# Publications Search Within Results Search Within Results search ## 112 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 112 results Download 112 citations download- [BibTeX](/node/1606801/export?format=bibtex) - [EndNote X3 XML](/node/1606801/export?format=endnote8) - [EndNote 7 XML](/node/1606801/export?format=endnote7) - [Endnote tagged](/node/1606801/export?format=tagged) - [Marc](/node/1606801/export?format=marc) - [PubMedId](/node/1606801/export?format=pubmed_id) - [RIS](/node/1606801/export?format=ris) ### 2020 C. L. Lai, C. Y. Chen, S. C. Ou, M. Prentiss, and B. M. Pettitt. 2020. “[Interactions Between Identical DNA Double Helices](/publications/interactions-between-identical-dna-double-helices)”. PHYSICAL REVIEW E, 101 C. L. Lai, C. Y. Chen, S. C. Ou, M. Prentiss, and B. M. Pettitt. 2020. “[Interactions Between Identical DNA Double Helices](/publications/interactions-between-identical-dna-double-helices)”. PHYSICAL REVIEW E, 101 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1103/PhysRevE.101.032414) 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... - [ descriptionPublisher's Version](https://www.doi.org/10.1103/PhysRevE.101.032414) ### 2019 B. Boyer, C. Danilowicz, M. Prentiss, and C. Prevost. 2019. “[Weaving DNA Strands: Structural Insight on ATP Hydrolysis in RecA-Induced Homologous Recombination](/publications/weaving-dna-strands-structural-insight-atp-hydrolysis-reca-induced-homologous)”. NUCLEIC ACIDS RESEARCH, 47, Pp. 7798-7808 B. Boyer, C. Danilowicz, M. Prentiss, and C. Prevost. 2019. “[Weaving DNA Strands: Structural Insight on ATP Hydrolysis in RecA-Induced Homologous Recombination](/publications/weaving-dna-strands-structural-insight-atp-hydrolysis-reca-induced-homologous)”. NUCLEIC ACIDS RESEARCH, 47, Pp. 7798-7808 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gkz667) 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... - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gkz667) D. Lu, C. Danilowicz, T. F. Tashjian, C. Prevost, V. G. Godoy, and M. Prentiss. 2019. “[Slow Extension of the Invading DNA Strand in a D-Loop Formed by RecA-Mediated Homologous Recombination May Enhance Recognition of DNA Homology](/publications/slow-extension-invading-dna-strand-d-loop-formed-reca-mediated-homologous)”. JOURNAL OF BIOLOGICAL CHEMISTRY, 294, Pp. 8606-16 D. Lu, C. Danilowicz, T. F. Tashjian, C. Prevost, V. G. Godoy, and M. Prentiss. 2019. “[Slow Extension of the Invading DNA Strand in a D-Loop Formed by RecA-Mediated Homologous Recombination May Enhance Recognition of DNA Homology](/publications/slow-extension-invading-dna-strand-d-loop-formed-reca-mediated-homologous)”. JOURNAL OF BIOLOGICAL CHEMISTRY, 294, Pp. 8606-16 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1074/jbc.RA119.007554) 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... - [ descriptionPublisher's Version](https://www.doi.org/10.1074/jbc.RA119.007554) T. F. Tashjian, C. Danilowicz, A. E. Molza, B. H. Nguyen, C. Prevost, M. Prentiss, and V. G. Godoy. 2019. “[Residues in the Fingers Domain of the Translesion DNA Polymerase DinB Enable Its Unique Participation in Error-Prone Double-Strand Break Repair](/publications/residues-fingers-domain-translesion-dna-polymerase-dinb-enable-its-unique)”. JOURNAL OF BIOLOGICAL CHEMISTRY, 294, Pp. 7588-7600 T. F. Tashjian, C. Danilowicz, A. E. Molza, B. H. Nguyen, C. Prevost, M. Prentiss, and V. G. Godoy. 