Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution

Samantha Weerasinghe, Paul E. Smith, V. Mohan, Y. K. Cheng, Bernard Pettitt

Research output: Contribution to journalArticle

87 Citations (Scopus)

Abstract

The structure and stability of a DNA triple helix was examined by molecular dynamics (MD) simulation using an all-atom force field. A 1.3 ns simulation was performed on a d(CG·G)7 triple helix in a 1 M saltwater solution. The Ewald method was used to calculate the electrostatic interactions of the system. The behavior of the DNA in the saltwater solution was determined by examining the structure, energetics, and mobility of water and ions in the system. The simulation results for the helical parameters support the validity of a model-built triplex-DNA structure. A low root mean square deviation of the dynamic structure from the initial structure demonstrates the stability of the triplex in the salt solution. The sugar pseudorotation, the backbone conformations, and the average helical parameters suggest that the conformation of strands I and III is strictly neither A-form nor B-form, whereas the conformation of strand II remains near the A-form. A higher mobility of both the cytosine strand and the triplex-forming guanine strand and also a longer residence time of water molecules in the spine of hydration were observed and are consistent with available NMR results.

Original languageEnglish (US)
Pages (from-to)2147-2158
Number of pages12
JournalJournal of the American Chemical Society
Volume117
Issue number8
StatePublished - Mar 1 1995
Externally publishedYes

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Conformations
DNA
Water
Cytosine
Guanine
Molecular Dynamics Simulation
Coulomb interactions
Static Electricity
Sugars
Hydration
Molecular dynamics
Spine
Salts
Nuclear magnetic resonance
Ions
Atoms
Molecules
Computer simulation
triplex DNA

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution. / Weerasinghe, Samantha; Smith, Paul E.; Mohan, V.; Cheng, Y. K.; Pettitt, Bernard.

In: Journal of the American Chemical Society, Vol. 117, No. 8, 01.03.1995, p. 2147-2158.

Research output: Contribution to journalArticle

Weerasinghe, Samantha ; Smith, Paul E. ; Mohan, V. ; Cheng, Y. K. ; Pettitt, Bernard. / Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution. In: Journal of the American Chemical Society. 1995 ; Vol. 117, No. 8. pp. 2147-2158.
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