@article {2019|2064, title = {Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology}, journal = {J Biol Chem}, volume = {294}, year = {2019}, month = {May}, pages = {8606-8616}, abstract = {

DNA recombination resulting from RecA-mediated strand exchange aided by RecBCD proteins often enables accurate repair of DNA double-strand breaks. However, the process of recombinational repair between short DNA regions of accidental similarity can lead to fatal genomic rearrangements. Previous studies have probed how effectively RecA discriminates against interactions involving a short similar sequence that is embedded in otherwise dissimilar sequences but have not yielded fully conclusive results. Here, we present results of in vitro experiments with fluorescent probes strategically located on the interacting DNA fragments used for recombination. Our findings suggest that DNA synthesis increases the stability of the recombination products. Fluorescence measurements can also probe the homology dependence of the extension of invading DNA strands in D-loops formed by RecA-mediated strand exchange. We examined the slow extension of the invading strand in a D-loop by DNA polymerase (Pol) IV and the more rapid extension by DNA polymerase LF-Bsu We found that when DNA Pol IV extends the invading strand in a D-loop formed by RecA-mediated strand exchange, the extension afforded by 82 bp of homology is significantly longer than the extension on 50 bp of homology. In contrast, the extension of the invading strand in D-loops by DNA LF-Bsu Pol is similar for intermediates with \≥50 bp of homology. These results suggest that fatal genomic rearrangements due to the recombination of small regions of accidental homology may be reduced if RecA-mediated strand exchange is immediately followed by DNA synthesis by a slow polymerase.

}, keywords = {cooperativity, DNA damage, DNA polymerase, DNA recombination, double-strand break (DSB), fluorescence resonance energy transfer (FRET), heteroduplex formation, molecular dynamics, RecA, strand displacement synthesis}, doi = {10.1074/jbc.RA119.007554}, author = {Lu, Daniel and Danilowicz, Claudia and Tashjian, Tommy F and Chantal Pr{\'e}vost and Godoy, Veronica G and Prentiss, Mara} } @article {2016|1763, title = {Structure of ring-shaped Aβ42 oligomers determined by conformational selection}, journal = {Sci. Rep.}, volume = {6}, year = {2016}, pages = {21429}, abstract = {

The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a critical role in the pathogenesis of Alzheimer\&$\#$39;s disease. However, it has been challenging to characterize the tertiary and quaternary structures of Aβ peptides due to their disordered nature and high aggregation propensity. In this work, replica exchange molecular dynamics simulations were used to explore the conformational space of Aβ42 monomer. Among the most populated transient states, we identified a particular conformation which was able to generate ring-shaped pentamers and hexamers, when docked onto itself. The structures of these aggregates were stable during microsecond all-atom MD simulations in explicit solvent. In addition to high resolution models of these oligomers, this study provides support for the conformational selection mechanism of Aβ peptide self-assembly.

}, issn = {2045-2322}, doi = {10.1038/srep21429}, author = {Tran, Linh and Basdevant, Nathalie and Chantal Pr{\'e}vost and Ha-Duong, T{\^a}p} } @article {2015|1641, title = {Structure/function relationships in RecA protein-mediated homology recognition and strand exchange}, journal = {Crit. Rev. Biochem. Mol. Biol.}, volume = {50}, year = {2015}, pages = {453{\textendash}76}, abstract = {RecA family proteins include RecA, Rad51, and Dmc1. These recombinases are responsible for homology search and strand exchange. Homology search and strand exchange occur during double-strand break repair and in eukaryotes during meiotic recombination. In bacteria, homology search begins when RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site to form the presynaptic filament. The filament is a right-handed helix, where the initiating strand is bound deep within the filament. Once the presynaptic filament is formed, it interrogates nearby double-stranded DNA (dsDNA) to find a homologous sequence; therefore, we provide a detailed discussion of structural features of the presynaptic filament that play important functional roles. The discussion includes many diagrams showing multiple filament turns. These diagrams illustrate interactions that are not evident in single turn structures. The first dsDNA interactions with the presynaptic filament are insensitive to mismatches. The mismatch insensitive interactions lead to dsDNA deformation that triggers a homology testing process governed by kinetics. The first homology test involves {\^a}ˆ{\textonequarter}8 bases. Almost all interactions are rejected by this initial rapid test, leading to a new cycle of homology testing. Interactions that pass the initial rapid test proceed to a slower testing stage. That slower stage induces nonhomologous dsDNA to reverse strand exchange and begin a new cycle of homology testing. In contrast, homologous dsDNA continues to extend the heteroduplex strand-exchange product until ATP hydrolysis makes strand exchange irreversible.}, keywords = {Double-strand break repair, meiosis, meiotic recombination, Rad51, recombinase}, doi = {10.3109/10409238.2015.1092943}, author = {Prentiss, Mara and Chantal Pr{\'e}vost and Danilowicz, Claudia} } @article {2012|1527, title = {{S}tructure-function analysis of the {NFL}-{TBS}.40-63 peptide corresponding to the binding site of tubulin on the light neurofilament subunit}, journal = {Plos One}, volume = {7}, year = {2012}, pages = {e49436}, author = {Berges, R. and Balzeau, J. and Takahashi, M. and Chantal Pr{\'e}vost and Eyer, J.} } @inbook {2008|1651, title = {Searching for Homology by Filaments of RecA-like Proteins}, booktitle = {Genome Dynamics \& Stability}, volume = {Recombination and Meiosis. Models, Means and Evolution}, number = {3}, year = {2008}, pages = {65{\textendash}89}, publisher = {Springer Verlag}, organization = {Springer Verlag}, edition = {Richard Egel and Dirk-Henner Lankenau}, address = {Berlin Heidelberg}, abstract = {

