title: Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.
abstract: We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Fujimoto
authors.forename: Shu-ichi
authors.initials: S
authors.lastname: Nakano
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
mesh_terms: D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D008958:Models, Molecular; D012964:Sodium / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D004247:DNA; D012964:Sodium