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.
PaczkowskiJ.KabatcJ.JedrzejewskaB.. “Polymethine Dyes as Fluorescent Probes and Visible-Light Photoinitiators for Free Radical Polymerization”. In: GuptaR.R., editor. Topics in Heterocyclic Chemistry. Berlin, Germany: Springer-Verlag, 2008. Vol. 14, Pp. 183–220.
2.
MishraA.BeheraR.K.BeheraP.K.MishraB.K.BeheraG.B.. “Cyanines During the 1990s: A Review”. Chem. Rev.2000. 100(6): 1973–2012.
3.
OwenD.J.VanDerveerD.SchusterG.B.. “Cyanine Borate Penetrated Ion Pair Structures in Solution and the Solid State: Induced Circular Dichroism”. J. Am. Chem. Soc.1998. 120(8): 1705–1717.
4.
MurphyS.SauerweinB.DrickamerH.G.SchusterG.B.. “Spectroscopy of Cyanine Dyes in Fluid Solution at Atmospheric and High Pressure: The Effect of Viscosity on Nonradiative Processes”. J. Phys. Chem.1994. 98(51): 13476–13480.
5.
ChatterjeeS.DavisP.D.GottschalkP.KurzM.E.SauerweinB.YangX.SchusterG.B.. “Photochemistry of Carbocyanine Alkyltriphenylborate Salts: Intra Ion-Pair Electron Transfer and the Chemistry of Boranyl Radicals”. J. Am. Chem. Soc.1990. 112(17): 6329–6338.
6.
WangM.Holmes-DavisR.RafinskiZ.JedrzejewskaB.ChoiK.Y.ZwickM.BuppC.IzmailovA.PaczkowskiJ.WarnerB.KoshinskyH.. “Accelerated Photobleaching of a Cyanine Dye in the Presence of a Ternary Target DNA, PNA Probe, Dye Catalytic Complex. A Molecular Diagnostic”. Anal. Chem.2009. 81(6): 2043–2052.
7.
DeligeorgievT.G.. “Molecular Probes Based on Cyanine Dyes for Nucleic Acid Research”. In: DaehneS.Resch-GengerU.WolfbeisO.S., editors. Near-Infrared Dyes for High Technology Applications (NATO ASI Series). Dordrecht, the Netherlands: Kluwer, 1998. Pp. 125.
GlazerA.N.RyeH.S.. “Stable Dye-DNA Intercalation Complexes as Reagents for High-Sensitivity Fluorescence Detection”. Nature.1992. 359(6398): 859–861.
10.
RyeH.S.GlazerA.N.. “Interaction of Dimeric Intercalating Dyes with Single Stranded DNA”. Nucleic Acids Res.1995. 23(7): 1215–1222.
11.
BiverT.De BiasiA.SeccoF.VenturiniM.YarmolukS.. “Cyanine Dyes as Intercalating Agents: Kinetic and Thermodynamic Studies on the DNA/Cyan40 and DNA/Cyan2 Systems”. Biophys. J.2005. 89(1): 374–383.
12.
HannahK.C.GilR.R.ArmitageB.A.. “1H NMR and Optical Spectroscopic Investigation of the Sequence-Dependent Dimerization of a Symmetrical Cyanine Dye in the DNA Minor Groove”. Biochemistry.2005. 44(48): 15924–15929.
13.
MikheikinA.L.ZhuzeA.L.ZasedatelevA.S.. “Binding of Symmetrical Cyanine Dyes into the DNA Minor Groove”. J. Biomol. Struct. Dyn.2000. 18(1): 59–72.
14.
YarmolukS.M.LukashovS.S.Ogul'ChanskyT.Y.LosytskyyM.Y.KornyushynaO.S.. “Interaction of Cyanine Dyes with Nucleic Acids. XXI. Arguments for Half-Intercalation Model of Interaction”. Biopolymers.2001. 62(4): 219–227.
15.
LeeL.G.ChenC.LiuL.A.. “Thiazole Orange: A New Dye for Reticulocyte Analysis”. Cytometry.1986. 7(6): 508–517.
16.
RenikuntlaB.R.RoseH.C.EldoJ.WaggonerA.S.ArmitageB.A.. “Improved Photostability and Fluorescence Properties Through Polyfluorination of a Cyanine Dye”. Org. Lett.2004. 6(6): 909–912.
17.
