DNA dynamics in aqueous solution : opening the double helix
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 simulation...
| Publié dans: | The international journal of supercomputer applications. - 1990. - 4(1990), 3 vom: 15., Seite 81-96 |
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| Auteur principal: | |
| Autres auteurs: | , , |
| Format: | Article |
| Langue: | English |
| Publié: |
1990
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| Accès à la collection: | The international journal of supercomputer applications |
| Sujets: | Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. NASA Center ARC NASA Discipline Exobiology NASA Discipline Number 52-20 NASA Program Exobiology Water 059QF0KO0R Guanine plus... |
| Résumé: | 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 |
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| Description: | Date Completed 25.03.1996 Date Revised 27.10.2019 published: Print Citation Status MEDLINE |
| ISSN: | 0890-2720 |