Molecular Docking Study of the Interactions Between Cyanine Dyes And DNA

Abstract

Among the various fluorescent probes currently used for biomedical and biochemical studies, significant attention attracts cyanine dyes possessing advantageous properties upon their complexation with biomolecules, particularly nucleic acids. Given the wide range of cyanine applications in DNA studies, a better understanding of their binding mode and intermolecular interactions governing dye-DNA complexation would facilitate the synthesis of new molecular probes of the cyanine family with optimized properties and would be led to the development of new cyanine-based strategies for nucleic acid detection and characterization. In the present study molecular docking techniques have been employed to evaluate the mode of interaction between one representative of monomethines (AK12-17), three trimethines (AK3-1, AK3-3, AK3-5), three pentamethines (AK5-1, AK5-3, AK5-9) and one heptamethine (AK7-6) cyanine dyes and B–DNA dodecamer d(CGCGAATTCGCG)2 (PDB ID: 1BNA). The molecular docking studies indicate that: i) all cyanines under study (excepting AK5-9 and AK7-6) form the most stable dye-DNA complexes with the minor groove of double-stranded DNA; ii) cyanines AK5-9 and AK7-6 interact with the major groove of the DNA on the basis of their more extended structure and higher lipophilicity in comparison with other dyes; iii) cyanine dye binding is governed by the hydrophobic and Van der Waals interactions presumably with the nucleotide residues C9A, G10A (excepts AK3-1, AK3-5), A17B (excepts AK3-5, AK5-3) and A18B in the minor groove and the major groove residues С16B, A17B, A18B, C3A, G4A, A5A, A6A (AK5-9 and AK7-6); iv) all dyes under study (except AK3-1, AK3-5 and AK5-39 possess an affinity to adenine and cytosine residues, whereas AK3-1, AK3-5 and AK5-3 also interact with thymine residues of the double-stranded DNA.