Fluorescent Properties of Pentamethine Cyanine Dyes with Cyclopentene and Cyclohexene Group in Presence of Biological Molecules

Abstract

A series of pentamethine cyanine dyes with cyclohexene or cyclopentene group in polymethyne chain, assumed as DNA groove-binders, were studied as fluorescent probes for nucleic acids as well as for native and denatured proteins. It was revealed that the presence of methyl or dimethyl substituent in 5 position of the cyclohexene group hinders the formation of dye-DNA fluorescent complex, while the methyl substituent in 2 position leads to the increasing of the dye-DNA complex fluorescence intensity. The dyes SL-251, SL-1041, and SL-1046 containing methyl group in the 2 position of the cyclic group, are reported as bright DNA-sensitive dyes. The study of the dyes DNA-binding specificity demonstrated significant AT-preference that points to the groove-binding interaction mode. At the same time, the dyes SL-251, SL-377, and SL-957 with the 2-methyl substituted cyclohexene group were shown to be sensitive fluorescent dyes both for nonspecific (in SDS presence) proteins detection and for native BSA.

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA

“…We chose also cyanine dyes, known to change their fluorescence properties (quantum yield and emission wavelength) upon the interaction with DNA. [35][36][37]62,63 Two commercially available cyanine fluorophores Cy3 and Cy5 were used. 64 They display the desirable properties and can be eventually used for FRET experiments.…”

“…In order to circumvent background problems in non-permeabilized cells, a possible way is to use fluorescent probes that are able to modulate their emission spectra upon the interaction with the target DNA, that is, to increase the probe fluorescence intensity ("light-up probes") or/and to modify the emission spectra with a red or blue shift. [32][33][34][35][36][37] The other way is the use of FRET (Fluorescence Resonance Energy Transfer) approach, 38 when two fluorophores (donor and acceptor) attached to two neighboring probes are located in a close proximity on the target. Excitation of the donor results in the transfer of the energy to the acceptor, which emits light with a different spectrum compared to donor's one.…”

Interaction of Crown Ether‐Annelated Styryl Dyes with Double‐Stranded DNA

“…by complexation of cations from the DNA backbone upon intercalation of the aromatic part. Nevertheless, the experimental data and comparison with results obtained for mono‐ and bisstyryl dyes of similar structure allow the conclusion that such an effect is only marginal. Most likely, the effect of oxa crown ether moiety is too small in aqueous solution under physiological conditions, and the interaction of the corresponding dyes with ct DNA is only due to the π − π stacking and electrostatic contributions of the positive charged heteroaromatic moiety.…”

Recent advances in the development of synthetic chemical probes for glycosidase enzymes

“…Selective cleavage of the glycosidic bond triggers a dye-protein interaction accompanied by a fluorescence enhancement. [110][111][112] The squarylium hydrolysis product of 27, 6SqOH, displayed a significant spectral change upon enzymatic action and subsequent protein interaction. Moreover, 27 exhibited a binding parameter of two orders of magnitude lower than hydrolysis product 6SqOH confirming that the glycan moiety suppresses the protein-dye binding affinity.…”