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Article ; Online: Modeling the Homologous Recombination Process: Methods, Successes and Challenges.

Sabei, Afra / Prentiss, Mara / Prévost, Chantal

International journal of molecular sciences

2023 Volume 24, Issue 19

Abstract: Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The ... ...

Abstract	Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information.
MeSH term(s)	Rec A Recombinases/metabolism ; Homologous Recombination ; DNA, Single-Stranded/genetics ; Nucleoproteins/genetics ; DNA Breaks, Double-Stranded
Chemical Substances	Rec A Recombinases (EC 2.7.7.-) ; DNA, Single-Stranded ; Nucleoproteins
Language	English
Publishing date	2023-10-04
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241914896
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Article ; Online: Finding the infectious dose for COVID-19 by applying an airborne-transmission model to superspreader events.

Prentiss, Mara / Chu, Arthur / Berggren, Karl K

PloS one

2022 Volume 17, Issue 6, Page(s) e0265816

Abstract: We probed the transmission of COVID-19 by applying an airborne transmission model to five well-documented case studies-a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. For all events the ...

Abstract	We probed the transmission of COVID-19 by applying an airborne transmission model to five well-documented case studies-a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. For all events the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. Applying the model to those events yields results that suggest the following: (1) transmission was airborne; (2) superspreading events do not require an index patient with an unusually high viral load; (3) the viral loads for all of the index patients were of the same order of magnitude and consistent with experimentally measured values for patients at the onset of symptoms, even though viral loads across the population vary by a factor of >108. In particular we used a Wells-Riley exposure model to calculate q, the total average number of infectious quanta inhaled by a person at the event. Given the q value for each event, the simple airborne transmission model was used to determined Sq, the rate at which the index patient exhaled infectious quanta and N0, the characteristic number of COVID-19 virions needed to induce infection. Despite the uncertainties in the values of some parameters of the superspreading events, all five events yielded (N0∼300-2,000 virions), which is similar to published values for influenza. Finally, this work describes the conditions under which similar methods can provide actionable information on the transmission of other viruses.
MeSH term(s)	COVID-19/epidemiology ; Exhalation ; Humans ; Influenza, Human ; Serologic Tests ; Viral Load
Language	English
Publishing date	2022-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0265816
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Article ; Online: Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination.

Prentiss, Mara / Wang, Dianzhuo / Fu, Jonathan / Prévost, Chantal / Godoy-Carter, Veronica / Kleckner, Nancy / Danilowicz, Claudia

PloS one

2023 Volume 18, Issue 7, Page(s) e0288611

Abstract: In E. coli, double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting that RecA should ... ...

Abstract	In E. coli, double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting that RecA should rapidly reject mismatched recombination products; however, this is not the case. Decades of work have shown that long lasting recombination products can include many mismatches. In this work, we show that in vitro RecA forms readily observable recombination products when 16% of the bases in the product are mismatched. We also consider various theoretical models of mismatch-tolerant homology testing. The models test homology by comparing the sequences of Ltest bases in two single-stranded DNAs (ssDNA) from the same genome. If the two sequences pass the homology test, the pairing between the two ssDNA becomes permanent. Stringency is the fraction of permanent pairings that join ssDNA from the same positions in the genome. We applied the models to both randomly generated genomes and bacterial genomes. For both randomly generated genomes and bacterial genomes, the models show that if no mismatches are accepted stringency is ∼ 99% when Ltest = 14 bp. For randomly generated genomes, stringency decreases with increasing mismatch tolerance, and stringency improves with increasing Ltest. In contrast, in bacterial genomes when Ltest ∼ 75 bp, stringency is ∼ 99% for both mismatch-intolerant and mismatch-tolerant homology testing. Furthermore, increasing Ltest does not improve stringency because most incorrect pairings join different copies of repeats. In sum, for bacterial genomes highly mismatch tolerant homology testing of 75 bp provides the same stringency as homology testing that rejects all mismatches and testing more than ∼75 base pairs is not useful. Interestingly, in vivo commitment to recombination typically requires homology testing of ∼ 75 bp, consistent with highly mismatch intolerant testing.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; DNA ; Rec A Recombinases/genetics ; Rec A Recombinases/metabolism ; Base Pairing ; DNA, Single-Stranded/genetics ; Recombination, Genetic
Chemical Substances	DNA (9007-49-2) ; Rec A Recombinases (EC 2.7.7.-) ; DNA, Single-Stranded
Language	English
Publishing date	2023-07-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0288611
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Article: Influences of ssDNA-RecA Filament Length on the Fidelity of Homologous Recombination

Danilowicz, Claudia / Vietorisz, Evan / Godoy-Carter, Veronica / Prévost, Chantal / Prentiss, Mara

Journal of molecular biology. 2021 Sept. 03, v. 433, no. 18

2021

Abstract: Chromosomal double-strand breaks can be accurately repaired by homologous recombination, but genomic rearrangement can result if the repair joins different copies of a repeated sequence. Rearrangement can be advantageous or fatal. During repair, a broken ...

