Dynamic properties of DNA

The static and dynamic properties of DNA have been studied by the temperature-dependent Stokes shift of the intercalated dye acridine orange [192] and by molecular dynamic simulation [193]. A large part of the Stokes shift of the intercalated dye in DNA is found to be frozen out at low temperature, as in the solution. Thus, the interior of DNA is found to have the diffusive and viscous dynamic characteristics of a fluid rather than the purely vibrational characteristics of a crystal. The results suggest that the probe dye molecule senses the movement of DNA and at high viscosity the rate of DNA motion is limited by the rate of solvent motion. 

This is referred to as end effects that must be taken into account in describing colligative and dynamical properties of DNA. 

For the analysis of the dynamical properties of the water and ions, the simulation cell is divided into eight subshells of thickness 3.0A and of height equal to the height of one turn of DNA. The dynamical properties, such as diffusion coefficients and velocity autocorrelation functions, of the water molecules and the ions are computed in various shells. From the study of the dipole orientational correlation function... 

Physical Properties of DNA Affect the Nucleosome Stability and Dynamics... 

Matsumoto, A. and Go, N. (1999) Dynamic properties of double-stranded DNA by normal mode analysis. J. Chem. Phys. 110, 11070-11075. 

Chirico, G. and Langowski, J. (1992) Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm. Macromolecules 25, 769-775. 

The year 2003 is the tenth anniversary of the first Femtochemistry Conference and the fiftieth anniversary of Watson and Crick s celebrated discovery of the DNA double helix [1], Remarkable progress has been made in both fields femtosecond spectroscopy has made decisive contributions to Chemistry and Biology, and advances in the elucidation of static nucleic acid structures have profoundly transformed the biosciences. However, much less is known about the dynamical properties of these complex macromolecules. This is especially true of the dynamics of the excited electronic states, including their evolution toward the photoproducts that are the end result of DNA photodamage [2],... 

The comparison between the several purine species discussed above suggests a fine tuning of the structure/tautomerism on the excited state electronic properties. Because several excited states of various polarisabilities are involved, solvation is expected to play a role on this dynamics. Complexes of DNA bases with various solvent or with other bases, easily isolated in the gas phase, are an ideal laboratory... 

In order to delineate the structural and dynamic properties of PAH diol epoxide-DNA adducts and their correlations to DNA repair susceptibility, a powerful array of complementary methods have been employed (e.g., [78]) ... 

Abstract In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids. 

Harris, S.A., Sands, Z.A., and Laughton, C.A., 2005. Molecular dynamics Simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys. J. 88 1684-1691. 

The exciting properties of nucleic acids have opened new scenarios in the field of nanotechnology and sensor development. In particular, the dynamic properties of nucleic acids and the thermally indnced sequence-dependent separation of double-stranded DNA allow the utilization of nucleic acids with machinelike functions that can perform different motions or act as switches and motors (Beissenhirtz and Willner, 2006). The same principles have been applied for the development of aptamer-based machines, which can amplify the recognition event between the aptamer and the substrate through operation of the machine (Shlyahovsky et al., 2007). A scheme for the assay developed for cocaine is reported in Figure 8.10. 

S.K. Sinha and S. Bandyopadhyay, Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J. Chem. Phys., 135 (2011), 135101. 

DNA is a highly charged, semi-flexible polyelectrol)Ae. In eukaiyotic cells, DNA chains are packed inside the microscopic volume of the nucleus in an ordered, yet dynamical way. To overcome the electrostatic repulsion that hinders compaction, DNA molecules associate with a variety of counterions and proteins to condensate into a hierarchical and tunable architecture named chromatin. Besides DNA condensation, chromatin also plays a key role in gene regulation by making DNA accessible for transcription in a dynamical and specific way. Consequently, understanding the physicochemical properties of DNA chains at the molecular and mesoscopic scales is a required step to elucidate how cells regulate... 

Moir, R. D., Montag-Lowy, M., and Goldman, R. D. (1994). Dynamic properties of nuclear lamins Lamin B is associated with sites of DNA replication. J. Cell BioL 125,1201-1212. 

Functional analyses have suggested that lamins are involved in a number of biological processes, including DNA replication, chromatin organization, cellular differentiation during development, nuclear envelope reassembly following mitosis, and the structural stabilization of the nuclear membrane during interphase (for review, see Moir et al., 1995). Here we describe two methods that we have successfully applied in our laboratories and that have allowed us to analyze functional and dynamic properties of lamins in vivo by the microinjection of cultured cells with either affinity-purified lamin antibodies or with fluorescently labeled lamins. 

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