Hydration of Watson−Crick Base Pairs and Dehydration of Hoogsteen Base Pairs Inducing Structural Polymorphism under Molecular Crowding Conditions Export

@article{citeulike:4202806, 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 °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.}, author = {Miyoshi, Daisuke and Nakamura, Kaori and Tateishi-Karimata, Hisae and Ohmichi, Tatsuo and Sugimoto, Naoki}, citeulike-article-id = {4202806}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ja805972a}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ja805972a}, day = {18}, doi = {10.1021/ja805972a}, journal = {Journal of the American Chemical Society}, keywords = {dna\_topology}, month = {March}, number = {10}, pages = {3522--3531}, posted-at = {2009-03-21 16:06:41}, priority = {2}, title = {Hydration of Watson−Crick Base Pairs and Dehydration of Hoogsteen Base Pairs Inducing Structural Polymorphism under Molecular Crowding Conditions}, url = {http://dx.doi.org/10.1021/ja805972a}, volume = {131}, year = {2009} }

TY - JOUR ID - citeulike:4202806 L3 - citeulike-article-id:4202806 N2 - 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 °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. IS - 10 JF - Journal of the American Chemical Society EP - 3531 TI - Hydration of Watson−Crick Base Pairs and Dehydration of Hoogsteen Base Pairs Inducing Structural Polymorphism under Molecular Crowding Conditions VL - 131 SP - 3522 KW - dna_topology AU - Miyoshi, Daisuke AU - Nakamura, Kaori AU - Tateishi-Karimata, Hisae AU - Ohmichi, Tatsuo AU - Sugimoto, Naoki PY - 2009/03/18/ UR - http://dx.doi.org/10.1021/ja805972a ER -