The thermodynamics of DNA structural motifs.
DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
SantaLucia
John
J
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA. jsl@chem.wayne.edu
Hicks
Donald
D
D000465:Algorithms; D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D016208:Databases, Factual; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
D015342:DNA Probes; D004247:DNA