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 (DeltaG mean errors of 4.5 and 5.4%, respectively).
Bashford
J D
JD
School of Mathematics and Physics, University of Tasmania, P. O. Box 252-37, Hobart 7001, Tasmania, Australia. James.Bashford@utas.edu.au
Jarvis
P D
PD
D020029:Base Pairing; D004247:DNA / Q000737:chemistry; D008433:Mathematics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D012313:RNA / Q000737:chemistry; D013816:Thermodynamics
D012313:RNA; D004247:DNA