Charge Structure and Counterion Distribution in Hexagonal DNA Liquid Crystal
Dai Liang 1, Yuguang Mu 2, Lars Nordenskiold 2, Alain Lapp 3 and Johan RC van der Maarel 1*
1 National University of Singapore
2 Nanyang Technological University
3 Laboratoire Léon Brillouin
* To whom correspondence should be addressed. E-mail: phyjrcvd{at}nus.edu.sg.
Submitted on August 22, 2006
Revised on September 24, 2006
Accepted on 13 October 2006
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Abstract |
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A hexagonal liquid crystal of DNA fragments (double stranded, 150 base pairs) with tetramethylammonium (TMA) counterions was investigated with small angle neutron scattering (SANS). We obtained the structure factors pertaining to the DNA and counterion density correlations with contrast matching in the water. Molecular Dynamics (MD) computer simulation of a hexagonal assembly of nine DNA molecules showed that the inter-DNA distance fluctuates with a correlation time around 2 ns and a standard deviation of 8.5 % of the interaxial spacing. The MD simulation also showed a minimal effect of the fluctuations in inter-DNA distance on the radial counterion density profile and significant penetration of the grooves by TMA. The radial density profile of the counterions was also obtained from a Monte Carlo (MC) computer simulation of a hexagonal array of charged rods with fixed interaxial spacing. Strong ordering of the counterions between the DNA molecules and the absence of charge fluctuations at longer wavelengths was shown by the SANS number and charge structure factors. The DNA-counterion and counterion structure factors are interpreted with the correlation functions derived from the Poisson-Boltzmann (PB) equation, MD, and MC simulation. Best agreement is observed between the experimental structure factors and the prediction based on the PB equation and/or MC simulation. The SANS results show that TMA is too large to penetrate the grooves to a significant extent, in contrast to what is shown by MD simulation.
Key Words:
molecular dynamics, monte carlo, neutron scattering, poisson boltzmann, structure factors
