Oligonucleotide-polyamide hybrid molecules containing multiple pyrene residues exhibit significant excimer fluorescence

Article abstract of DOI:10.1021/ja00154a015

Oligonucleotide-polyamide hybrid molecules bearing multiple pyrene residues in the polyamide moiety were prepared. These molecules were designed to promote pyrene excimer formation and avoid intercalation of the label into the DNA duplex. Significant excimer fluorescence was observed, and this was shown to increase with the number of pyrene residues present. Hence, there is potential for further increasing of the fluorescence intensity by incorporation of additional label residues. Excimer fluorescence intensity was also shown to be sensitive to duplex formation. Fluorescence measurements and melting temperature studies gave no evidence of intercalation of the pyrene residues into duplex DNA. The hybridization properties of these hybrid molecules are similar to those of unmodified oligonucleotides. It seems, then, likely that pyrenylated oligonucleotide-polyamide hybrids may be useful as oligonucleotide probes.