2019. “[Residues in the Fingers Domain of the Translesion DNA Polymerase DinB Enable Its Unique Participation in Error-Prone Double-Strand Break Repair](/publications/residues-fingers-domain-translesion-dna-polymerase-dinb-enable-its-unique)”. JOURNAL OF BIOLOGICAL CHEMISTRY, 294, Pp. 7588-7600 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1074/jbc.RA118.006233) The evolutionarily conserved Escherichia coli translesion DNA polymerase IV (DinB) is one of three enzymes that can bypass potentially deadly DNA lesions on the template strand during DNA replication. Remarkably, however, DinB is the only known... - [ descriptionPublisher's Version](https://www.doi.org/10.1074/jbc.RA118.006233) C. Li, C. Danilowicz, T. F. Tashjian, V. G. Godoy, C. Prevost, and M. Prentiss. 2019. “[The Positioning of Chi Sites Allows the RecBCD Pathway to Suppress Some Genomic Rearrangements](/publications/positioning-chi-sites-allows-recbcd-pathway-suppress-some-genomic)”. NUCLEIC ACIDS RESEARCH, 47, Pp. 1836-46 C. Li, C. Danilowicz, T. F. Tashjian, V. G. Godoy, C. Prevost, and M. Prentiss. 2019. “[The Positioning of Chi Sites Allows the RecBCD Pathway to Suppress Some Genomic Rearrangements](/publications/positioning-chi-sites-allows-recbcd-pathway-suppress-some-genomic)”. NUCLEIC ACIDS RESEARCH, 47, Pp. 1836-46 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gky1252) Bacterial recombinational repair of double-strand breaks often begins with creation of initiating 3 single-stranded DNA (ssDNA) tails on each side of a double-strand break (DSB). Importantly, if the RecBCD pathway is followed, RecBCD creates a gap between... - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gky1252) ### 2017 C. Danilowicz, L. Hermans, V. Coljee, C. Prevost, and M. Prentiss. 2017. “[ATP Hydrolysis Provides Functions That Promote Rejection of Pairings Between Different Copies of Long Repeated Sequences](/publications/atp-hydrolysis-provides-functions-promote-rejection-pairings-between-different)”. NUCLEIC ACIDS RESEARCH, 45, Pp. 8448-62 C. Danilowicz, L. Hermans, V. Coljee, C. Prevost, and M. Prentiss. 2017. “[ATP Hydrolysis Provides Functions That Promote Rejection of Pairings Between Different Copies of Long Repeated Sequences](/publications/atp-hydrolysis-provides-functions-promote-rejection-pairings-between-different)”. NUCLEIC ACIDS RESEARCH, 45, Pp. 8448-62 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gkx582) During DNA recombination and repair, RecA family proteins must promote rapid joining of homologous DNA. Repeated sequences with >100 base pair lengths occupy more than 1% of bacterial genomes; however, commitment to strand exchange was believed to occur... - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gkx582) A. Bitran, W. Y. Chiang, E. Levine, and M. Prentiss. 2017. “[Mechanisms of Fast and Stringent Search in Homologous Pairing of Double-Stranded DNA](/publications/mechanisms-fast-and-stringent-search-homologous-pairing-double-stranded-dna)”. PLOS COMPUTATIONAL BIOLOGY, 13 A. Bitran, W. Y. Chiang, E. Levine, and M. Prentiss. 2017. “[Mechanisms of Fast and Stringent Search in Homologous Pairing of Double-Stranded DNA](/publications/mechanisms-fast-and-stringent-search-homologous-pairing-double-stranded-dna)”. PLOS COMPUTATIONAL BIOLOGY, 13 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1371/journal.pcbi.1005421) Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with... - [ descriptionPublisher's Version](https://www.doi.org/10.1371/journal.pcbi.1005421) C. L. Liu, C. Danilowicz, N. Kleckner, and M. Prentiss. 2017. “[Single Molecule Identification of Homology-Dependent Interactions Between Long SsRNA and DsDNA](/publications/single-molecule-identification-homology-dependent-interactions-between-long)”. NUCLEIC ACIDS RESEARCH, 45, Pp. 894-901 C. L. Liu, C. Danilowicz, N. Kleckner, and M. Prentiss. 