MatsuiM.KawamuraS.ShibataK.MuramatsuH.. “Synthesis and Characterization of Mono-, Bis-, and Trissubstituted Pyridinium and Pyrylium Dyes”. Bull. Chem. Soc. Jpn.1992. 65(1): 71–74.
18.
CaoY.HeX.-Wen. “Studies of Interaction Between Safranine T and Double Helix DNA by Spectral Methods”. Spectrochim. Acta A Mol. Biomol. Spectrosc.1998. 54(6): 883–892.
19.
WolfeA.Jr.ShimerG.H.MeehamT.. “Polycyclic Aromatic Hydrocarbons Physically Intercalate into Duplex Regions of Denatured DNA”. Biochemistry.1987. 26(20): 6392–6396.
20.
HuangC.Z.LiY.F.FengP.. “A Spectrophotometric Study on the Interaction of Neutral Red with Double-Stranded DNA in Large Excess”. Talanta.2001. 55(2): 321–328.
21.
ChenL.-M.LiuJ.ChenJ.-C.ShiS.TanC.-P.ZhengK.-C.JiL.-N.. “Experimental and Theoretical Studies on the DNA-Binding and Spectral Properties of Water-Soluble Complex [Ru(MeIm)4(dpq)]2+”. J. Mol. Struct.2008. 881(1-3): 156–166.
22.
HamerF.M.. “Some Chain-Substituted Methincyanines and Styryl Dyes”. J. Chem. Soc.1956. 1480–1498.
23.
KabatcJ.JedrzejewskaB.PaczkowskiJ.. “New Heterobicationic Hemicyanine Dyes: Synthesis, Spectroscopic Properties, and Photoinitiating Ability”. J. Polym. Sci. A Polym. Chem.2006. 44(21): 6345–6359.
24.
MurphyS.YangX.ShusterG.B.. “Cyanine Borate Salts That Form Penetrated Ion Pairs in Benzene Solution: Synthesis, Properties, and Structure”. J. Org. Chem.1995. 60(8): 2411–2422.
25.
VenkataramanK.. “Cyanine Dyes”. In: VenkataramanK., editor. The Chemistry of Synthetic Dyes. New York: Academic Press, 1952. Vol. 2, Chap. XXXVIII. Pp. 1143–1188.
26.
ChenX.PengX.CuiA.WangB.WangL.ZhangR.. “Photostabilities of Novel Heptamethine 3H-Indolenine Cyanine Dyes with Different N-Substituents”. J. Photochem. Photobiol. A Chem.2006. 181(1): 79–85.
27.
SongB.ZhangQ.MaW.-H.PengX.-J.FuX.-M.WangB.-S.. “The Synthesis and Photostability of Novel Squarylium Indocyanine Dyes”. Dyes Pigm.2009. 82(3): 396–400.
28.
PingC.ShuqingS.YunfengH.ZhiguoQ.DeshuiZ.. “Structure and Solvent Effect on the Photostability of Indolenine Cyanine Dyes”. Dyes Pigm.1999. 41(3): 227–231.
29.
BartonJ.K.DanishefskyA.GoldbergJ.. “Tris(phenanthroline)ruthenium(II): Stereoselectivity in Binding to DNA”. J. Am. Chem. Soc.1984. 106(7): 2172–2176.
30.
IslamM.M.SinhaR.KumarG.S.. “RNA Binding Small Molecules: Studies on t-RNA Binding by Cytotoxic Plant Alkaloids Berberine, Palmatine and the Comparison to Ethidium”. Biophys. Chem.2007. 125(2-3): 508–520.
31.
KumarC.V.AsuncionE.H.. “DNA Binding Studies and Site Selective Fluorescence. Sensitization of an Anthryl Probe”. J. Am. Chem. Soc.1993. 115(19): 8547–8553.
32.
LongE.C.BartonJ.K.. “On Demonstrating DNA Intercalation”. Acc. Chem. Res.1990. 23(9): 271–273.
33.
HusainN.N.AgbariaR.A.WarnerI.M.. “Spectroscopic Analysis of the Binding of Doxorubicin to Human a-1 Acid Glycoprotein”. J. Phys. Chem.1993. 97(41): 10857–10861.
34.
ZhongW.YuJ.-S.LiangY.. “Chlorobenzylidine-Herring Sperm DNA Interaction: Binding Mode and Thermodynamic Studies”. Spectrochim. Acta A Mol. Biomol. Spectrosc.2003. 59(6): 1281–1288.
