Silver nanocrystals grown on a poly(dG)-poly(dC) double stranded DNA scaffold displayed circular dichroism at their surface plasmon excitation band. This chiral plasmon signature was not observed in a control experiment where silver nanocrystals of similar size were produced without the DNA template and adsorbed to the DNA. It is concluded that the DNA templated Ag nanocrystals had a preferred structural handedness.

Interaction of Thiazole Orange (TO) with double-, triple-, and quadruple-stranded forms of DNA was studied. We have demonstrated by UV-vis absorption, circular dichroism (CD), and fluorescence spectroscopy that TO binds with much higher affinity to triplex and G-quadruplex DNA structures compared to double-stranded (ds) DNA. Complexes of the dye with DNA triplexes and G-quadruplexes are very stable and do not dissociate during chromatography and gel electrophoresis. TO binding to either triple- or quadruple-stranded DNA structures results in a >1000-fold increase in dye fluorescence. The fluorescence titration data showed that TO to triad and tetrad ratios, in tight complexes with the triplex and the G-quadruplex, are equal to 0.5 and 1, respectively. Preferential binding of TO to triplexes and G-quadruplexes enables selective detection of only these DNA forms in gels in the absence of free TO in electrophoresis running buffer. We have also demonstrated that incubation of U2OS cells with submicromolar concentrations of TO results in preferential staining of certain areas in the nucleus in contrast to DAPI which binds to dsDNA and efficiently stains regions that are unstained with TO. We suggest that TO staining may be useful for the detection of noncanonical structural motifs in genomic DNA.

Interaction of meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) with G4-wires composed of approximately 1000 stacked tetrads (Kotlyar, A. B., Borovok, N., Molotsky, T., Cohen, H., Shapir, E., and Porath, D. (2005) Long monomolecular G4-DNA nanowires, Adv. Mater. 17, 1901-1905) was studied. These wires exist in either K (Na)-free or K forms in contrast to short telomeric G-quadruplexes, which are stable only in the presence of monovalent cations. We showed that a stable complex between K-free G4-wires and the porphyrin is formed at a TMPyP to tetrad molar ratio of 0.5. A 19 nm shift and a hypochromicity of 58% in the absorption spectrum, the induced CD of the porphyrin, and efficient energy transfer between TMPyP and K-free G4-wires suggest an intercalative mechanism of TMPyP binding. The K form interacts with TMPyP much weaker than the K-free form of the wires. Binding of TMPyP to the K form is characterized by a small (3 nm) shift of the Soret band, a weak positive induced CD in the Soret region, and the absence of energy transfer between the G-bases and the porphyrin. These parameters reflect a nonintercalative binding of TMPyP to the K form of the wires. We suggest that K ions positioned in the center space between the adjacent tetrads limit the access of TMPyP and other organic molecules to this region, thus enabling only nonintercalative modes of ligand binding to G-quadruplex DNAs.

Steady-state and time-resolved emission techniques were employed to study the nonradiative process of deoxygunaosine monophosphate (dGMP) and novel uniform continuous G4 wires containing hundreds of stacked tetrads. We found that the time-resolved emissions of both dGMP and G4 wires decay nonexponentialy. At room temperature, the short-time decay of the G4 wires is about 10 ps. At low temperatures in ice, the fluorescence quantum yields of both dGMP and G4 wires increase as the temperature decreases. For the G4 wires, the fluorescence quantum yield increases from about 10 -3 at room temperature to about 0.03 at liquidnitrogen temperatures. The asymptotic long-time decay of the lifetime-corrected emission of the G4 wires obeys a power law. At all temperatures, the average fluorescence decay time of G4 wires is longer than that of dGMP. We successfully used an inhomogeneous nonradiative model to fit the experimental results.

Two of earlier reported dsDNA sensitive cyanine dyes-monomethine Cyan 40 and meso-substituted trimethine Cyan 2 were studied for their ability to interact with non-canonical DNA conformations. These dyes were characterized by spectral-luminescent methods in the presence of G-quadruplex, triplex and dsDNA motifs. We have demonstrated that Cyan 2 binds strongly and preferentially to triple- and quadruple-stranded DNA forms that results in a strong enhancement of the dye fluorescence, as compared to dsDNA, while Cyan 40 form fluorescent complexes preferentially only with the triplex form. Highly fluorescent complexes of Cyan 2 with DNA triplexes and G-quadruplexes and Cyan 40 with DNA triplexes are very stable and do not dissociate during gel electrophoresis, leading to preferential staining of the above DNA forms in gels. The data presented point to the intercalation mechanism of the Cyan 2 binding to G4-DNA, while the complexes of Cyan 40 and Cyan 2 with triplex DNA are believed to be formed via groove binding mode. The Cyan dyes can provide a highly sensitive method for detection and quantification of non-canonical structures in genome.