A model for simulating dynamics of DNA denaturation

Karen Drukker; George C. Schatz

doi:10.1021/jp000550j

A model for simulating dynamics of DNA denaturation

Karen Drukker, George C. Schatz^*

^*Corresponding author for this work

Chemistry

Research output: Contribution to journal › Article › peer-review

63 Scopus citations

Abstract

We present a simplified model of DNA for computer simulation of melting dynamics. This model is simple enough to allow simulation times up to the microsecond range for DNA duplexes with tens of base pairs, while its level of detail is sufficient to describe individual base pairs and individual hydrogen bond formation and breakage. We have applied this model to the simulation of the melting of two model B-DNA decamers. The DNA melting profiles are similar to those seen in experiment, as are the differences between duplexes containing only AT pairs versus those with only CG pairs.

Original language	English (US)
Pages (from-to)	6108-6111
Number of pages	4
Journal	Journal of Physical Chemistry B
Volume	104
Issue number	26
DOIs	https://doi.org/10.1021/jp000550j
State	Published - Jun 6 2000

ASJC Scopus subject areas

Physical and Theoretical Chemistry
Surfaces, Coatings and Films
Materials Chemistry

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10.1021/jp000550j

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abstract = "We present a simplified model of DNA for computer simulation of melting dynamics. This model is simple enough to allow simulation times up to the microsecond range for DNA duplexes with tens of base pairs, while its level of detail is sufficient to describe individual base pairs and individual hydrogen bond formation and breakage. We have applied this model to the simulation of the melting of two model B-DNA decamers. The DNA melting profiles are similar to those seen in experiment, as are the differences between duplexes containing only AT pairs versus those with only CG pairs.",

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AB - We present a simplified model of DNA for computer simulation of melting dynamics. This model is simple enough to allow simulation times up to the microsecond range for DNA duplexes with tens of base pairs, while its level of detail is sufficient to describe individual base pairs and individual hydrogen bond formation and breakage. We have applied this model to the simulation of the melting of two model B-DNA decamers. The DNA melting profiles are similar to those seen in experiment, as are the differences between duplexes containing only AT pairs versus those with only CG pairs.

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A model for simulating dynamics of DNA denaturation

Abstract

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