Nucleic acid structural parameters

Saenger W, Shakked Z, Sklenar H, Soumpasis DM, Tung C-S, Wang AH-J, Zhurkin VB. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 1989 208 787-791. 

M. S. Babcock, E. P. D. Pendault, and W. K. Olson,/ Mol. Biol., 237,125 (1994). Nucleic Acid Structure Analysis. Mathematics for Local Cartesian and Helical Structure Parameters That Are Truly Comparable Between Structures. 

Lavery R and H Sklenar 1988. The Definition of Generalized Helicoidal Parameters and of A> Curvature for Irregular Nucleic Acids. Journal of Biomolecular Structure and Dynamics 5 63-91. 

There are therefore four adjustable parameters per atom in the refinement (xy, yy, Zj, By). In the computer experiments we have carried out to test the assumptions of the nucleic acid refinement model we have generated sets of observed structure factors F (Q), from the Z-DNA molecular dynamics trajectories. The thermal averaging implicit in Equation III.3 is accomplished by averaging the atomic structure factors obtained from coordinate sets sampled along the molecular dynamics trajectories at each temperature ... 

Case58 investigated the effect of ring currents on NMR shielding constants by means of the DFT calculations. The studied rings included the ones commonly found in proteins and nucleic acids. The shielding constants were calculated for methane molecule placed in several positions relative to the ring. The calculations provided data needed to derive structural parameters from measured chemical shifts in proteins and nucleic acids. 

Since NMR data may reflect the conformational averaging resulting from a substantial flexibility of DNA/RNA fragments, the parameters of the ensemble of structures obtained by MD refinement and experimental NMR restraints can display internal inconsistency. James and coworkers developed a method to determine the family of structural conform-ers and their populations based on NMR data [83]. This approach applies multiple-copy refinement with floating weights, which better reflects the conformational dynamics of nucleic acids. 

Fluorescence is also a powerful tool for investigating the structure and dynamics of matter or living systems at a molecular or supramolecular level. Polymers, solutions of surfactants, solid surfaces, biological membranes, proteins, nucleic acids and living cells are well-known examples of systems in which estimates of local parameters such as polarity, fluidity, order, molecular mobility and electrical potential is possible by means of fluorescent molecules playing the role of probes. The latter can be intrinsic or introduced on purpose. The high sensitivity of fluo-rimetric methods in conjunction with the specificity of the response of probes to their microenvironment contribute towards the success of this approach. Another factor is the ability of probes to provide information on dynamics of fast phenomena and/or the structural parameters of the system under study. 

The database would present all known protein sequences and structures nucleic acid sequences exosporium structure metric parameters such as mean density and size spectral properties such as the fluorescence, fluorescence... 

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