Molecular Dynamics Study of Small PNA Molecules in Lipid-Water System

¹ Los Alamos National Laboratory

^* To whom correspondence should be addressed. E-mail: pawel{at}lanl.gov.

Submitted on September 12, 2006
Revised on November 9, 2006
Accepted on 27 December 2006

	Abstract

We present the results of Molecular Dynamics simulations of small peptide nucleic acid (PNA) molecules, synthetic analogues of DNA, at a lipid bilayer in water. At neutral pH, without any salt, and in the NP_nT ensemble, two similar PNA molecules (6-mers) with the same nucleic base sequence and different terminal groups are investigated at the interface between water and a 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) lipid bilayer. The results of our simulations suggest that at low ionic strength of the solution, both PNA molecules adsorb at the lipid-water interface. In the case where the PNA molecule has charged terminal groups, the main driving force of adsorption is the electrostatic attraction between the charged groups of PNA and the lipid heads. The main driving force of adsorption of the PNA molecule with neutral terminal groups is the hydrophobic interaction of the non-polar groups. Our simulations suggest that the system free energy change associated with PNA adsorption at the lipid-water interface is on the order of several tens of kT per PNA molecule in both cases.

Key Words: 1PUP, PNA adsorption, POPC, free energy profile, lipid bilayer, peptide nucleic acid