title: Conformational analysis of the single-helical DNA fragment d(T-A-A-T) in aqueous solution. The combined use of NMR proton chemical shifts and coupling constants obtained at 300 MHz and 500 MHz.
abstract: Proton NMR studies at 300 MHz and 500 MHz were carried out on the tetranucleoside trisphosphate d(T-A-A-T). The thermodynamics of the three stacking interactions, derived from chemical shift versus temperature profiles, were used to extrapolate the observed coupling constants, measured at a range of temperatures, to values appropriate to the fully stacked forms of the molecule. The data were interpreted in terms of N and S pseudorotational ranges [ Altona , C. and Sundaralingham , M. (1972) J. Am. Chem. Soc. 94, 8205-8212]. It is shown that the stacked state of the molecule cannot be described by one conformer, but consists of one major structure (60%) in which all sugar rings have S-type geometry and another structure (30%) in which residue dT(4) has an N-type sugar. The remainder of the stacked states consists of one or more conformers with two or three sugar residues in the N-type pseudorotational range. Detailed geometrical models are proposed for the major stacked conformers encountered in aqueous solution.
mesh_terms: D004277:DNA, Single-Stranded; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D011522:Protons; D012996:Solutions; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D011522:Protons; D012996:Solutions; C041463:deoxy-(thymidylyl-adenylyl-adenylyl-thymidylic acid)