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

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Abstract
Synthesis of the nucleoside building block of the 6-keto derivative of 2′-deoxy-5-methylcytidine (m5oxC) as an analog of an N3-protonated cytosine derivative is described. A series of 15mer oligonucleotides containing either four or six m5oxC residues has been prepared by chemical synthesis. Complexation of the 15 residue oligonucleotides with target 25mer duplexes results in DNA triplexes containing T-A-T and m5oxC-G-C base triplets. When the m5oxC-G-C base triplets are present in sequence positions that alternate with TAT base triplets, DNA triplexes are formed with Tm values that are pH independent in the range 6.4–8.5. A 25mer DNA duplex containing a series of five contiguous G-C base pairs cannot be effectively targeted with either m5C or m5oxC in the third strand. In the former case charge-charge repulsion effects likely lead to destabilization of the complex, while in the latter case ineffective base stacking may be to blame. However, if the m5C and m5oxC residues are present in the third strand in alternate sequence positions, then DNA triplexes can be formed with contiguous G-C targets even at pH 8.0.