USE OF A PYRIMIDINE NUCLEOSIDE THAT FUNCTIONS AS A BIDENTATE HYDROGEN-BOND DONOR FOR THE RECOGNITION OF ISOLATED OR CONTIGUOUS G-C BASE-PAIRS BY OLIGONUCLEOTIDE-DIRECTED TRIPLEX FORMATION

Synthesis of the nucleoside building block of the 6-keto derivative of 2'-deoxy-5-methylcytidine (m(5ox)C) as an analog of an N-3-protonated cytosine derivative is described. A series of 15mer oligonucleotides containing either four or six m(5ox)C residues has been prepared by ch emical synthesis. Complexation of the 15 residue oligonucleotides with target 25mer duplexes results in DNA triplexes containing T-A-T and m (5ox)C-G-C base triplets. When the m(5)oxC-G-C base triplets are prese nt in sequence positions that alternate with TAT base triplets, DNA tr iplexes are formed with T-m values that are pH independent in the rang e 6.4-8.5, A 25mer DNA duplex containing a series of five contiguous G -C base pairs cannot be effectively targeted with either m(5)C or m(5o x)C in the third strand. In the former case charge-charge repulsion ef fects likely lead to destabilization of the complex, while in the latt er case ineffective base stacking may be to blame. However, if the m(5 )C and m(5ox)C residues are present in the third strand in alternate s equence positions, then DNA triplexes can be formed with contiguous G- C targets even at pH 8.0.