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Biophys. J. BioFAST: First Published April 29, 2005. doi:10.1529/biophysj.105.059790
© 2005 by the Biophysical Society.

A more recent version of this article appeared on July 1, 2005.
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NUCLEIC ACIDS

Cyanine Dyes as Intercalating Agents: Kinetic and Thermodynamic Studies on the DNA/Cyan40 and DNA/CCyan2 Systems

Fernando Secco 1*, Tarita Biver 2, Angela De Biasi 2, Marcella Venturini 2 and Sergiy M Yarmoluk 3

1 Universitá di Pisa,
2 Dipartimento di Chimica e Chimica Industriale - Universitá di Pisa
3 Institute of Molecular Biology and Genetics of NAS of Ukraine

* To whom correspondence should be addressed. E-mail: ferdi{at}dcci.unipi.it.

Submitted on January 25, 2005
Revised on March 2, 2005
Accepted on 20 April 2005


  Abstract
The interaction of cyanines with nucleic acids is accompanied by intense variations of their optical properties. Consequently these molecules find numerous applications in biology and medicine. Since no detailed information on the binding mechanism of DNA/cyanines systems is available, a T-jump investigation of the kinetics and equilibria of binding of the cyanines Cyan40 [3-methyl-2-(1,2,6-trimethyl-4(1H)pyridinylidenmethyl)-benzothiazolium ion] and CCyan2 [3-methyl-2-[2-methyl-3-(3-methyl-2(3H)-benzothiazolylidene)-1-propenyl]-benzothiazolium ion] with CT-DNA is performed at 25°C, pH 7 and various ionic strengths. Bathochromic shifts of the dye absorption band upon DNA addition, polymer melting point displacement ({Delta}T = 8-10°C), site size determination (n = 2) and stepwise kinetics concur in suggesting that the investigated cyanines bind to CT-DNA primary by intercalation. Measurements with poly(dA-dT)•poly(dA-dT) and poly(dG-dC)•poly(dG-dC) reveal fair selectivity of CCyan2 towards G-C basepairs. T-jump experiments show two kinetic effects for both systems. The binding process is discussed in terms of the sequence D + S = D,S = DSI = DSII, which leads first to fast formation of an external complex D,S and then to a partially intercalated complex DSI which, in turn, converts to DSII, a more stable intercalate. Absorption spectra reveal that both dyes tend to self-aggregate; the kinetics of CCyan2 self-aggregation is studied by T-jump relaxation and the results are interpreted in terms of dimer formation.

Key Words: DNA, cyanine dyes, intercalation, kinetics, melting, self-aggregation






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Copyright © 2005 by the Biophysical Society.