Abstract	Chromosomal double-strand breaks can be accurately repaired by homologous recombination, but genomic rearrangement can result if the repair joins different copies of a repeated sequence. Rearrangement can be advantageous or fatal. During repair, a broken double-stranded DNA (dsDNA) is digested by the RecBCD complex from the 5′ end, leaving a sequence gap that separates two 3′ single-stranded DNA (ssDNA) tails. RecA binds to the 3′ tails forming helical nucleoprotein filaments.A three-strand intermediate is formed when a RecA-bound ssDNA with L nucleotides invades a homologous region of dsDNA and forms a heteroduplex product with a length ≤ L bp. The homology dependent stability of the heteroduplex determines how rapidly and accurately homologous recombination repairs double-strand breaks. If the heteroduplex is sufficiently sequence matched, repair progresses to irreversible DNA synthesis. Otherwise, the heteroduplex should rapidly reverse. In this work, we present in vitro measurements of the L dependent stability of heteroduplex products formed by filaments with 90 ≤ L ≤ 420 nt, which is within the range observedin vivo. We find that without ATP hydrolysis, products are irreversible when L > 50 nt. In contrast, with ATP hydrolysis when L < 160 nt, products reverse in < 30 seconds; however, with ATP hydrolysis when L ≥ 320 nt, some products reverse in < 30 seconds, while others last thousands of seconds. We consider why these two different filament length regimes show such distinct behaviors. We propose that the experimental results combined with theoretical insights suggest that filaments with 250 ≲ L ≲ 8500 nt optimize DSB repair.
Keywords	DNA repair ; DNA replication ; genomics ; homologous recombination ; hydrolysis ; molecular biology ; nucleoproteins ; single-stranded DNA
Language	English
Dates of publication	2021-0903
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167143
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Article ; Online: Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination.

Boyer, Benjamin / Danilowicz, Claudia / Prentiss, Mara / Prévost, Chantal

Nucleic acids research

2019 Volume 47, Issue 15, Page(s) 7798–7808

Abstract: Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation ...

Abstract	Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.
MeSH term(s)	Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Binding Sites ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/genetics ; DNA, Single-Stranded/metabolism ; Homologous Recombination ; Hydrolysis ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/chemistry ; Nucleic Acid Heteroduplexes/genetics ; Nucleic Acid Heteroduplexes/metabolism ; Protein Binding ; Protein Conformation ; Rec A Recombinases/chemistry ; Rec A Recombinases/genetics ; Rec A Recombinases/metabolism
Chemical Substances	DNA, Single-Stranded ; Nucleic Acid Heteroduplexes ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Rec A Recombinases (EC 2.7.7.-)
Language	English
Publishing date	2019-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkz667
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Article ; Online: Influences of ssDNA-RecA Filament Length on the Fidelity of Homologous Recombination.

Danilowicz, Claudia / Vietorisz, Evan / Godoy-Carter, Veronica / Prévost, Chantal / Prentiss, Mara

Journal of molecular biology

2021 Volume 433, Issue 18, Page(s) 167143

Abstract	Chromosomal double-strand breaks can be accurately repaired by homologous recombination, but genomic rearrangement can result if the repair joins different copies of a repeated sequence. Rearrangement can be advantageous or fatal. During repair, a broken double-stranded DNA (dsDNA) is digested by the RecBCD complex from the 5' end, leaving a sequence gap that separates two 3' single-stranded DNA (ssDNA) tails. RecA binds to the 3' tails forming helical nucleoprotein filaments.A three-strand intermediate is formed when a RecA-bound ssDNA with L nucleotides invades a homologous region of dsDNA and forms a heteroduplex product with a length ≤ L bp. The homology dependent stability of the heteroduplex determines how rapidly and accurately homologous recombination repairs double-strand breaks. If the heteroduplex is sufficiently sequence matched, repair progresses to irreversible DNA synthesis. Otherwise, the heteroduplex should rapidly reverse. In this work, we present in vitro measurements of the L dependent stability of heteroduplex products formed by filaments with 90 ≤ L ≤ 420 nt, which is within the range observedin vivo. We find that without ATP hydrolysis, products are irreversible when L > 50 nt. In contrast, with ATP hydrolysis when L < 160 nt, products reverse in < 30 seconds; however, with ATP hydrolysis when L ≥ 320 nt, some products reverse in < 30 seconds, while others last thousands of seconds. We consider why these two different filament length regimes show such distinct behaviors. We propose that the experimental results combined with theoretical insights suggest that filaments with 250 ≲ L ≲ 8500 nt optimize DSB repair.
MeSH term(s)	Adenosine Triphosphate/metabolism ; DNA/chemistry ; DNA/genetics ; DNA Repair ; DNA Replication ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/genetics ; Homologous Recombination ; Models, Molecular ; Rec A Recombinases/genetics ; Rec A Recombinases/metabolism
Chemical Substances	DNA, Single-Stranded ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Rec A Recombinases (EC 2.7.7.-)
Language	English
Publishing date	2021-07-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167143
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Article ; Online: Superspreading Events Without Superspreaders: Using High Attack Rate Events to Estimate N o for Airborne Transmission of COVID-19

PRENTISS, MARA G. / Chu, Arthur / Berggren, Karl K.

medRxiv

Abstract: We study transmission of COVID-19 using five well-documented case studies : a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. In all cases the likely index patients were pre-symptomatic ... ...

