Structure and mechanical properties of DNA play a key role in its biological functioning. A lot of well-established conclusions about the DNA structure and its sequence-dependent variabil- ity came from various experimental and computational studies of the Dickerson-Drew dodecamer (DD), a prototypic B-DNA molecule of the sequence (5')CGCGAATTCGCG(3'). In this study we present a detailed analysis of structural and mechan- ical properties of DD based on extensive atomistic molecular dynamics (MD) simulations with explicit representation of wa- ter and ionic environment. We analyze three simulated systems covering different ionic conditions and water models. Two MD trajectories are reported for the first time, one of them being 2.4 µs long. An extensive comparsion with one recent NMR struc- ture and four recent X-ray structures is made. It is found that the end basepairs can adopt two different pairing motifs dur- ing the simulation: the canonical Watson-Crick pair or a non- canonical trans Watson-Crick/Sugar Edge pair. These states can significantly influence the structure of DD even at the third step from the end. A clear relationship is found between the BI/BII backbone substates and the basepair step conformation. A model of rigid bases is used to study mechanical properties of the DNA. The non-local...
| Identifer | oai:union.ndltd.org:nusl.cz/oai:invenio.nusl.cz:310194 |
| Date | January 2012 |
| Creators | Dršata, Tomáš |
| Contributors | Lankaš, Filip, Jurečka, Petr |
| Source Sets | Czech ETDs |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/masterThesis |
| Rights | info:eu-repo/semantics/restrictedAccess |
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