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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Chandler, David Chakraborty, Arup K. Dinner, Aaron R. Hagan, Michael F. |
| Description | Author Affiliation: Hagan MF ( Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA.); |
| Abstract | We combine free-energy calculations and molecular dynamics to elucidate a mechanism for DNA base-pair binding and unbinding in atomic detail. Specifically, transition-path sampling is used to overcome computational limitations associated with conventional techniques to harvest many trajectories for the flipping of a terminal cytosine in a 3-bp oligomer in explicit water. Comparison with free-energy projections obtained with umbrella sampling reveals four coordinates that separate true dynamic transition states from stable reactant and product states. Unbinding proceeds via two qualitatively different pathways: one in which the flipping base breaks its intramolecular hydrogen bonds before it unstacks and another in which it ruptures both sets of interactions simultaneously. Both on- and off-pathway intermediates are observed. The relation of the results to coarse-grained models for DNA-based biosensors is discussed. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 24 |
| Volume Number | 100 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2003-12-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | DNA Chemistry Metabolism Base Pairing Biophysical Phenomena Biophysics Hydrogen Bonding Kinetics Models, Molecular Nucleic Acid Conformation Thermodynamics Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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