Biomolecular Structure - Structure Determination

Structure Determination

Structure probing is the process by which biochemical techniques are used to determine biomolecular structure. This analysis can be used to define the patterns which can infer the molecular structure, experimental analysis of molecular structure and function, and further understanding on development of smaller molecules for further biological research. Structure probing analysis can be done through many different methods, which include chemical probing, hydroxyl radical probing, nucleotide analog interference mapping (NAIM), and in-line probing.

DNA structures can be determined using either nuclear magnetic resonance spectroscopy or X-ray crystallography. The first published reports of A-DNA X-ray diffraction patterns-- and also B-DNA—employed analyses based on Patterson transforms that provided only a limited amount of structural information for oriented fibers of DNA isolated from calf thymus. An alternate analysis was then proposed by Wilkins et al. in 1953 for B-DNA X-ray diffraction/scattering patterns of hydrated, bacterial oriented DNA fibers and trout sperm heads in terms of squares of Bessel functions. Although the `B-DNA form' is most common under the conditions found in cells, it is not a well-defined conformation but a family or fuzzy set of DNA-conformations that occur at the high hydration levels present in a wide variety of living cells. Their corresponding X-ray diffraction & scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder (>20%), and concomitantly the structure is not tractable using only the standard analysis.

On the other hand, the standard analysis, involving only Fourier transforms of Bessel functions and DNA molecular models, is still routinely employed for the analysis of A-DNA and Z-DNA X-ray diffraction patterns.