Biopolymers and cell. 2001; 17 (4): 331 - 336

Interacion of cyanine dyes with nucleic acids. 23. Computer simulation of «half-intercalative» interaction of monomethyne cyanine dyes with DNA

S. S. Lukashov, G. O. Kachkovsky, S. M. Yarmoluk, G. Kh. Matsuka

Computer simulation of interaction with DNA of six monomethyne cyanine dyes was carried out using MM+, AMBER, PM3 and CNDO/2 methods from Hyperchem 5.0 program packet. Geometry optimization of complexes was carried out, charge density for ground S0 and exited 5] states and potential energies of heterocyeles' rotation around the bonds of methyne group for unbound dyes and dyes in complexes with DNA were calculated. Obtained energies of complexes are in agreement with observed fluorescent intensities of dyes in presence of DNA, Calculated electron density distribution changes in dyes' molecules upon DNA binding diverge with observed Stocks' shift values changes. Rotation potential energy values show that rigidity of fixation of dye's molecule planar conformation increases strongly upon binding to DNA.