Synthesis and properties of oligodeoxynucleotides incorporating 5-carboxydeoxycytidine

We synthesized oligodeoxynucleotide derivatives containing 5-carboxydeoxycytidine (1) as a new deoxynucleoside derivative having an anionic residue at the base part. The base pairing properties of the 5-carboxycytosine base were evaluated by use of ab initio calculations at the MP2/6-31G++(2d,p)//HF/6-31G(d) level. These calculations suggest that the Hoogsteen-type hydrogen bond in DNA triplex is less stable than that of the canonical C(+)-G pair and that the Watson-Crick base pair of this modified base with G is slightly more stable than the natural G-C base pair. These expectations were confirmed by T(m) experiments of duplexes and triplexes formed by hybridization of an oligodeoxynucleotide 14mer incorporating 5-carboxydeoxycytidine with ssDNA and dsDNA oligomers, respectively.