How long does DNA keep the memory of its conformation? A time-dependent canonical correlation analysis of molecular dynamics simulation.

Abstract

The time dependence of the correlation between motions of different parts 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 furanose ring (SU), the base (BA), and the backbone (SK). The motion of each subunit is considered as the superimposition of rigid body translation, rigid body rotation, and internal deformation. Canonical time-dependent correlation functions calculated with coordinates describing the different components of the subunits motion are defined and computed. This allows us to probe how long a particular type of motion of one subunit influences the other types of motions of other subunits (cross correlation functions) or how long a particular subunit keeps the memory of its own conformation or location (autocorrelation functions). From autocorrelation analysis it is found that deformation decorrelates within a few tenths of picoseconds, rotational correlation times are on the order of 8 ps, while translational motions are long-time correlated. The deformation of a subunit is not correlated to the deformation of another one (at the 200 ps time scale of our simulation), but influences slightly their translation and orientation as time increases.