HOW LONG DOES DNA KEEP THE MEMORY OF ITS CONFORMATION - A TIME-DEPENDENT CANONICAL CORRELATION-ANALYSIS OF MOLECULAR-DYNAMICS SIMULATION

The time dependence of the correlation between motions of different pa rts of DNA is analyzed from a 200 ps molecular dynamics simulation of the double-stranded self-complementary d(CTGATCAG) in the B form. Each nucleotide is decomposed into three subunits corresponding to the fur anose ring (SU), the base (BA), and the backbone (SK). The motion of e ach subunit is considered as the superimposition of rigid body transla tion, rigid body rotation, and internal deformation. Canonical time-de pendent correlation functions calculated with coordinates describing t he different components of the subunits motion are defined and compute d. This allows us to probe how long a particular type of motion of one subunit influences the other types of motions of other subunits (cros s correlation functions) or how long a particular subunit keeps the me mory of its own conformation or location (autocorrelation functions). From autocorrelation analysis it is found that deformation decorrelate s within a few tenths of picoseconds, rotational correlation times are on the order of 8 ps, while translational motions are long-time corre lated. The deformation of a subunit is not correlated to the deformati on of another one (at the 200 ps time scale of our simulation), but in fluences slightly their translation and orientation as time increases. (C) 1996 John Wiley & Sons, Inc.