Bolhuis, P.G.

Swenson, D.W.H.

Vreede, J.

English

International Migration, Integration and Social Cohesion online publications

UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl)UvA-DARE (Digital Academic Repository)Path Sampling Simulations of the Mechanisms and Rates of Transitionsbetween Watson-Crick and Hoogsteen Base Pairing in DNAVreede, J.; Bolhuis, P.G.; Swenson, D.W.H.DOI10.1016/j.bpj.2016.11.1181Publication date2017Document VersionFinal published versionPublished inBiophysical JournalLicenseOtherLink to publicationCitation for published version (APA):Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2017). Path Sampling Simulations of theMechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing inDNA. Biophysical Journal, 112(3, Supplement 1), 214a.https://doi.org/10.1016/j.bpj.2016.11.1181General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s)and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an opencontent license (like Creative Commons).Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, pleaselet the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the materialinaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letterto: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. Youwill be contacted as soon as possible.Download date:09 Mar 2023214a Monday, February 13, 20171058-Pos Board B126Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNAJocelyne Vreede, Peter G. Bolhuis, David W.H. Swenson.van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands.DNA duplexes predominantly contain Watson-Crick (WC) base pairs. Howev-er, at any time, a non-negligible fraction of base pairs exhibit a different inter-action pattern, called Hoogsteen (HG) where the purine base is rotated approximately 180o relative to its orientation in the WC pairing. The conver-sion from WC to HG alters the conformation of DNA, and may play a role in several processes, including recognition and replication. The transient nature of these transitions hamper thorough experimental investigation. Molecular dy-namics simulations complement experimental work by providing insights at very high spatial and temporal resolution. Path sampling methods focus the mo-lecular dynamics effort on the dynamics during a transition, thus avoiding the long waiting times in stable states. We apply two different path sampling tech-niques to study the transitions between the WC and HG base pairing motifs. By using transition path sampling we observed that the WC to HG conversion can proceed along several mechanistic routes with varying degrees of exposure of the purine. We computed the rate for each process by employing transition interface sampling.

Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA

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Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA

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International Migration, Integration and Social Cohesion online publications