An Algebraic Model of RNA Duplex Formation

We propose a simple algebraic description of the two-body interactions of bases in RNA thermodynamics showing in detail qualitative equivalence with conventional nearest-neighbor models. The process of obtaining base content, polymer, and oligomer parameters is illustrated, and for duplexes containing Watson-Crick pairs, fits to oligonucleotide duplex heat-of-formation data are shown to be statistically equivalent to existing models. © 2004 Wiley Periodicals, Inc.