A model for simulating dynamics of DNA denaturation

Karen Drukker, George C Schatz

Research output: Contribution to journalArticle

62 Citations (Scopus)

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 languageEnglish
Pages (from-to)6108-6111
Number of pages4
JournalJournal of Physical Chemistry B
Volume104
Issue number26
Publication statusPublished - Jun 6 2000

Fingerprint

Denaturation
biopolymer denaturation
DNA
deoxyribonucleic acid
Melting
melting
B-Form DNA
Hydrogen bonds
simulation
computerized simulation
hydrogen bonds
Computer simulation
profiles
Experiments

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Engineering(all)

Cite this

A model for simulating dynamics of DNA denaturation. / Drukker, Karen; Schatz, George C.

In: Journal of Physical Chemistry B, Vol. 104, No. 26, 06.06.2000, p. 6108-6111.

Research output: Contribution to journalArticle

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