Year: 2005
Type: article
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 (ΔG mean errors of 4.5 and 5.4%, respectively). © 2005 Wiley Periodicals, Inc. Biopolymers 78: 287–297, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected]
Source: Biopolymers
DOI: 10.1002/bip.20282
Authors: J.D. Bashford, P.D. Jarvis
Institution: University of Tasmania
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2030310608