Nanosecond Molecular Dynamics of Hybrid Triplex and Duplex of Polycation Deoxyribonucleic Guanidine Strands with a Complimentary DNA Strand

Replacement of the phosphodiester linkages of the polyanion DNA with guanidinium linkers provides the polycation deoxyribonucleic guanidine (DNG). Molecular dynamics studies to 1120 ps of the hybrid triplex and 1420 ps of the hybrid duplex formed from octameric DNG strands d(Tg)8 with a complementary DNA oligomer strand d(Ap)8 have been carried out with water explicitly as solvent and Na+Cl- as counterions under periodic boundary conditions using the CHARMM force field and Ewald summation method. The Watson−Crick and Hoogstein hydrogen-bonding patterns of the A/T tracts remained intact without any structural restraints for both hybrid duplex and triplex structures throughout the simulation. And for the hybrid duplex and triplex structures, both 5‘ and 3‘ ends were only partially frayed. In agreement with our previous thermodynamic study the hybrid triplex is more favorable than the hybrid duplex in the simulations. This conclusion is reached by the comparison of the extent of 5‘ end fraying and the bifurc...