ORIGINAL PAPER Specificity of Cyanine Dye L-21 Aggregation in Solutions with Nucleic Acids G. Ya. Guralchuk & A. V. Sorokin & I. K. Katrunov & S. L. Yefimova & A. N. Lebedenko & Yu. V. Malyukin & S. M. Yarmoluk Received: 8 November 2006 / Accepted: 4 May 2007 / Published online: 13 June 2007 # Springer Science + Business Media, LLC 2007 Abstract Optical spectroscopy experiments were used to study the features of cyanine dye 3,3′-dimethyl-9-(2- thienyl)-thiacarbocyanine iodide (L-21) aggregation in binary solutions DMF:Tris–HCl buffer (pH=8) containing nucleic acids (DNA or RNA). The appearance of absorp- tion and luminescence bands associated with J-aggregates and dimers that are formed within the minor groove of DNA has been observed. The model of L-21 J-aggregate structure is proposed. It has been found that dimers are the building blocks of L-21 J-aggregates. Disorientation in dimers caused by the minor groove curvature is reason of observation of Davydov splitting in absorption spectrum of L-21 J-aggregates. In the solution containing DNA the absorption and luminescence bands of L-21 J-aggregates exhibit the specific properties that allows the dye L-21 to be used as a fluorescent probe for DNA detection. Keywords Nucleic acids . Minor groove binding . J-aggregates . Cyanine dye . Fluorescence labels Introduction Various chemical structures of different nature such as proteins, synthetic organic molecules, fluorescent dyes and ions interact with NA and interfere with NA functions [1]. Cyanine dyes are very popular as fluorescent probes for DNA and RNA detection due to their extraordinary increase in fluorescence intensity upon binding to NA as a result of rigid fixation of trans-conformation [1–9]. There are two important ways in which cyanines can reversibly bind to DNA: by intercalation between the base pairs [1, 10–12] or by binding in the minor groove [1, 6, 7, 13]. Intercalation is inserting and stacking of molecules between the base pairs of the DNA duplex due to hydrophobic and van der Waals interaction. Intercalation is a noncovalent interaction in which the molecule is held perpendicular to the helix axis. As a rule, intercalating cyanine dyes do not exhibit specificity to DNA sequences and reveal weak GC- specificity. Also disadvantages of intercalating cyanine dyes are that they elongate the DNA helix and that they are fluorescent both in single stranded DNA and double stranded DNA [1, 10–12]. At groove binding in addition to hydrophobic and van der Waals interaction, electrostatic interaction between a dye molecule and phosphate ions takes place as well as hydrogen bonds formation with the base pairs and hydroxyl groups of sugar residua. Groove binders can be sequence specific due to the fact that they can be elongated by aggregation to extend the interactions within the groove [1, 6, 7, 13]. As a rule, monomethine dyes act as intercalators [10–12, 14], while increase in polymethine chain length leads to increasing the part of groove binders [7, 15, 16]. At groove binding, cyanine dyes can interact forming aggregates, mainly, face-to-face dimers [1, 15–17]. Dimer formation results in the appearance of a new absorption band hypsochromically shifted with respect to the monomer band. Such associates are called H-aggregates [18, 19]. For some cyanine dyes an end-to-end aggregation in minor groove of DNA was observed [16, 20–22] that results in the appearance of a new bathochromically shifted absorption J Fluoresc (2007) 17:370–376 DOI 10.1007/s10895-007-0201-5 G. Y. Guralchuk : A. V. Sorokin (*) : I. K. Katrunov : S. L. Yefimova : A. N. Lebedenko : Y. V. Malyukin Institute for Scintillation Materials, STC “Institute for Single Crystals”, NAS of Ukraine, 60 Lenin Ave., 61001 Kharkov, Ukraine e-mail: sorokin@isc.kharkov.com S. M. Yarmoluk Institute for Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo str., 03143 Kyiv, Ukraine