Determination of High-Resolution, Sequence-Dependent DNA Duplex Structures in Solution

Abstract

There can be rather subtle structural variations in the DNA double helix which are sequence-dependent; but these subtle structural differences may direct protein, mutagen or drug recognition. These subtle variations demand detailed knowledge of the structure. This has not been easy to achieve, but the ability to determine an accurate, high-resolution structure of nearly any DNA double helix of length less than 15 base pairs (bp) is now possible if sufficient care and effort are expended. The structure of any molecule can be determined with a sufficient number of structural restraints, e.g., internuclear distances and bond torsion angles, in conjunction with holonomic constraints of bond lengths, bond angles, and steric limitations. NMR, in conjunction with appropriate computational algorithms, has become the method of choice for determination of the high-resolution solution structure of proteins, nucleic acids and complexes. Multidimensional NMR has the capability of yielding interpro- ton distances and bond torsion angles as experimental structural restraints (James and Basus, 1991; Oppenheimer and James, 1989; Wagner et al, 1992). These structural restraints per se do not constitute a structure. However, use of algorithms, such as distance geometry (DG) and restrained molecular dynamics (rMD), which search conformational space to define structures consistent with the experimental restraints will provide a “structure” or envelope of closely related structures. Structure determination via NMR is distinctly different from the situation with x-ray crystallographic determination of structure, where Fourier transformation of the diffraction pattern basically yields an atomic array (assuming the phase problem has been solved).

This work was supported by the National Institutes of Health via grants GM39247, GM41639, and RR01695.

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