This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.106.095745v1 92/3/947    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Dai, L. Articles by van der Maarel, J. R. C. Search for Related Content PubMed PubMed Citation Articles by Dai, L. Articles by van der Maarel, J. R. C.

Charge Structure and Counterion Distribution in Hexagonal DNA Liquid Crystal

Liang Dai ^*, Yuguang Mu , Lars Nordenskiöld , Alain Lapp  and Johan R. C. van der Maarel ^*

^* National University of Singapore, Department of Physics, Singapore; Nanyang Technological University, School of Biological Sciences, Singapore; and Laboratoire Léon Brillouin, CEA/CNRS, Gif-sur-Yvette, France

Correspondence: Address reprint requests to Johan R. C. van der Maarel, Dept. of Physics, National University of Singapore, 2 Science Dr. 3, Singapore 117542. Tel.: 65-6874-4396; Fax: 65-6777-6126; E-mail: phyjrcvd{at}nus.edu.sg.

A hexagonal liquid crystal of DNA fragments (double-stranded, 150 basepairs) 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 equation, MD, and MC simulation. Best agreement is observed between the experimental structure factors and the prediction based on the Poisson-Boltzmann 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.