Sequence specificity of the non-natural pyrido[2,3-d]pyrimidine nucleoside in triple helix formation.
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.
Staubli
A B
AB
Beckman Institute, California Institute of Technology, Pasadena 91125.
Dervan
P B
PB
D001482:Base Composition; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000737:chemistry*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines / Q000737:chemistry*
D009705:Nucleosides; D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines; D004247:DNA