Structure and Conformational Dynamics of (dA:dT dA)₆
with Antiparallel Adenine Chains

S. Yu. Tsybenko¹, I. A. Il’icheva¹, E. A. Silin², and V. L. Florent’ev¹

¹ Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 117984 Russia
² Moscow Physicotechnical Institute, Dolgoprudnyi, Moscow Region, 141700 Russia

Received June 15, 1998

Abstract—For a hexamer fragment of triple-stranded helix dA · dT:dA with antiparallel adenine chains, all
admissible conformations were found, and the molecular dynamics along nanosecond trajectories was mod-
eled. All possible schemes of base bonding in a triple were studied with regard for both anti and syn adenine
orientations in the third chain. The most stable structures of the triplex were revealed to be such that the adenine
in the third chain is in the anti orientation and is hydrogen-bonded with the Watson–Crick adenine via the
reverse Hoogsteen scheme. Statistics were obtained for conformations of these structures along the equilibrium
trajectory for 2.4 ns. The statistical weights of the N and S states of the furanose ring depend on the number of
the chain in the triplex. In the Watson–Crick adenine chain, N:S = 60:40; in the thymine chain, N:S = 66:34;
and in the third adenine chain, N:S = 3:96. This triplex is additionally stabilized by approach of fragments of
the thymine and third adenine sugar-phosphate chains from different monomeric units to the van der Waals dis-
tances. This approach is accompanied by characteristic transitions in furanose rings. Since advantageous con-
tacts involve donors and acceptors of hydrogen bonds, the water–cation environment can be assumed to sub-
stantially affect not only the triplex stability, but also the statistics of the equilibrium N-to-S furanose state
ratios. An alternative structure is a triplex where the adenine in the third chain is in the syn orientation, and its
bonding to the adenine of the duplex is described by a twofold axis passing through the center of the square
formed by the pairs of N₆ and N₇ atoms. Additional mechanisms were found for the intramolecular stabilization
of the structure with the syn orientation of adenines in the third chain. These mechanisms consist in hydrogen
bonding between the hydrogen of the amino group in the third adenine chain and the oxygen of a phosphate
group in the Watson–Crick adenine chain.

Key words: triplexes, molecular dynamics, conformational analysis, equilibrium structure, correlation of
intramolecular movements

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