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A Base-Pairing Model of Duplex Formation. I. Watson-Crick Pairing Geometries
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 (ΔG mean errors of 4.5 and 5.4%, respectively). © 2005 Wiley Periodicals, Inc.
Funding
Australian Research Council
History
Publication title
BiopolymersVolume
78Issue
6Pagination
287-297ISSN
0006-3525Department/School
School of Natural SciencesPublisher
John Wiley & Sons IncPlace of publication
Hoboken, USA, NJRepository Status
- Restricted