David A. Pearlman

Conformational studies of nucleic acids. I. A rapid and direct method for generating furanose coordinates from the pseudorotation angle.

The greatest difficulty in modeling a nucleic acid is generating the coordinates of its furanoses. This difficulty arises from constraints imposed by the closed ring geometries of these sugars. We have developed a new method for modeling these furanose rings. Using this method, the coordinates of a sugar can be obtained quickly and unambiguously for any point on the pseudorotational pathway from one parameter: the phase angle of pseudorotation P. The significant difference between this and previous sugar modeling schemes is that here the endocyclic bond lengths of the five-membered sugar ring are allowed to vary a small amount according to simple, explicit, and experimentally reasonable analytic functions of P. The coefficients of these functions follow from the empirical behavior of the endocyclic bond angles and from geometrical constraints due to ring closure. The ability to model the sugars directly from one parameter greatly facilitates carrying out the global conformational studies on nucleic acid constituents which will be attempted in subsequent papers of this series.

Refinement of Three-Dimensional Protein and DNA Structures in Solution from NMR Data

Two-dimensional NMR, in particular two-dimensional nuclear Overhauser effect (2D NOE) spectra, when used in conjunction with distance geometry and energy refinement calculations can be used to determine the high-resolution structure of DNA fragments and small proteins. To understand functional interactions of proteins and nucleic acids, it is important to know their solution structures to high-resolution. Problems addressed with DNA structure and with protein structure studies are often of a different nature. In general, we are interested in fairly subtle structural changes in the DNA helix which are sequence-dependent and, consequently, guide protein, mutagen or drug recognition. These subtle variations demand detailed knowledge of the structure and, therefore, accurate internuclear distance and perhaps torsion angle constraints. But one can define a protein tertiary structure with moderate accuracy using distance geometry or restrained molecular dynamics calculations without accurately determining interproton distances; a qualitative assessment of 2D NOE intensities is often all that is needed. However, in proteins possessing less common structural features, it may be especially valuable to have additional structural constraints and more accurate constraints for use with the computational techniques. And, even more importantly, we will want better defined structures at ligand binding sites (with and without ligand bound).

The Conformational Effects of UV Induced Damage on DNA

Energy minimization techniques are used in conjunction with the results of small molecule crystallographic studies on relevant compounds to propose structural models for photodamaged DNAs. Specifically, we present models both for a DNA molecule containing a psoralen photo-crosslink and for a DNA molecule containing a thymine photodimer. In both models, significant distortions of the nucleic acid helix are observed, including kinking and unwinding at the damage site and numerous changes in the backbone torsion angles relative to their standard conformations.

The conformations and energetics of photodamaged DNA

Energy minimization techniques are used in conjunction with the results of small molecule crystallographic studies on relevant compounds to propose structural models for photodamaged DNAs. Specifically, we present models both for a DNA molecule containing a psoralen photo-crosslink and for a DNA molecule containing a thymine photodimer. In both models, significant distortions of the nucleic acid helix are observed, including kinking and unwinding at the damage site and numerous changes in the backbone torsion angles relative to their standard conformations. Both the torsion angle geometries and the energetics of the models are presented in detail.