Interactions of cyanine dyes with DNA or PNA duplexes: Formation of supramolecular structures and application in DNA probing

This thesis presents the results of spectroscopic studies on the binding of two cyanine dyes, DiSC₃₊(5) and DiSC₃₋(5) to DNA or PNA duplexes. The phenomena of aggregation of cyanine dyes in solution, on surface or in porous solid have attracted much research interest in the past decades. The J-aggregate formation of certain cyanine dyes provides a possibility of non-covalently synthesize novel materials with non-linear optical effects. We observed the formation of DiSC₃₊(5) J-aggregate on the thread of poly(dI-dC)₂. The aggregate shows sharp and strong red-shifted UV-vis absorbance, as well as strong CD excition splitting, due to the helical oligomers it adapted to on the DNA template. The rules beyond the binding mode interest us. Small molecules that bind to DNA in minor groove have been studied intensively in order to find out the codes governing binding. Such molecules are potential antigene or antisense drugs, and may also be used in DNA probing. Thus we continue the study by synthesizing DiSC₃₋(5), which has negatively charged side chains, instead of the positive substituents in DiSC₃₊(5). We found that although this dye has no affinity to DNA duplexes, it does show high affinity for PNA duplexes. The specific binding mode was characterized. Furthermore, by combining the two dyes together, hetero mode binding was accomplished on both the DNA and PNA templates. Models were proposed on the different types of aggregates formed of these two dyes on DNA or PNA templates based on CD spectra.; We also designed two systems for DNA probing. The first one uses DiSC ₃₋(5) as the signal molecule, together with a PNA hairpin, based on its higher affinity for PNA duplexes. Thus the fluorescence of the dye will be enhanced once the PNA hairpin hybridizes to DNA target and release the dye. The system was examined on its sensitivity. The other system is based on FET (Fluorescence Energy Transfer) and includes two fluorophore modified PNA strands. Upon hybridization to the target, FET will be observed to indicate the presence of certain target. Various targets were used to find out the sensitivity of this system.