Origins of Sequence Selectivity in Homologous Genetic Recombination: Insights from Rapid Kinetic Probing of RecA-mediated DNA Strand Exchange

Lee, Andrew M.; Xiao, Jie; Singleton, Scott F.

doi:10.1016/j.jmb.2006.04.065

Cited by 21 publications

(14 citation statements)

References 51 publications

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“…In conclusion, multiple factors suggest that the total search time is probably optimized when 1 < n initial,BRW ⩽ 4, consistent with known experimental results for RecA [19,21,28]; however, more experimental and structural information would be required for meaningful optimization of the total search time if factors governing n initial,BRW are to be accurately included.…”

Section: Resultssupporting

confidence: 81%

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

2013

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Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.

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Section: Resultssupporting

confidence: 81%

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

2013

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“…It has been proposed by Radding and collaborators (53,54) as a result of studies on RecA or its human homolog Rad51, showing that A,T bases exchange their pairing as soon as they encounter. The kinetic studies of Singleton and collaborators (36,55) support the mixed scenario model.…”

Section: Discussionmentioning

confidence: 75%

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Saladin

Amourda

Poulain

et al. 2010

Nucleic Acids Research

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Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.

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“…ATP hydrolysis is not needed for either step, because the spontaneous breathing of the duplex appears to sample all of the required conformational space (Savir and Tlusty 2010). Rapid kinetics data support the idea that the RecA-ssDNA filament binds to a deformed conformation of the duplex in which the sequence may be sampled via the formation of Watson-Crick base pairs (Lee et al 2006). The propagation of heteroduplex formation occurs in three-base-pair increments (Ragunathan et al 2011), consistent with the organization of the ssDNA observed in the RecA-ssDNA-ADPAlF 4 crystal structure (Chen et al 2008).…”

Section: Dna Pairing and Annealingmentioning

confidence: 76%

“…Cite this article as Cold Spring Harb Perspect Biol 2015;7:a016444 the idea that the filament senses both WatsonCrick base pairing and DNA conformation in the recognition process, a mechanism referred to as "conformational proofreading" (Lee et al 2006;Takahashi et al 2007; see comments in Rambo et al 2010;Savir and Tlusty 2010;Ragunathan et al 2011). The atomic structure of the RecA-ssDNA filament, in its active, ATP-bound form, reveals that the ssDNA exists in a deformed conformation, with the sugar-phosphate backbone extended between trinucleotide units, which are held in a B-like conformation (Chen et al 2008; see comments by Kowalczykowski 2008).…”

Section: Dna Pairing and Annealingmentioning

confidence: 99%

DNA-Pairing and Annealing Processes in Homologous Recombination and Homology-Directed Repair

Morrical

2015

Cold Spring Harb Perspect Biol

112

127

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The formation of heteroduplex DNA is a central step in the exchange of DNA sequences via homologous recombination, and in the accurate repair of broken chromosomes via homology-directed repair pathways. In cells, heteroduplex DNA largely arises through the activities of recombination proteins that promote DNA-pairing and annealing reactions. Classes of proteins involved in pairing and annealing include RecA-family DNA-pairing proteins, single-stranded DNA (ssDNA)-binding proteins, recombination mediator proteins, annealing proteins, and nucleases. This review explores the properties of these pairing and annealing proteins, and highlights their roles in complex recombination processes including the double Holliday junction (DhJ) formation, synthesis-dependent strand annealing, and singlestrand annealing pathways-DNA transactions that are critical both for genome stability in individual organisms and for the evolution of species.

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Origins of Sequence Selectivity in Homologous Genetic Recombination: Insights from Rapid Kinetic Probing of RecA-mediated DNA Strand Exchange

Cited by 21 publications

References 51 publications

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

DNA-Pairing and Annealing Processes in Homologous Recombination and Homology-Directed Repair

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