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Nucleic Acids Research, Vol 27, Issue 20 4034-4039, Copyright © 1999 by Oxford University Press

ARTICLES

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

JG Hacia, EA Novotny, RA Mayer, SA Woski, MA Ashlock and FS Collins
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

A series of dye-labeled oligonucleotide probes containing base and sugar modifications were tested for the ability to detect telomeric repeat sequences in FISH assays. These modified oligonucleotides, all 18 nt in length, were complementary to either the cytidine-rich (C(3)TA(2))(n)or guanosine-rich (T(2)AG(3))(n)telomere target sequences. Oligonucleotides were modified to either increase target affinity by enhancing duplex stability [2'-OMe ribose sugars and 5-(1- propynyl)pyrimidine residues] or inhibit the formation of inter- or intramolecular structures (7-deazaguanosine and 6-thioguanosine 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 in a specific manner. Such probes could be used as an alternative to peptide nucleic acids for investigating the dynamics of telomere length and maintenance. In principle, these relatively inexpensive and readily synthesized modified oligonucleotides could be used for other FISH-related assays.
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