NO SLIDING DURING HOMOLOGY SEARCH BY RECA PROTEIN

The RecA protein of Escherichia coli is a prototype of the RecA/Rad51 family of proteins that exist in virtually all the organisms. In a pro cess called DNA synapsis, RecA first polymerizes onto a single-strande d DNA (ssDNA) molecule; the resulting RecA-ssDNA complex then searches for and binds to a double-stranded DNA (dsDNA) molecule containing th e almost identical, or ''homologous,'' sequence. The RecA-ssDNA comple x thus can be envisioned as a sequence-specific binding entity. How do es the complex search for its target buried within nonspecific sequenc es? One possible mechanism is the sliding mechanism, in which the comp lex first binds to a dsDNA molecule nonspecifically and then linearly diffuses, or slides, along the dsDNA To understand the mechanism of ho mology search by RecA, this sliding model was tested. A plasmid contai ning four homologous targets in tandem was constructed and used as the dsDNA substrate in the synapsis reaction. If the sliding is the predo minant search mode, the two outermost targets should act as more effic ient targets than the inner targets. No such positional preference was observed, indicating that a long range sliding of the RecA-ssDNA comp lex does not occur. These and other available data can be adequately e xplained by a simple three-dimensional random collision mechanism.