Two-dimensional proton and phosphorus-31 NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex

Abstract

Assignment of the 1H and 31P NMR spectra of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d(CGCAGAATTCGCG)2, has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The downfield 31P resonance previously noted by Patel et al. (1982) has been assigned by both 17O labeling of the phosphate as well as a pure absorption phase constant-time heteronuclear 31P-1H correlated spectrum and has been associated with the phosphate on the 3' side of the extrahelical adenosine. JH3'-P coupling constants for each of the phosphates of the tridecamer were obtained from the 1H-31P J-resolved selective proton-flip 2D spectrum. By use of a modified Karplus relationship the C4-C3'-O3-P torsional angles (epsilon) were obtained. There exists a good linear correlation between 31P chemical shifts and the epsilon torsional angle. The 31P chemical shifts and epsilon torsional angles follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. Because the extrahelical adenosine significantly distorts the deoxyribose phosphate backbone conformation even several bases distant from the extrahelical adenosine, 31P chemical shifts show complex site- and sequence-specific variations. Modeling and NOESY distance-restrained energy minimization and restrained molecular dynamics suggest that the extrahelical adenosine stacks into the duplex. However, a minor conformation is also observed in the 1H NMR, which could be associated with a structure in which the extrahelical adenosine loops out into solution.

Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on phosphorus-31 NMR spectra

“…While X-ray crystallography has provided much of our understanding of these DNA structural variations, increasingly, high-resolution NMR (particularly 'H/IH NOESY) has also begun to provide detailed three-dimensional structural information on duplex oligonucleotides (Broido et al, 1984;Feigon et al, 1983;Frechet et al, 1983;Hare et al, 1983;Kearns, 1984;Scheek et al, 1984;Schroeder et al, 1986Schroeder et al, , 1987van de Ven & Hilbers, 1988). Importantly, NMR experiments have suggested that the duplex conformation in solution (Assa-Munt & Kearns, 1984;Clore et al, 1985;Gorenstein et al, 1988;Nikonowicz et al, 1989;Patel et al, 1987;Rinkel et al, 1987) may not be identical with the static picture provided by X-ray diffraction in the crystal state. This has raised the question whether some of the sequence-specific structural variations observed in the X-ray crystallographic studies are the result of less profound crystal packing forces.…”

“…Recently we have attempted to utilize 31P N M R to define sequence-specific variations in the backbone conformation of oligonucleotides Nikonowicz et al, 1989;Schroeder et al, 1989). Variations of 31P chemical shifts of individual phosphates in duplex oligonucleotides have been suggested to be attributable to torsional angle changes in the deoxyribose phosphate backbone.…”

Structure determination of [d(ATATATAUAT)]2 via two‐dimensional NOE spectroscopy and molecular dynamics calculations

“…Twodimensional (2D) NMR, in particular 2D NOE spectra, when used in conjunction with energy-refinement calculations, can be used to determine the high-resolution structure of DNA fragments where subtle changes in structure can be detected (Zhou et al, 1987;Nilges et al, 1987;Nikonowicz et al, 1989;Pieters et al, 1990). A major obstacle to accurately depicting a structure using this methodology is the problem of extracting a large number of accurate interproton distances from the 2D NOE cross-peak intensities.…”

TWo-Dimensional1H and31P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

“…In general there is a slight decrease in the R factor during the refinement cycles (decreasing from approximately 0.4 to 0.3). We believe our %RMSvol factor better represents the quality of the NMR refinement than the R factor (3,20,28,62). The latter heavily weighs the large NOESY volumes.…”

“…A "crankshaft" motion interconverts BI and BII conformations with only a modest movement of the phosphate. It is largely this variation in ε and ζ (as well as 8,3,36,39,62,68) that allows the sugar phosphate backbone to "stretch" or "contract" to allow for variations in the local structure of B-DNA.…”