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Nucleic Acids Research, 1994, Vol. 22, No. 13 2637-2642
© 1994

RNA

Sequence specificity of the non-natural pyrido[2,3-d]pyrimidine nucleoside in triple helix formation

Andrea B. Staubli and Peter B. Dervan*

The Beckman Institute, California Institute of Technology Pasadena, CA 91125, USA

*To whom correspondence should be addressed

Received March 4, 1994. Revised May 17, 1994. Accepted May 17, 1994.

The non-natural pyrido[2,3-d]pyrimidine nucleoside F, which pairs preferentially with guanine (G) and adenine (A) within double-helical DNA, recognizes with high selectivity AT base pairs within triple-helical complexes. These observations suggest that F may exist in different tautomeric forms within double-helical and triple-helical complexes. Analysis of the base stacking properties of this extended ring system using two oligodeoxyribonucleotides containing terminal thymines and/or pyrido[2,3-d]pyrimidines bound to adjacent sites showed a decrease in free energy of binding in a triple-helical complex in the order (5' – 3') TT > FT > TF > FF.


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