Paper Citing NAMD - Abstract
Karachevtsev, Maxim V.; Karachevtsev, Victor A.
Peculiarities of Homooligonucleotides Wrapping around Carbon Nanotubes: Molecular Dynamics Modeling
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9271-9279, JUL 28 2011
Spontaneous adsorption of homooligonucleotides dC(25), dT(25), dG(25), and dA(25) on the surface of the carbon nanotube (16,0) has been simulated by the molecular dynamics method. It was demonstrated that the rate of pyrimidine oligonucleotide wrapping around the nanotube is higher than that of purine ones which do not form a complete pitch even after the maximum simulation time (50 ns). This behavior can be explained by a stronger self-stacking between the purines than pyrimidines, which prevents the reorientation of the polymer required for the acquisition of a more energetically favored conformation on the nanotube. Estimations obtained from modeling allowed to establish the oligonucleotide row which demonstrates decreasing interaction energies between oligonucleotides and the carbon nanotube: d(T)(25) > d(C)(25) > d(A)(25) approximate to d(G)(25). It was shown that the temperature growth increases the rate of oligonucleotides to reach the maximum binding energy mainly due to the destruction of nitrogen base self-stacking. Ribonucleic oligonucleotides r(C)(25), r(A)(25), and r(G)(25) do not make a pitch around the nanotube for SO ns. The presence of the additional hydroxyl group in ribose restricts the conformational flexibility of ribonucleic oligonucleotides in comparison with their deoxy analogues and this reduces the possibility of rapid occupation of the stable conformation on the nanotube surface.
