title: Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.
abstract: It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Kaori
authors.initials: K
authors.lastname: Nakamura
authors.forename: Hisae
authors.initials: H
authors.lastname: Tateishi-Karimata
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Ohmichi
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D002942:Circular Dichroism; D017931:DNA Primers; D004591:Electrophoresis, Polyacrylamide Gel; D008958:Models, Molecular; D015394:Molecular Structure; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D017931:DNA Primers; D014867:Water