Design of modified oligodeoxyribonucleotide probes to detect telomere repeat sequences in FISH assays

A series of dye-labeled oligonucleotide probes containing base and sugar mo difications were tested for the ability to detect telomeric repeat sequence s in FISH assays. These modified oligonucleotides, all 18 nt in length, wer e complementary to either the cytidine-rich (C(3)TA(2))(n) or guanosine-ric h (T(2)AG(3))(n) telomere target sequences, Oligonucleotides were modified to either increase target affinity by enhancing duplex stability [2'-OMe ri bose sugars and 5-(1-propynyl)pyrimidine residues] or inhibit the formation of inter- or intramolecular structures (7-deazaguanosine and 6-thioguanosi ne residues), which might interfere with binding to the target. Several dye -labeled oligonucleotide probes were found that could effectively stain the telomeric repeat sequences of either cytidine- or guanosine-rich strands i n a specific manner. Such probes could be used as an alternative to peptide nucleic acids for investigating the dynamics of telomere length and mainte nance. In principle, these relatively inexpensive and readily synthesized m odified oligonucleotides could be used for other FISH-related assays.