Nucleic acids, solvent relaxation

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Selected entries from Methods in Enzymology [vol, page(s)] Anisotropy effects, 261, 427-430 determination by dynamic laser light scattering (quasi-elastic light scattering), 261, 432-433 determination for nucleic acids by NMR [accuracy, 261, 432-433 algorithms, 261, 11-13, 425, 430 carbon-13 relaxation, 261, 11-12, 422-426, 431, 434-435 cross-relaxation rates, 261,419-422, 435 error sources, 261, 430-432 phosphorus-31 relaxation, 261, 426-427, 431 proton relaxation, 261,51,418-422 relaxation matrix calculations, 261,12] deuterium solvent viscosity effects, 261,433 effect... 

So far, a large number of low-molar-mass systems have been studied by ultrafast fluorescence techniques in sub-nanosecond time regions [35-39]. Recently, a relatively slow (nanosecond) relaxation process proceeding in mixed low-molar-mass solvents, consisting in redistribution of components of the solvent mixture in the solvate shell of the fluorophore upon the excitation, has also been reported [40-43, 46, 47]. However, an important part of experimental studies is still concerned with relatively slowly relaxing biological systems, such as lipid membranes [48-50], proteins [51, 52], nucleic acids [53], and also colloidal [54] and polymer systems [55-57]. 

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