Sequence dependence of DNA structure in solution.

Fedoroff OYu; B R Reid; V P Chuprina

doi:10.1016/s0022-2836(05)80036-1

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Sequence dependence of DNA structure in solution.

Fedoroff OYu·B R Reid·V P Chuprina

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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.

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Base Sequence DNA Hydrogen Magnetic Resonance Spectroscopy Molecular Sequence Data Nucleic Acid Conformation Oligodeoxyribonucleotides Solutions Structure-Activity Relationship Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

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Fedoroff OYu, B R Reid, V P Chuprina. 1994-01-07. Sequence dependence of DNA structure in solution.. https://doi.org/10.1016/s0022-2836(05)80036-1

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