Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

Abstract

The solution structure of the self-complementary D N A hexamer 5'd(GCATGC)2 comprising the specific target site for the restriction endonuclease Sphl is investigated by using nuclear magnetic resonance spectroscopy and restrained molecular dynamics. All the nonexchangeable proton resonances are assigned sequentially, and from time-dependent nuclear Overhauser enhancement measurements a set of 158 approximate interproton distances are determined. These distances are used as the basis of a structure refinement using restrained molecular dynamics in which the interproton distances are incorporated into the total energy function of the system in the form of an effective potential term. Two restrained molecular dynamics simulations are carried out, starting from classical B-and A-DNA [atomic root mean square (rms) difference 3.3 A]. In both cases convergence is achieved to essentially identical structures satisfying the experimental restraints and having a root mean square difference of only 0.3 A between them, which is within the rms fluctuations of the atoms about their average positions. These results suggest that the restrained molecular dynamics structures represent reasonable approximations of the solution structure. The converged structures are of the B type and exhibit clear sequence-dependent variations of helical parameters, some of which follow Calladine's rules and can be attributed to the relief of interstrand purine-purine clash at adjacent base pairs. In addition, the converged restrained dynamics structures appear bent with a radius of curvature of approximately 20 A. This bending appears to be due almost entirely to the large positive base roll angles, particularly a t the Pyr-Pur steps. Further, the global and local helix axes are not coincident, and the global helix axis represents a superhelical axis which the bent DNA, when extended into an "infinite" helix by repeated translation and rotation, wraps around.

Sequence effects on local DNA topology.

“…Fig. 2 shows histograms for all these steps, including data taken from the literature (12)(13)(14)(15)17). Several trends and consistent patterns are observed.…”

Structure and conformation in solution of the parallel-stranded hybrid α-d(CGCAATTCGC)·β-d(GCGTTAAGCG) by high-resolution 2D NMR

“…Shifted sine bells were used to apodize the data in both dimensions. The baseline was corrected according to the procedure of Otting (Otting et al, 1986). COSY spectra with delays set to emphasize small-or long-range couplings (Bax and Freeman, 1982) were acquired with identical parameters but with a fixed delay during the evolution period and prior to acquisition.…”

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

“…In addition, while base pairing and stacking interactions can often be adequately defined from NOESY-derived distances (Nilges et al, 1987), detailed sequence-specific conformational information with regard to the deoxyribose phosphate backbone is often not available (van de Ven & Hilbers, 1988). 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).…”