3] Distance geometry in NMR determination of solution conformation of nucleic acids: Application of d-ACCGTTAACGGT

Abstract

Publisher Summary This chapter discusses distance geometry in nuclear magnetic resonance (NMR) determination of solution conformation of nucleic acids. Quantitative analysis of two-dimensional (2D) nuclear Overhauser effect (NOE)-correlated and J-correlated spectra for the extraction of structural parameters and interpretation of these parameters, in terms of three-dimensional (3D) structures, constitute the two most important elements of solution structure determination of nucleic acids by NMR spectroscopy. The cross-peak fine structures in J-correlated spectra carry information, regarding J-coupling constants, that are best extracted by iterative simulation of the fine structure patterns. The derived J-values can then be translated into torsion-angle information, using Karplus-type relations. With regard to interproton distances, the elongated nature of the DNA molecule poses some problems. There are six backbone torsion angles, sugar geometry, and a glycosidic torsion angle for each nucleotide unit and all of these influences the interproton distances. The conformational search to fit the observed interproton distances, therefore, necessarily must take place in a multidimensional torsion angle space and the number of distances available that are mostly intranucleotide or between adjacent nucleotides only.