title: Sequence dependence of DNA structure in solution.
abstract: Sequence-dependent structural variations in DNA can influence its binding by ligands and proteins. However, relatively little is known about sequence-structure relationship for arbitrary DNA sequences. The 1H two-dimensional NOESY data presented here for ten oligonucleotide duplexes show pronounced sequence-dependent changes in at least two types of internucleotide distances commonly used in sequential connectivity assignments, namely the H-6/H-8 to preceding (5') H-1' distance (S1) and the H-6/H-8 to preceding (5') H-2'' distance (S2). On the basis of these two measured distances, all dinucleotide steps can be divided into four different groups: Y-R, R-Y, R-R and Y-Y, where R is purine and Y is pyrimidine. These data suggest some rules for the variation in these distances along DNA duplexes. Correlations between these distances and helical parameters of DNA are discussed in comparison to well-resolved X-ray structures of B-type DNA.
authors.affiliation: Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Moscow Region.
authors.lastname: Fedoroff OYu
authors.forename: B R
authors.initials: BR
authors.lastname: Reid
authors.forename: V P
authors.initials: VP
authors.lastname: Chuprina
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D006859:Hydrogen; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012996:Solutions; D013329:Structure-Activity Relationship
chemical_list: D009838:Oligodeoxyribonucleotides; D012996:Solutions; D006859:Hydrogen; D004247:DNA