The recombinase proteins of the RecA family perform tasks that are essential for cell survival and for the maintenance of genetic diversity. They are able to rearrange genes in new combinations and to repair DNA double-strand breaks in an almost error-free fashion. Their function in homologous recombination is performed in an original way that has no equivalent in the DNA processing machinery: They form long helical filaments on a target DNA, capable of recognizing homologous DNA sequences in the genome and of exchanging DNA strands. How the DNA sequences are recognized during this process and how the DNA strands are exchanged remain matters of investigation. This chapter reviews the information that has been accumulated on recognition and strand exchange, together with the models that aim at organizing this data, viewed at different levels: that of the nucleus, the molecule, or the atom. Altogether, a picture begins to emerge on a multiscale dimension, which presents the search for homology as a complex process with important dynamic components.

}, author = {Chantal Pr{\'e}vost}, editor = {Richard Egel and Dirk Henner-Lankenau} } @article {1995|1941, title = {Solution structure of oligonucleotides covalently linked to a psoralen derivative.}, journal = {Nucleic Acids Res.}, volume = {23}, number = {5}, year = {1995}, month = {mar}, pages = {788{\textendash}795}, abstract = {

Psoralen (pso) was attached via its C-5 position to the 5\&$\#$39;-phosphate group of an oligodeoxynucleotide d(TAAGCCG) by a hexamethylene linker (m6). Complex formation between pso-m6-d(TAAGCCG) and the complementary strands d(CGGCTTA)[7-7mer] or d(CGGCTTAT)[7-8mer] was investigated by nuclear magnetic resonance in aqueous solution. Structural informations derived from DQF-COSY and NOESY maps, revealed that the mini double helix adopts a B-form conformation and that the deoxyriboses preferentially adopt a C2\&$\#$39;-endo conformation. The nOe connectivities observed between the protons of the bases or the sugars in each duplex, and the protons of the psoralen and the hexamethylene chain, led us to propose a model involving an equilibrium between two conformations due to different locations of the psoralen. Upon UV-irradiation, the psoralen moiety cross-linked the two DNA strands at the level of 5\&$\#$39;TpA3\&$\#$39; sequences. NMR studies of the single major photo-cross-linked duplex pso-m6-d(TAAGCCG) and d(CGGCTTA) were performed. The stereochemistry of the diadduct is indeed cis-syn at both cyclobutane rings. In addition, the effects of this diadduct on the helical structure are analyzed in detail.

}, keywords = {Base Sequence, chemistry, chemistry/radiation effects, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Psoralens, Solutions}, author = {O. Bornet and Chantal Pr{\'e}vost and F. Vovelle and M. Chassignol and N. T. Thuong and G. Lancelot} } @inbook {1989|1579, title = {Stereospecific Ion-Molecule reactions in the collision cell induced by nucleophilic gas phase reagents on CI/NH4+ protonated diastereoisomeric tetracyclic terpenes.}, booktitle = {Advances in Mass Spectrometry}, volume = {11}, year = {1989}, pages = {1056}, edition = {P. Longevialle, Heyden and Son, Ed, New York}, author = {Cole, RB and Chantal Pr{\'e}vost and Tabet, JC} }