title: The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick.
abstract: Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5'-d-[(A)10TAATTTTAAATATTT]-3' (D1) and 5'-d[(T)10ATTAAAATTTATAAA]-3' (D2) in H2O and D2O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5'-d(AAATATTTAAAATTA-(T)10]-3' (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly[d(A)].poly[d(T)] and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due to changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region (1600-1700 cm-1) implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent wtih formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogenous sequence and high A,T content are observed at 843 and 1092 cm-1 in the spectra of the parallel-stranded duplex. The 843-cm-1 band is due to the presence of a sizable population of furanose rings in the C2'-endo conformation. Significant changes observed in the regions from 1150 to 1250 cm-1 and from 1340 to 1400 cm-1 in the spectra of the parallel-stranded duplex are attributed to variations in backbone torsional and glycosidic angles and base stacking.
authors.affiliation: Department of Chemistry, University of Oregon, Eugene 97403.
authors.forename: C
authors.initials: C
authors.lastname: Otto
authors.forename: G A
authors.initials: GA
authors.lastname: Thomas
authors.forename: K
authors.initials: K
authors.lastname: Rippe
authors.forename: T M
authors.initials: TM
authors.lastname: Jovin
authors.forename: W L
authors.initials: WL
authors.lastname: Peticolas
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA; D006859:Hydrogen / Q000737:chemistry*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013059:Spectrum Analysis, Raman
chemical_list: D006859:Hydrogen; D004247:DNA