase I, we have identified a distinct region that exhibits a strong electropositive potential contour. The examination of the distribution of the electropositive and negative potential across the two‐dimensional slices of the modeled structure revealed that the positive potential was concentrated around the cleft. The approximate size and shape of the region appears well suited to accommodate eight base pairs of duplex DNA and is consistent with the position of the dsDNA binding cleft reported in the crystal structure [Beese et al., Science (1993) 260, 352–355].