A base-pairing model of duplex formation. I. Watson–Crick pairing geometries

✍ Scribed by J.D. Bashford; P.D. Jarvis

• Publisher: Wiley (John Wiley & Sons)
• Year: 2005
• Tongue: English
• Weight: 139 KB
• Volume: 78
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.20282

✦ Synopsis

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

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