title: Synthesis and properties of a new oligonucleotide analogue containing an internucleotide squaryl amide linkage.
abstract: We report here the synthesis and properties of a new oligonucleotide analogue (5'-CGCATsqTAGCC-3') containing a squaryl group in place of the fifth phosphate group from the 5'-terminus. The modified thymidine dimer building unit was synthesized by use of 5'-amino-5'-deoxythymidine and a 3'-amino-3'-deoxythymidine derivative. This building unit was phosphitylated and incorporated into the oligonucleotide by the phosphoramidite method. The hybridization ability of this modified oligomer with the complementary oligonucleotide was studied in detail by using Tm experiments and CD spectroscopy as well as computer simulations. These results suggest that this modified duplex has a unique bend conformation.
authors.affiliation: Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Sato
authors.forename: K
authors.initials: K
authors.lastname: Seio
authors.forename: M
authors.initials: M
authors.lastname: Sekine
mesh_terms: D000577:Amides / Q000737:chemistry; D001483:Base Sequence; D002942:Circular Dichroism; D019295:Computational Biology; D003198:Computer Simulation; D003503:Cyclobutanes / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry; D011740:Pyrimidine Dimers / Q000138:chemical synthesis / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000577:Amides; D003503:Cyclobutanes; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D011740:Pyrimidine Dimers; C434331:phosphoramidite; C030042:squaric acid