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

Pawe Weroski ^* , Yi Jiang ^* and Steen Rasmussen  

^* Theoretical Division and Center for Nonlinear Studies, and Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico; Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland; and Santa Fe Institute, Santa Fe, New Mexico

Correspondence: Address reprint requests to Pawe Weroski, Theoretical Division, Los Alamos National Laboratory, MS-B284, Los Alamos, NM 87545. Tel.: 505-667-9956; Fax: 505-665-2659; E-mail: pawel{at}lanl.gov.

We present the results of molecular dynamics simulations of small peptide nucleic acid (PNA) molecules, synthetic analogs 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 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 nonpolar 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.