Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

RecA Mediated Homology Recognition Offers Lessons for Sequence Dependent Protein Recognition, Protein Folding, and Artificial Self-Assembly

In vivo, RecA mediated homology recognition must stringently reject non-homologous pairings, but it must also allow strand exchange to progress through non-homologous regions within homologous pairings. We propose a new model of homology recognition that explains how the statistical distribution of accidental matches in a bacterial genome could allow RecA mediated homology recognition to provide both of these seemingly contradictory features. RecA bound DNA is divided into triplets separated by large rises. Recent theory and experiment suggest that in vivo the vast majority of mismatched pairings can be very rapidly rejected without forming a metastable strand exchange intermediate.We propose that this rapid initial rejection occurs in transition states in which no complete base pair triplets occupy the post-strand exchange RecA-heteroduplex. Simulations suggest that in these transition states the base pairing in the strand exchange product is much more unstable than B-form pairing. In contrast, both theory and experiment indicate that when complete triplets occupy the heteroduplex, the base pairing is more stable and homology insensitive than pairing in B-form dsDNA. . Despite the stability and homology insensitivity of the heteroduplex, experiments show that even rare mismatches can be rejected as a result of the sparsity of accidentally matched triplets in a bacterial genome.


Figure 1: Experiments FRET to study the homology sensitivity of strand exchange (a,b), dsDNA binding to site I (c,d), and free ssDNA annealing (e,f) . We compare results for a homolog (blue), a heterolog(black), and a near match (magenta). Also shown are >10 ns MD simulations of the time evolution of matched (g) and mismatched (h) sequences in the heteroduplex.

This research has been supported by NSF Research Fellowship Grant No. DGE-1144152; IDEX DYNAMO Grant ANR-11-LABX-0011-01. The work used the computer resources of Stampede at the Texas Advanced Computing Center (TACC) under an XSEDE startup allocation (TG-MCB130076).

Claudia Danilowicz, Darren Yang, Craig Kelley,, Chantal Prévost, Mara Prentiss Accurate RecA-mediated homologous pairing is not dominated by the inherent stringency of pairing in the RecA-heteroduplex complex. to be submitted

Darren Yang1
Claudia Danilowicz2
Benjamin Boyer3
Chantal Prevost 3
Mara Prentiss2

1School of Engineering and Applied Sciences
Harvard University
Cambridge, USA
2Department of Physics
Harvard University
Cambridge, USA MA 02138,
Univ Paris Diderot
Sorbonne Paris Cite
Paris, France

Ph: (617) 495-2910 prentiss@fas.harvard.edu