No abstract

3,3′-Diethylthiadicarbocyanine (DiSC 2 (5)) is a symmetrical cationic cyanine dye consisting of two N-ethylated benzothiazole groups linked by a pentamethine bridge. Spectroscopic analysis indicates dimerization of the dye in the presence of duplex DNA sequences consisting of alternating adenine/thymine (A/T) or inosine/ cytosine (I/C) residues, based on the following observations: (i) the absorption maximum shifts from 647 to 590 nm, (ii) exciton splitting is observed in the induced circular dichroism spectrum, and (iii) fluorescence from the dye is strongly quenched. Dimerization on I/C, but not G/C sequences indicates that the cyanine dimers insert into the minor groove, a conclusion that is supported by viscometric analysis. Spectroscopic studies with short synthetic oligonucleotide duplexes demonstrate that dimerization is highly cooperative: binding of one dimer greatly facilitates binding of a second dimer. For longer binding sites, this cooperativity leads to the formation of extended helical cyanine dye aggregates consisting of dimers aligned in an end-to-end fashion within the minor groove of the DNA. The DNA structure strictly controls the dimensions of the aggregate, permitting distinction between inter-and intradimer interactions.

UV−vis and CD spectroscopy reveal that a tricationic cyanine dye spontaneously assembles into a helical J-aggregate in the presence of a double-helical DNA template. The stability of the J-aggregate is strongly dependent on the dye concentration and DNA length in a manner that reflects a high degree of cooperativity in formation of the aggregate. Slight changes in environmental conditions such as temperature and ionic strength result in interconversion between J- and H-aggregates. The aggregate likely consists of dimeric units assembled in an offset, face-to-face orientation within the minor groove of the DNA template, analogous to an earlier report of H-aggregation on DNA by a related cyanine dye. A model is proposed that relates the two aggregate structures by translation of one monomer from a given dimer along the floor of the minor groove. This translation requires adjacent monomers to also translate, leading to the observed cooperativity.

Developed in the early 1990's, PNA has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity towards DNA and RNA, and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol (`miniPEG') unit at the γ-backbone transforms a randomly-folded PNA into a right-handed helix. Synthesis of optically pure R-MPγPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-L-serine. Once synthesized, R-MPγPNA oligomers are preorganized into a right-handed helix and hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have important implications for the future design and application of PNA in biology, biotechnology and medicine, as well as in other disciplines including drug discovery and molecular engineering.

Symmetrical cationic cyanine dyes assemble in cooperative fashion into helical supramolecular polymers using DNA as a template. The dyes assemble into cofacial dimers within the minor groove of the DNA and assembly of one dimer facilitates assembly of additional dimers directly adjacent to the first. Growth of the polymer ceases when the end of the DNA is reached or when the DNA sequence blocks dimerization of the dye. Thus, this process can be thought of as a supramolecular analogue of a chain polymerization. This Account describes how polymerization depends on the dye structure and DNA sequence and also summarizes the interesting optical properties exhibited by these chiral, helical materials.