Hydration Regulates The Thermodynamic Stability Of Dna Structures Under Molecular Crowding Conditions

Abstract

Although water is an integral part of DNA structures, the effects of water molecules on various DNA structures which are formed by not only Watson-Crick but also Hoogsteen base pairs are still unclear. Here, we studied quantitatively the effects of molecular crowding on the thermodynamics of a parallel G-quadruplex formation of [d(TG ₄ )₂] ₄ with Hoogsteen base pairs. It was demonstrated that molecular crowding conditions stabilized the parallel G-quadruplex. Moreover, the plot of stability of the parallel G-quadruplex structure versus water activity suggested that water molecules were released through the G-quadruplex formation. The stabilization of the DNA structures consisting of Hoogsteen base pairs under cell-like conditions may lead to a structural polymorphism of various DNA sequences regulated by water molecules.

Keywords:

• DNA G-quadruplex
• molecular crowding
• hydration
• thermodynaimics

Acknowledgments

The authors thank Yumi Ueda for data collection. H.K. received a Research Fellowship from the Japan Society for the Promotion of Science for Young Scientists. This work was supported in part by Grants-in-Aid for Scientific Research and for the Academic Frontier Project (2004–2009) from MEXT, Japan.