Interaction of Carbocyanine Dyes with DNA: Synthesis and Spectroscopic Studies

Abstract

Six carbocyanine dyes have been synthesized and their interactions with DNA have been investigated for their prospective use as fluorescent markers in molecular biology. The noncovalent binding of the compounds with DNA was explored by fluorescence spectroscopy, ultraviolet/visible spectrophotometry, and photobleaching. The electron-withdrawing ability of the substituents in N-position of free thio- and selenocarbocyanines strongly affected their photostabilities. Changes in the experimental conditions, such as the presence or absence of oxygen, had an impact on the rate of photobleaching. In the presence of DNA, absorbance photofading and fluorescence photobleaching occurred. It appears that the reduction of fluorescence intensity was due to quenching of the dye fluorescence by interaction with DNA.

Electrospray ionization collision induced dissociation of thiocarbocyanine and selenocarbocyanine dyes

“…All the necessary reagents and solvents were purchased from Aldrich‐Chemical Co. and used without further purification. The methods applied for the synthesis of thiocarbocyanine and selenocarbocyanine dyes (shown at Scheme ) have been described in detail elsewhere …”

“…The methods applied for the synthesis of thiocarbocyanine and selenocarbocyanine dyes (shown at Scheme 1) have been described in detail elsewhere. 19…”

“…The development of general rules of CID fragmentation of dyes will allow for a fast and simple structural analysis of unknown molecules and confirmation of the structure of newly synthesized compounds. The analysed carbocyanine dyes were used as effective visible‐wavelength initiators of the radical polymerization of acrylic monomers and were also tested as fluorescent markers in molecular biology . The structures of all of the examined carbocyanine dyes are shown in Scheme .…”

“…The analysed carbocyanine dyes were used as effective visible-wavelength initiators of the radical polymerization of acrylic monomers 18 and were also tested as fluorescent markers in molecular biology. 19 The structures of all of the examined carbocyanine dyes are shown in Scheme 1.…”

Structure and electronic absorption spectra of cyanine dyes – derivatives of tetrazolo- and triazoloisoindole

“…Indeed their applications in biochemistry and medicine are becoming numerous, especially as they show a peculiar ability to act as effective marker of biomolecules [1][2][3][4][5][6][7][8][9][10].…”