ION TRANSFER IN G4-WIRES

P. Kulhánek,^1,2 Z. Střelcová,² and J. Koča^1,2

¹CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic

²National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic

G4-wires are guanine quadruple helices of various length studied both experimentally and theoretically [1] [2]. In this work, we present results of molecular dynamics simulation of infinitively long G4-wires. The infinitive length is achieved by a periodic boundary condition applied on 12-steps long G4-fragment, which is covalently bound to its neighboring images. The main purpose of such setup is to disable possible penetration of interior channel by water or cations from bulk solution. Under these well defined conditions, the transfer of cations in various scenarios through the channel was studied by the means of potential of mean force calculations using the Adaptive Biasing Force method [3].

This work was realized in CEITEC - Central European Institute of Technology with research infrastructure supported by the project CZ.1.05/1.1.00/02.0068 financed from European Regional Development Fund (P.K., J.K.). The work has been supported by the Grant Agency of Czech Republic (GD301/09/H0040) (Z.S). The access to the MetaCentrum computing facilities provided under the program "Projects of Large Infrastructure for Research, Development, and Innovations" LM2010005 funded by the Ministry of Education, Youth, and Sports of the Czech Republic is acknowledged.

[1] J.T. Davis, Angewandte Chemie International Edition , 43, (2004), 668-698.

[2] M. Cavallari, A. Calzolari, A. Garbesi, R. Di Felice, J Phys Chem B , 110, (2006), 26337-26348.

[3] E. Darve, D. Rodriguez-Gomez, A. Pohorille, J. Chem. Phys. , 128, (2008), 144120.