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DNA dynamics in aqueous solution: opening the double helixThe 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.
Document ID
20040090066
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
Authors
Pohorille, A.
(University of California Berkeley 94720, United States)
Ross, W. S.
Tinoco, I. Jr
MacElroy, R. D.
Date Acquired
August 21, 2013
Publication Date
September 1, 1990
Publication Information
Publication: The international journal of supercomputer applications
Volume: 4
Issue: 3
ISSN: 0890-2720
Subject Category
Exobiology
Funding Number(s)
CONTRACT_GRANT: DE-FG03-86ER60406
CONTRACT_GRANT: GM 10840
CONTRACT_GRANT: NCA-2 315
Distribution Limits
Public
Copyright
Other
Keywords
NASA Discipline Number 52-20
NASA Center ARC
NASA Program Exobiology
NASA Discipline Exobiology

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