Abstract	We study transmission of COVID-19 using five well-documented case studies : a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. In all cases the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. An estimate of N 0 , the characteristic number of COVID-19 virions needed to induce infection in each case, is found using a simple physical model of airborne transmission. We find that the N 0 values are similar for five COVID-19 superspreading cases (~300-2,000 viral copies) and of the same order as influenza A. Consistent with the recent results of Goyal et al , these results suggest that viral loads relevant to infection from presymptomatic or mildly symptomatic individuals may fall into a narrow range, and that exceptionally high viral loads are not required to induce a superspreading event [1,2] . Rather, t he accumulation of infective aerosols exhaled by a typical pre-symptomatic or mildly symptomatic patient in a confined, crowdedspace (amplified by poor ventilation, particularly activity like exercise or singing, or lack of masks) for exposure times as short as one hour are sufficient. We calculate that talking and breathing release ~460 N 0 and ~10 N 0 (quanta)/hour, respectively, providing a basis to estimate the risks of everyday activities. Finally, we provide a calculation which motivates the observation that fomites appear to account for a smallpercentage of total COVID-19 infection events.
Keywords	covid19
Language	English
Publishing date	2020-10-23
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.10.21.20216895
Database	COVID19

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Article ; Online: Interactions between identical DNA double helices.

Lai, Chun-Liang / Chen, Chuanying / Ou, Shu-Ching / Prentiss, Mara / Pettitt, B Montgomery

Physical review. E

2020 Volume 101, Issue 3-1, Page(s) 32414

Abstract: The molecular mechanism of specific interactions between double stranded DNA molecules has been investigated for many years. Problems remain in how confinement, ions, and condensing agents change the interactions. We consider how the orientational ... ...

Abstract	The molecular mechanism of specific interactions between double stranded DNA molecules has been investigated for many years. Problems remain in how confinement, ions, and condensing agents change the interactions. We consider how the orientational alignment of DNAs contributes to the interactions via free energy simulations. Here we report on the effective interactions between two parallel DNA double helices in 150-mM NaCl solution using all atom models. We calculate the potential of mean force (PMF) of DNA-DNA interactions as a function of two coordinates, interhelical separation of parallel double helices and relative rotation of a DNA molecule with respect to the other about the helical axis. We generate the two-dimensional PMF to better understand the effective interactions when a DNA molecule is in juxtaposition with another. The analysis of the ion and solvent distributions around the DNA and particularly in the interface region shows that certain alignments of the DNA pair enhance the interactions. At local free energy minima in distance and alignment, water molecules and Na^{+} ions form a hydrogen bonded network with the phosphates from each DNA. This network contributes an attractive energy component to the DNA-DNA interactions. Our results provide a molecular mechanism whereby local DNA-DNA interactions, depending on the helical orientation, give a potential mechanism for stabilizing pairing of much larger lengths of homologous DNA that have been seen experimentally. The study suggests an atomically detailed local picture of relevance to certain aspects of DNA condensation or aggregation.
MeSH term(s)	DNA/chemistry ; DNA/metabolism ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Rotation
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2020-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.101.032414
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Article ; Online: RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers.

Jiang, Lili / Prentiss, Mara

Physical review. E, Statistical, nonlinear, and soft matter physics

2014 Volume 90, Issue 2, Page(s) 22704

Abstract: Ideally, self-assembly should rapidly and efficiently produce stable correctly assembled structures. We study the tradeoff between enthalpic and entropic cost in self-assembling systems using RecA-mediated homology search as an example. Earlier work ... ...

Abstract	Ideally, self-assembly should rapidly and efficiently produce stable correctly assembled structures. We study the tradeoff between enthalpic and entropic cost in self-assembling systems using RecA-mediated homology search as an example. Earlier work suggested that RecA searches could produce stable final structures with high stringency using a slow testing process that follows an initial rapid search of ∼9-15 bases. In this work, we will show that as a result of entropic and enthalpic barriers, simultaneously testing all ∼9-15 bases as separate individual units results in a longer overall searching time than testing them in groups and stages.
MeSH term(s)	DNA/metabolism ; Decision Trees ; Entropy ; Models, Genetic ; Nucleic Acid Conformation ; Rec A Recombinases/metabolism ; Sequence Homology ; Time Factors
Chemical Substances	DNA (9007-49-2) ; Rec A Recombinases (EC 2.7.7.-)
Language	English
Publishing date	2014-08-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1550-2376
ISSN (online)	1550-2376
DOI	10.1103/PhysRevE.90.022704
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Article ; Online: Binding energies of nucleobase complexes: Relevance to homology recognition of DNA.

León, Sergio Cruz / Prentiss, Mara / Fyta, Maria

Physical review. E

2016 Volume 93, Issue 6, Page(s) 62410

Abstract: The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and ... ...

Abstract	The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.
MeSH term(s)	Base Pairing ; DNA/chemistry ; DNA/metabolism ; Energy Metabolism ; Sequence Homology, Nucleic Acid
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2016-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.93.062410
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