title: Oligonucleotide model with non-identical complementary strands for chromatographic studies of structure-dependent photosusceptibility.
abstract: In a previous work, we used a quantitative chromatographic analysis of two self-complementary oligonucleotides to correlate the conformational differences between the oligonucleotide duplexes and photochemical susceptibilities of constituent oligomers. In this work we describe a new double-stranded oligonucleotide model with non-identical complementary strands. To separately analyze photoproducts in two strands, one of them is used in a partially protected form (the hydrophobic 5'-dimethoxytrityl group uncleaved). Using a reversed-phase column, the oligomers and products of their UV photomodification are separated into two groups of peaks. This facilitates the quantitation of photoproducts in each of the complementary strands. Three 15-mer oligonucleotides, 5'-TTTTTAT-TAAATATA-3' (F5), 5'-AAAAATAATTTATAT-3' (F6) and 5'-TATATTTAATAAAAA-3' (F7) form the parallel-stranded (ps) F5.F6 and the ordinary antiparallel-stranded (aps) F5.F7 duplexes. For these particular sequences, the rate of cyclobutane thymine dimer formation in the ps DNA has been estimated as ca. 1.5-2 times that in the ordinary aps DNA.
authors.affiliation: Department of Biology, George Mason University, Fairfax, VA 22030.
authors.forename: V N
authors.initials: VN
authors.lastname: Potaman
authors.forename: V N
authors.initials: VN
authors.lastname: Soyfer
mesh_terms: D001483:Base Sequence; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000528:radiation effects; D010777:Photochemistry; D014466:Ultraviolet Rays
chemical_list: D009841:Oligonucleotides