Sequence-dependent structural variation in single-helical DNA. Proton NMR studies of d(T-A-T-A) and d(A-T-A-T) in aqueous solution.
The two deoxyribotetranucleoside triphosphates d(T-A-T-A) and d(A-T-A-T) were investigated in aqueous solution by one- and two-dimensional proton NMR at 300 and 500 MHz. It is demonstrated that both compounds occur predominantly in the single-helical form. Accurate coupling constants are obtained by computer simulation of several 500-MHz spectra. The data are interpreted in terms of N and S pseudorotational ranges. The geometry of the major S-type conformers displays a clear sequence dependence, as expressed by variation of the endocyclic backbone angle delta (C5'-C4'-C3'-O3'). A simple sum rule is proposed to predict delta variation in single-helical DNA fragments. Comparisons are made with other sequence-dependent geometries as observed in a double-helical B-DNA fragment in the crystalline state. Furthermore, one- and two-dimensional nuclear Overhauser effect (NOE) spectroscopy was carried out on d(T-A-T-A). An inventory is made of the observed intra- and inter-residue NOEs. The NOE data confirm the presence of a highly stacked single-helical conformation of d(T-A-T-A) in solution. No indications are found for the formation of a bulge-out structure as observed for analogous alternating purine-pyrimidine oligoribonucleotides.
D001483:Base Sequence; D055598:Chemical Phenomena; D002621:Chemistry; D004277:DNA, Single-Stranded; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D009994:Osmolar Concentration; D012996:Solutions
D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D012996:Solutions; C042640:deoxy-(thymidylyl-adenylyl-thymidylyl-adenylic acid); C042639:deoxy-(adenylyl-thymidylyl-adenylyl-thymidylic acid)