Dyes for fluorescent detection of non-canonical DNA structures (triplexes and quadruplexes)

In living organisms genomic DNAs mostly exist in a double-stranded (ds) helical form, but occurrence of some other conformations also seems possible. The guanine-rich nucleic acid sequences are known to fold into four-stranded (G-quadruplexes, G4-DNA) or triple-stranded (triplex) structures in which the nucleotide bases are connected by means of Hoogsteen base-pairing bonding (Fig. 7).

The problem of the possible role of triplex and quadruplex DNA motifs in gene regulation and genomic stability still remains unsolved. Therefore, development of a specific probe for distinguishing quadruplex or triplex conformations from a canonical ds one may have a significant scientific and practical importance.

Figure 7. Structures of G-G-C triad in poly(dG-dG)-poly(dC) (A) and G-tetrad in G4-DNA. (B).

Interaction of earlier reported DNA sensitive cyanine dyes monomethine Cyan 40 and trimethine Cyan 2 (Fig. 8), with dsDNA and non-canonical triplex and G-quadruplex DNA motifs was studied by spectral-luminescent methods. Cyan 40 demonstrated strong preference for triplex over duplexes and quadruplex DNA forms; whereas Cyan 2 was less specific with respect to non-cannonical DNA structures and binds with high affinity to either triplex or quadruplex DNA forms. We suggested that the complexes of Cyan 40 and Cyan 2 with triplex DNA are formed via groove binding mode, while Cyan 2 intercalates into G4-DNA.

Figure 8. Chemical structures of Cyan 40 and Cyan 2.

We consider the studied cyanine dyes can provide a highly sensitive method for detection and quantification of non-canonical DNA structures in genome and could be used for the search and development of agents that specifically bind with mentioned DNA motifs and inhibit their functioning.

• Mono and trimethine cyanines Cyan 40 and Cyan 2 as probes for highly selective fluorescent detection of non-canonical DNA structures / V. B. Kovalska, M. Yu. Losytskyy, S. M. Yarmoluk, I. Lubitz, A. B. Kotlyar // Journal of Fluorescence. – 2011. – Vol. 21, № 1. – P. 223–230.