title: Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop.
abstract: All 64 possible thermodynamic parameters for a single-bulge loop in the middle of a sequence were derived from optical melting studies. The relative stability of a single bulge depended on both the type of bulged base and its flanking base pairs. The contribution of the single bulge to helix stability ranged from 3.69 kcal/mol for a TAT bulge to -1.05 kcal/mol for an ACC bulge. Thermodynamics for 10 sequences with a GTG bulge were determined to test the applicability of the nearest-neighbor model to a single-bulge loop. Thermodynamic parameters for the GTG bulge and Watson-Crick base pairs predict, DeltaH degrees, DeltaS degrees, and T(M)(50 microM) values with average deviations of 3.0%, 4.3%, 4.7%, and 0.9 degrees C, respectively. The prediction accuracy was within the limits of what can be expected for a nearest-neighbor model. This certified that the thermodynamics for single-bulge loops can be estimated adequately using a nearest-neighbor model.
authors.affiliation: Graduate School of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo 060-8628, Japan. fumiaki@dna-comp.org
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Tanaka
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kameda
authors.forename: Masahito
authors.initials: M
authors.lastname: Yamamoto
authors.forename: Azuma
authors.initials: A
authors.lastname: Ohuchi
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D012313:RNA; D004247:DNA