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Nucleotides sequestered at different subsite loci within DNA-binding pockets of two OB-fold single-stranded DNA-binding proteins are unstacked to different extents.
MedLine Citation:
PMID:  23616216     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
The gene 5 protein (g5p) encoded by the Ff strains of Escherichia coli bacteriophages is a dimeric single-stranded DNA-binding protein (SSB) that consists of two identical OB-fold (oligonucleotide/oligosaccharide-binding) motifs. Ultrafast time-resolved fluorescence measurements were carried out to investigate the effect of g5p binding on the conformation of 2-aminopurine (2AP) labels positioned between adenines or cytosines in the 16-nucleotide antiparallel tails of DNA hairpins. The measurements revealed significant changes in the conformational heterogeneity of the 2AP labels caused by g5p binding. The extent of the changes was dependent on sub-binding-site location, but generally resulted in base unstacking. When bound by g5p, the unstacked 2AP population increased from ∼22% to 59-67% in C-2AP-C segments and from 39% to 77% in an A-2AP-A segment. The OB-fold RPA70A domain of the human replication protein A also caused a significant amount of base unstacking at various locations within the DNA binding site as evidenced by steady-state fluorescence titration measurements using 2AP-labeled 5-mer DNAs. These solution studies support the concept that base unstacking at most of a protein's multiple sub-binding-site loci may be a feature that allows non-sequence specific OB-fold proteins to bind to single-stranded DNAs (ssDNAs) with minimal preference for particular sequences. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 484-496, 2013.
Authors:
Hieu N Nguyen; Liang Zhao; Carla W Gray; Donald M Gray; Tianbing Xia
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Biopolymers     Volume:  99     ISSN:  0006-3525     ISO Abbreviation:  Biopolymers     Publication Date:  2013 Jul 
Date Detail:
Created Date:  2013-04-25     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0372525     Medline TA:  Biopolymers     Country:  United States    
Other Details:
Languages:  eng     Pagination:  484-96     Citation Subset:  IM    
Copyright Information:
Copyright © 2013 Wiley Periodicals, Inc.
Affiliation:
Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX, 75080.
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