Abstract
We show that certain DNA sequences have the ability to influence the positioning of RecA monomers in RecA-DNA complexes. A tendency for RecA monomers to be phased was observed in RecA protein complexes with several oligonucleotides containing a recombinational hotspot sequence, the chi-site from Escherichia coli. This influence was observed in both the 5' to 3' and 3' to 5' directions with respect to chi. A 5'-end phosphate group and probably some other features in DNA also influence the phasing of RecA monomers. We conclude that natural DNAs contain a number of features that influence the positioning of RecA monomers. The ability of specific DNA sequences to influence the positioning of RecA monomers demonstrates some specificity in the binding of individual bases at different sites within a RecA monomer and, most likely, reflects the stereochemical non-equivalence of these sites. The possible biological implications of the phasing of RecA monomers in presynaptic DNA-protein cofilaments are discussed.
Highlights
RecA protein is the central component of homologous recombination in Escherichia coli
The oligonucleotides used for the formation of complexes with RecA protein contained a chi-site sequence at different locations and a DNA sequence located in the same position within the oligonucleotide
To apply the DNA chemical modification method, two shorter oligonucleotides complementary to different regions in the chi-site containing oligonucleotide were added after formation of RecA1⁄7ssoligonucleotide presynaptic complexes (Fig. 1B)
Summary
Vol 277, No 2, Issue of January 11, pp. 1614 –1618, 2002 Printed in U.S.A. Influence of DNA Sequence on the Positioning of RecA Monomers in RecA-DNA Cofilaments*. The chi-site is a recombination hot spot in E. coli [7] with the sequence -GCTGGTGG [8] that contains two 3-base repeats that conform with the RecA protein-DNA binding stoichiometry and might provide a physical basis for the ordered arrangement of RecA monomers in RecA protein complexes with chi-containing DNA. For these reasons the chi-site sequence has been chosen in the present study as an example of a DNA sequence that may influence the positioning of RecA monomers along a DNA strand.
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