title: Synthesis and properties of oligodeoxynucleotides containing 5-carboxy-2'-deoxycytidines.
abstract: 5-Carboxy-2'-deoxycytidine (dC(COO-)) was synthesized as an anion-carrier to seek a new possibility of modified oligodeoxynucleotides capable of stabilization of duplexes and triplexes. The base pairing properties of this compound were evaluated by use of ab initio calculations. These calculations suggest that the Hoogsteen-type base pair of dC(COO-)-G is less stable than that of the canonical C+-G pair and the Watson-Crick-type base pair of dC(COO-)-G is slightly more stable than the natural G-C base pair. The modified cytosine base showed a basicity similar to that of cytosine (pKa 4.2). It turned out that oligodeoxynucleotides 13mer and 14mer incorporating dC(COO-) could form duplexes with the complementary DNA oligomer, which were more stable than the unmodified duplex. In contrast, it formed a relatively unstable triplex with the target ds DNA.
authors.affiliation: Department of Life Science, Tokyo Institute of Technology, CREST, JST, Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Sumino
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ohkubo
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Taguchi
authors.forename: Kohji
authors.initials: K
authors.lastname: Seio
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
mesh_terms: D004247:DNA / Q000737:chemistry / Q000235:genetics; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D003841:Deoxycytidine; D004247:DNA