Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye

Abstract

The interactions between the trinuclear cyanine all-trans-2,2'-[3-[(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)ethylidene]-1,4-pentadiene-1,5-diyl]-bis[1,3,3-trimethyl]-3H-indolium with representative G4-DNA sequences, namely, 22AG [d(AG3T2AG3T2AG3T2AG3)], c-myc [d(TGAG3TG3TAG3TG3TA2)], c-kit [d(AG3AG3CGCTG3AG2AG3)], and a2 [d(ACAG4TGTG4ACAG4TGTG4)] and with double-stranded DNA, ct DNA and ds26 [d(CA2TCG2ATCGA2T2CGATC2GAT2G)], are studied by photometric and fluorimetric titrations, CD-spectroscopic analysis, and 1H-NMR spectroscopy. It is demonstrated that the heptamethine cyanine binds to quadruplex DNA by terminal π-stacking and to duplex DNA by aggregation along the DNA backbone. The ligand does not bind selectively to quadruplex DNA as compared with duplex DNA, but the two DNA forms can be differentiated with this ligand based on the different development of its absorption and emission properties upon ligand-DNA association.