STABILITY OF TRIPLE-HELICAL POLY(DT)-POLY(DA)-POLY(DT) DNA WITH COUNTERIONS

Structural conformation of triple-helical poly(dT)-poly(dA)-poly(dT) h as been a very controversial issue recently. Earlier investigations, b ased on fiber diffraction data and molecular modeling, indicated an A- form conformation with C-3'-endo sugar pucker. On the other hand, Rama n, solution infrared spectral, and NMR studies show a B-form structure with C-2'-endo sugars. In accordance with these experimental results, a theoretical model with B-form, C-2'-endo sugars was proposed in 199 3, In the present work we investigate the dynamics and stability of th e two conformations within the effective local field approach applied to the normal mode calculations for the system. The presence of counte rions was explicitly taken into account. Stable equilibrium positions for the counterions were calculated by analyzing the normal mode dynam ics and free energy of the system. The breathing modes of the triple h elix are shifted to higher frequencies over those of the double helix by 4-16 cm(-1). The characteristic marker band for the B conformation at 835 cm(-1) is split up into two marker bands at 830 and 835 cm(-1). A detailed comparison of the normal modes and the free energies indic ates that the B-form structure, with C-2'-endo sugar pucker, is more s table than the A-form structure. The normal modes and the correspondin g dipole moments are found to be in close agreement with recent spectr oscopic findings.