Hydration pattern of A4T4 and T4A4 DNA: a molecular dynamics study

Abstract

Hydration pattern and energetics of ‘A-tract’ containing duplexes have been studied using molecular dynamics on 12-mer self-complementary sequences 5′-d(GCA4T4GC)-3′ and 5′-d(CGT4A4CG)-3′. The structural features for the simulated duplexes showed correlation with the corresponding experimental structures. Analysis of the hydration pattern confirmed that water network around the simulated duplexes is more conformation specific rather than sequence specific. The calculated heat capacity change upon duplex formation showed that the process is entropically driven for both the sequences. Furthermore, the theoretical free energy estimates calculated using MMPBSA approach showed a higher net electrostatic contribution for A4T4 duplex formation than for T4A4, however, energetically both the duplexes are observed to be equally stable.