Nucleic acids dynamics

Fluorescence Studies of Nucleic Acids Dynamics, Rigidities, and Structures... 

Miller, T. R., et ah (1995). A probe for sequence-dependent nucleic acid dynamics. J. Am. 

Detailed characterization of protein/nucleic acid dynamics... 

Schurr, J. M., Fujimoto. B. S., Wu, P., and Song, L., 1992, Fluorescence studies of nucleic acids Dynamics, rigidities, and structures, in Topics in Fluorescence Spectroscopy, Volume 3. Biochemical Applications, J. R. Lakowicz (ed.). Plenum Press, New York, pp. 137-229. 

Nucleic acids have two kinds of pentoses 2 -deoxy-D-ribose and D-ribose. Both of them are present in their furanose form in nucleic acids (Fig. 16.3). These sugar residues can easily bend and twist into different conformations thus making nucleic acids dynamic in structure. Depending on the kind of pentose, nucleotides are subclassified into deoxyribonucleotides and ribonucleotides (Fig. 16.4). Ribonucleotides might contain A, G, C, and U while deoxyribonucleotides contain A, G, C, and T. The bases of DNA and RNA are important for the structure and e distribution of nucleic acids. 

Nucleic acids Dynamics and structure, hybridization assays, DNA polymerase reactions, detection limits about picomolar level Sensitivity is enhanced combined with fluorescence resonance energy transfer... 

Li, HT, Ren, XJ, Iflng, LM, Balasubramanian, S, and Klenerman, D, Measuring single-molecule nucleic acid dynamics in solution by two-color filtered ratiometric fluorescence correlation spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 101 (2004) 14425-14430. 

Relaxation Behavior of Nucleic Acids Dynamics and Structure... 

J. McCammon and S. Harvey, Dynamics of proteins and nucleic acids, Cambridge University Press, Cambridge, U.K., 1987. 

McCammon and Harvey, 1987] McCammon, J. A., and Harvey, S. C. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, 1987. 

Volkov, S.N. Conformational transitions and the mechanism of transmission of long-range effects in DNA. Preprint ITP-88-12E, Kiev (1988) 22 Krumhansl, J.A., Alexander, D.M. Nonlinear dynamics and conformational exitations in biomolecular materials. In Structure and dynamics nucleic acids and proteins. (Clementi, E., Sarma, R.H., eds) Adenine Press, New York (1983) 61-80... 

Tolstorukov, M.Ye., Gatash, S.V., Maleev, V.Ya. Self-organization and non-iinear dynamics of nucleic acid-water system. Special Issue of Int. J. Bif. Chaos (in press)... 

J M 1992. Molecular Dynamics Simulation. Elementary Methods. New York, John Wiley Sons, ammon J A and S C Harvey 1987. Dynamics of Proteins and Nucleic Acids. Cambridge, Cambridge Jniversity Press. 

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. 

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

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