title: Iterative homology checking and non-uniform stepping during RecA-mediated strand exchange.
abstract: Recombinase-mediated homologous recombination (HR) in which strands are exchanged between two similar or identical DNA molecules is essential for maintaining genome fidelity and generating genetic diversity. It is believed that HR comprises two distinct stages: an initial alignment with stringent homology checking followed by stepwise heteroduplex expansion. If and how homology checking takes place during heteroduplex expansion, however, remains unknown. In addition, the number of base pairs (bp) involved in each step is still under debate. By using single-molecule approaches to catch transient intermediates in RecA-mediated HR with different degrees of homology, we show that (i) the expansion proceeds with step sizes of multiples of 3 bp, (ii) the step sizes follow wide distributions that are similar to that of initial alignment lengths, and (iii) each distribution can be divided into a short-scale and a long-scale part irrespective of the degree of homology. Our results suggest an iterative mechanism of strand exchange in which ssDNA-RecA filament interrogates double-stranded DNA using a short tract (6-15 bp) for quick checking and a long tract (>18 bp) for stringent sequence comparison. The present work provides novel insights into the physical and structural bases of DNA recombination.
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
authors.forename: Yu-Wei
authors.initials: YW
authors.lastname: Zhang
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
authors.forename: Da-Guan
authors.initials: DG
authors.lastname: Nong
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
authors.forename: Shuo-Xing
authors.initials: SX
authors.lastname: Dou
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China; Department of Physics, Emory University, Atlanta, GA, 30322, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yan
authors.affiliation: College of Life Sciences, Northwest A & F University, Xi'an, Shaanxi, 712100, China; LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, F-94235, Cachan, France.
authors.forename: Xu-Guang
authors.initials: XG
authors.lastname: Xi
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China. Electronic address: xch@iphy.ac.cn.
authors.forename: Chun-Hua
authors.initials: CH
authors.lastname: Xu
authors.affiliation: Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China. Electronic address: mingli@iphy.ac.cn.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
mesh_terms: D020137:Base Pair Mismatch; D031541:Fluorescence Resonance Energy Transfer; D059765:Homologous Recombination; D060328:Magnetic Phenomena; D009692:Nucleic Acid Heteroduplexes; D011938:Rec A Recombinases / Q000737:chemistry* / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D009692:Nucleic Acid Heteroduplexes; D011938:Rec A Recombinases
keywords: Heteroduplex expansion; Homologous recombination; Homology recognition; RecA; Single-molecule techniques