DYNAMICS OF COMPLEMENTARY BASE-PAIRS OF DREW-DICKERSON DODECAMER ON THE MILLIAND MICROSECOND TIME SCALE ACCORDING TO THE DATA OF NUCLEAR SPIN RELAXATION DISPERSION R1ρ OF IMINO PROTONS

Abstract

Drew-Dickerson Dodecamer (DDD) is one of the well-known DNA duplexes. It has been sufficiently well studied by various structure determination methods and appears to be a standard for developing new experimental techniques and molecular mechanical force fields. For this reason, the information about the dynamics of DDD on different time scales is important for constructing more accurate structural-dynamic models and carrying out molecular dynamics calculations of long-term time trajectories that allow simulation of real processes. In this work, the information on the dynamics of DDD base-pairs on the milli- and microsecond time scale, currently missing from the literature, was obtained by means of imino protons’ nuclear spin relaxation (R1ρ) dispersion. It is shown for all the base-pairs, except for terminal and pre-terminal ones, that any dynamic processes in the range of R1ρ method are not observed up to 300 K, but proceed on a faster time scale. For the pre-terminal GC pair, a pronounced dependence of the relaxation R1ρ on the applied spin-lock field strength is observed, which allowed us to extract the information about the pair closing dynamics using a fast exchange model with highly skewed state populations. These data supplement the information obtained previously on the dynamics of DDD complementary base-pairs by exchange-based water magnetization transfer experiments and provide a more complete view of the processes observed in DDD in relation to base-pair opening-closing.