Experimental and theoretical study of the interaction of single-stranded DNA homopolymers and a monomethine cyanine dye: nature of specific binding.
The photophysical properties of an intercalating unsymmetrical monomethine cyanine dye and single-stranded DNA homopolymers show strong association for poly(dA) and poly(dG), but not for poly(dC) and poly(dT), as determined by several spectroscopic techniques and molecular dynamics calculations. While poly(dA) and poly(dG) appear to bind the dye as a monomer (with dramatic increase in fluorescence), poly(dC) and poly(dT) bind only very weakly, and seem to promote dye aggregation. Only in the case of poly(dA) there seems to be a unique, well defined form of intercalation, that molecular dynamics calculations suggest involve the quinoline ring between two bases, in an arrangement that should favor pi-stacking; consistently with this, the decay of the fluorescence shows a single exponential, the absorption spectrum shows a shift in the dye maximum, the fluorescence is strong, and the induced circular dichroism follows a simple pattern.
Mikelsons
Larisa
L
Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
Carra
Claudio
C
Shaw
Michelle
M
Schweitzer
Claude
C
Scaiano
J C
JC
D002232:Carbocyanines / Q000737:chemistry*; D002942:Circular Dichroism; D004277:DNA, Single-Stranded / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry; D008958:Models, Molecular; D013050:Spectrometry, Fluorescence
D002232:Carbocyanines; D004277:DNA, Single-Stranded; D007364:Intercalating Agents