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Nucleic Acids Research, 1995, Vol. 23, No. 11 1936-1941
© 1995

MOLECULAR BIOLOGY

Overcoming potassium-mediated triplex inhibition

Wendy M. Olivas and L. James Maher, III*

Eppley Institute for Research in Cancer and Allied Diseases and the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center 600 South 42nd Street, Omaha, NE 68198-6805, USA

* To whom correspondence should be addressed

Received February 21, 1995. Revised March 23, 1995. Accepted March 23, 1995.

Sequence-specific duplex DNA recognition by oligonucleotlde-dlrected triple helix formation Is a possible approach to In vivo gene inhibition. However, triple helix formation involving guanlne-rich oligo-nucleotides is Inhibited by physiological Ions, particularly K+, most likely due to oligonucleotide aggregation via guanine quartets. Three ollgodeoxynucleotlde (ODN) derivatives were tested for their ability to resist guanine quartet-mediated aggregation, yet form stable triplexes. Electrophoretic mobility shift and dimethyl sulfate footprinting assays were used to analyze the formation of triplexes Involving these oligonucleotide derivatives. In the absence of K+, all ODNs had similar binding affinities for the duplex target Triplexes involving a 14mer ODN derivative containing 7-deazaxanthine substituted for three thymine bases or an 18mer ODN containing two additional thymlnes on both the 5' and 3' termini were abolished by 50 mM K+. Remarkably, triplexes Involving an ODN derivative containing four 6-thloguanine bases substituted for guanine resisted K+ inhibition up to 200 mM. We hypothesize that the Increased radius and decreased electronegativity of sulfur in the 6-posltlon of guanine destabilize potential guanine quartets. These results improve the prospects for creating ODNs that might serve as specific and efficient gene repressors In vivo.


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