Back to Search Start Over

DNA dynamics in aqueous solution: opening the double helix

Authors :
Pohorille, A
Ross, W. S
Tinoco, I. Jr
MacElroy, R. D
Source :
The international journal of supercomputer applications. 4(3)
Publication Year :
1990
Publisher :
United States: NASA Center for Aerospace Information (CASI), 1990.

Abstract

The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the molecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest reaction in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dynamics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water molecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.

Subjects

Subjects :
Exobiology

Details

Language :
English
ISSN :
08902720
Volume :
4
Issue :
3
Database :
NASA Technical Reports
Journal :
The international journal of supercomputer applications
Notes :
DE-FG03-86ER60406, , GM 10840, , NCA-2 315
Publication Type :
Report
Accession number :
edsnas.20040090066
Document Type :
Report