The Mechanism of Benzothiazole Styrylcyanine Dyes Binding with dsDNA: Studies by Spectral-Luminescent Methods

Abstract

In the presented work studies of the interaction mode of monomer and two homodimer benzothiazole styryl dyes containing spermine-like linkage/tail group with the double stranded (ds) DNA are reported. For these dyes, equilibrium constant of dye binding to DNA (K(b)), as well as the number of dsDNA base pairs occupied by one bound dye molecule (n) were determined. The data obtained show that the presence of spermine-like group containing quaternary nitrogen (Bos-5) results in increase of K(b) value as compared to this of unsubstituted analogue (Sbt). Besides, for the dimer dyes containing benzothiazole styryl chromophores, the K(b) value is either five times higher (DBos-13) or almost the same (DBsu-10) as compared to this of corresponding monomer Sbt, depending on the position in the benzothiazole ring where the linker is attached. Moreover, the n values for both dimers are significantly different as well, pointing to the bis-intercalative binding mechanism for DBos-13 and for the groove-binding one for DBsu-10. The conclusion about the dimer dyes-dsDNA binding mechanisms is also supported by the study of the fluorescent response of these dyes on the presence of AT- and GC-containing polynucleotides.

Exciton‐Controlled Hybridization‐Sensitive Fluorescent Probes: Multicolor Detection of Nucleic Acids

“…The DNA-binding ability of hemicyanines is known to be inherently lower than that of thiazole orange dyes. [12] The small shift in the absorption band suggests that the dissociation of the dye aggregate is inefficient in the hybrid with RNA, and that it is difficult for the dyes to bind independently to the hybrid structure. Similarly, D 640 and D 660 , which have relatively larger conjugated systems, showed low efficiency of dye-aggregate dissociation upon hybrid formation with RNA.…”

Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids

“…From the results in Table 2 , the small n values of BT+ , BT2+(NEt 2 ) , 4QL+ and 4QL2+ indicate that the dye is more likely to interact with DNA via intercalation. The larger n values of PY+ (4.4), PY2+(C4) (4.0) are more consistent with the groove-binding mode in which at least 3 base pairs would be required for the dye to occupy 52 . Consistent with the expectation, the larger binding constant of BT2+(NEt 2 ) than BT+ by an order of magnitude also confirms that the introduction of an additional positive charge improves the binding affinity of the dye towards DNA targets as proposed.…”

“…S17 52 ). Intercalators that bind to DNA usually have binding constants ( K b ) of less than 10 7 M −1 52 . Acridine orange (AO), thiazole orange (TO) 53 , and ethidium bromide 54 , have the K b values of 5.0 × 10 4 , 1 × 10 6 , and 1.5 × 10 5 M −1 , respectively.…”

“…5 ) (Fig. S17 52 ). Intercalators that bind to DNA usually have binding constants ( K b ) of less than 10 7 M −1 52 .…”

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

“…Among them, the most widely used are thiazole orange [77,100,117,118], Cy3 and Cy5 [121] (Figure 8). New synthetic polymethine cyanines developed by Yarmoluk’s laboratory are also promising [122,123,124,125,126]. They change both fluorescence intensity and emission spectra upon interaction with nucleic acid targets.…”