A study of model energetics and conformational properties of polynucleotide triplexes

H. W T Van Vlijmen, G. L. Rame, Bernard Pettitt

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

The formation of triple-stranded nucleic acid helices is studied by molecular mechanics and molecular dynamics calculations. Using standard TAT and CGG homopolymers, single, triple, and quintuple molecular replacements are made. Some of these replacements are expected to form Hoogsteen bonds and some are not. While the electrostatic and total energetic differences for base triplet mismatches were dependent on the electrostatic model chosen, clear trends in the local geometric distortions were apparent. Relationships between these model-built strand geometries and chemical probe experiments are discussed.

Original languageEnglish (US)
Pages (from-to)517-532
Number of pages16
JournalBiopolymers
Volume30
Issue number5-6
StatePublished - 1990
Externally publishedYes

Fingerprint

Polynucleotides
Static Electricity
Electrostatics
Molecular mechanics
Nucleic acids
Molecular Dynamics Simulation
Homopolymerization
Mechanics
Nucleic Acids
Molecular dynamics
Geometry
Experiments

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

A study of model energetics and conformational properties of polynucleotide triplexes. / Van Vlijmen, H. W T; Rame, G. L.; Pettitt, Bernard.

In: Biopolymers, Vol. 30, No. 5-6, 1990, p. 517-532.

Research output: Contribution to journalArticle

Van Vlijmen, H. W T ; Rame, G. L. ; Pettitt, Bernard. / A study of model energetics and conformational properties of polynucleotide triplexes. In: Biopolymers. 1990 ; Vol. 30, No. 5-6. pp. 517-532.
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