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A Base-Pairing Model of Duplex Formation. I. Watson-Crick Pairing Geometries

Citation

Bashford, JD and Jarvis, PD, A Base-Pairing Model of Duplex Formation. I. Watson-Crick Pairing Geometries, Biopolymers, 78, (6) pp. 287-297. ISSN 0006-3525 (2005) [Refereed Article]

DOI: doi:10.1002/bip.20282

Abstract

We present a base-pairing model of oligonucleotide duplex formation and show in detail its equivalence to the nearest-neighbor dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing only Watson-Crick pairs. For completeness, the corresponding RNA-RNA parameters are included. In this approach, the connection between rank-deficient polymer and rank-determinant oligonucleotide parameter sets for DNA duplexes is transparent. The method is generalized to include RNA-DNA hybrids where the rank-deficient model with 11 dimer parameters in fact provides slightly improved predictions relative to the standard method with 16 independent dimer parameters ("G mean errors of 4.5 and 5.4%, respectively). © 2005 Wiley Periodicals, Inc.

Item Details

Item Type:Refereed Article
Research Division:Physical Sciences
Research Group:Other Physical Sciences
Research Field:Physical Sciences not elsewhere classified
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Physical Sciences
Author:Bashford, JD (Dr James Bashford)
Author:Jarvis, PD (Dr Peter Jarvis)
ID Code:37473
Year Published:2005
Funding Support:Australian Research Council (DP0344996)
Web of Science® Times Cited:3
Deposited By:Physics
Deposited On:2005-08-01
Last Modified:2010-06-05
Downloads:0

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