2017. “[Single Molecule Identification of Homology-Dependent Interactions Between Long SsRNA and DsDNA](/publications/single-molecule-identification-homology-dependent-interactions-between-long)”. NUCLEIC ACIDS RESEARCH, 45, Pp. 894-901 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gkw758) Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long... - [ descriptionPublisher's Version](https://www.doi.org/10.1093/nar/gkw758) ### 2016 D. J. Lee, C. Danilowicz, C. Rochester, A. A. Kornyshev, and M. Prentiss. 2016. “[Evidence of Protein-Free Homology Recognition in Magnetic Bead Force-Extension Experiments](/publications/evidence-protein-free-homology-recognition-magnetic-bead-force-extension)”. PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 472 D. J. Lee, C. Danilowicz, C. Rochester, A. A. Kornyshev, and M. Prentiss. 2016. “[Evidence of Protein-Free Homology Recognition in Magnetic Bead Force-Extension Experiments](/publications/evidence-protein-free-homology-recognition-magnetic-bead-force-extension)”. PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 472 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1098/rspa.2016.0186) Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome... - [ descriptionPublisher's Version](https://www.doi.org/10.1098/rspa.2016.0186) S. C. Leon, M. Prentiss, and M. Fyta. 2016. “[Binding Energies of Nucleobase Complexes: Relevance to Homology Recognition of DNA](/publications/binding-energies-nucleobase-complexes-relevance-homology-recognition-dna)”. PHYSICAL REVIEW E, 93 S. C. Leon, M. Prentiss, and M. Fyta. 2016. “[Binding Energies of Nucleobase Complexes: Relevance to Homology Recognition of DNA](/publications/binding-energies-nucleobase-complexes-relevance-homology-recognition-dna)”. PHYSICAL REVIEW E, 93 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1103/PhysRevE.93.062410) 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... - [ descriptionPublisher's Version](https://www.doi.org/10.1103/PhysRevE.93.062410) ### 2015 D. R. Yang, B. Boyer, C. Prevost, C. Danilowicz, and M. Prentiss. 2015. “[Integrating Multi-Scale Data on Homologous Recombination into a New Recognition Mechanism Based on Simulations of the RecA-SsDNA DsDNA Structure](/publications/integrating-multi-scale-data-homologous-recombination-new-recognition)”. NUCLEIC ACIDS RESEARCH, 43, Pp. 10251-63 D. R. Yang, B. Boyer, C. Prevost, C. Danilowicz, and M. Prentiss. 2015. “[Integrating Multi-Scale Data on Homologous Recombination into a New Recognition Mechanism Based on Simulations of the RecA-SsDNA DsDNA Structure](/publications/integrating-multi-scale-data-homologous-recombination-new-recognition)”. NUCLEIC ACIDS RESEARCH, 43, Pp. 10251-63 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.1080/07391102.2015.1032752) RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these... - [ descriptionPublisher's Version](https://www.doi.org/10.1080/07391102.2015.1032752) M. Prentiss, C. Prevost, and C. Danilowicz. 2015. “[Structure/Function/Relationships/in/RecA/Protein-Mediated/Homology/Recognition/and/Strand/Exchange](/publications/structurefunction-relationships-reca-protein-mediated-homology-recognition-and)”. CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 50, Pp. 453-76 M. Prentiss, C. Prevost, and C. Danilowicz. 2015. “[Structure/Function/Relationships/in/RecA/Protein-Mediated/Homology/Recognition/and/Strand/Exchange](/publications/structurefunction-relationships-reca-protein-mediated-homology-recognition-and)”. CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 50, Pp. 453-76 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.doi.org/10.3109/10409238.2015.1092943) 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. 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