Structure and conformational dynamics of (dA.dT:dT) 6 with parallel oriented thymine chains
Tsybenko, S.I.; Il'icheva, I.A.; Florent'ev, V.L.
Molekuliarnaia Biologiia 31(2): 315-323
1997
ISSN/ISBN: 0026-8984 PMID: 9213760 Document Number: 481813
Optimization of intramolecular energy and molecular dynamic calculations on nanosecond trajectories were conducted for a hexameric fragment of triple-stranded helix dA cntdot dT : dT with parallel thymine chains. Possible pathways of hydrogen binding in triplets were investigated. It was shown that thymine oxygen interaction determined a certain and specific triplet scheme. Each of the three strands possessed a characteristic equilibrium conformer mixture. A-type conformers predominated in the purine chain. In this state, the system spends approximately 95% of the total time. Both thymine strands spend almost equal time in A- and B-type conformations. These thymine strands differ only with respect to the equilibrium population density of conformers with the E-type of sugar cycle. The area of the minimum on the potential energy surface of parallel triplexes is characterized by clearly pronounced irregularity of the third strand conformation. Nevertheless, the parameters of local coil transformations practically do not depend on dynamic conformational changes. Regularities were determined that controlled mutually correlated atomic movements. It is suggested that the probability of the formation of triple-stranded coils dA cntdot dT:dT with parallel orientation of thymine strands sharply decreases with the growth of the length of oligonucleotides. Relative stability of parallel and antiparallel triplexes is discussed.