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.
Sumino
Masanori
M
Department of Life Science, Tokyo Institute of Technology, Japan.
Itaru
Okamoto
O
Ohkubo
Akihiro
A
Taguchi
Haruhiko
H
Seio
Kohji
K
Sekine
Mitsuo
M
D020029:Base Pairing; D004247:DNA / Q000737:chemistry; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*
C528358:5-carboxydeoxycytidine; D009838:Oligodeoxyribonucleotides; C051802:triplex DNA; D003841:Deoxycytidine; D004247:DNA