Dynamics DNA

G. Ramachandran and T. Schlick. Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations. Phys. Rev. E, 51 6188-6203, 1995. 

DNA CT also permits chemistry at a distance. Oxidative DNA damage and thymine dimer repair can proceed in a DNA-mediated reaction initiated from a remote site. These reactions too are sensitive to intervening DNA dynamical structure, and such structures can serve to modulate DNA CT chemistry. The sensitivity of DNA CT to base pair stacking also provides the basis for the design of new DNA diagnostics, tools to detect mutations in DNA and to probe protein-DNA interactions. 

Overall, it can be envisioned that the Py-G group 47 represents an important label for the time-resolved studies of DNA dynamics and stacking interaction [123] and could be applied especially for assays in which conformational changes or base-flipping processes are essential in observation, such as in the investigation of DNA-protein complexes with DNA repair proteins. 

The reader is referred to other reviews for detailed discussions of the electronic states and luminescence of nucleic acids and their constituents/0 fluorescence correlation spectroscopy/2) spectroscopy of dye/DNA complexes/0 and ethidium fluorescence assays/4,0 A brief review of early work on DNA dynamics as well as a review of tRNA kinetics and dynamics have also appeared. The diverse and voluminous literature on the use of fluorescence techniques to assay the binding of proteins and antitumor drugs to nucleic acids and on the use of fluorescent DNA/dye complexes in cytometry and cytochemistry lies entirely outside the scope of this chapter. 

Sequence 3 examines chain-end effects on DNA dynamics. It contains the coumarin probe one base pair removed from the end of the sequence. This chain end sequence has the same base pair sequence as the normal sequence, but with entire sequence, including the coumarin, shifted towards one terminus. The Stokes shifts from the two sequences are displayed on a relative Stokes shift scale in Fig. 2b. 

Yoshikawa, K. and Matsuzawa, Y. (1995) Discrete phase transition of giant DNA Dynamics of globule formation from a single molecular chain. Physica D, 84, 220-227. 

Hustedt, E. J., et al. (1993). Motions of short DNA duplexes An analysis of DNA dynamics using an EPR-active probe. Biochemistry 32, 1774-1787. 

Liang, Z., et al. (2000). An electron spin resonance study of DNA dynamics using the slowly relaxing local structure model. J. Phys. Chem. 104, 5372-5381. 

Kuchta K, Barszcz D, Grzesiuk E et al (2012) DNAtraffic—a new database for systems biology of DNA dynamics during the cell life. Nucleic Acids Res 40 D1235-D1240... 

O Neill, M.A. and Barton, J.K. (2004) Sequence dependant DNA dynamics the regulator of DNA-mediated charge transport, in Charge Transfer in DNA From Mechanisms to Application (ed. 

Blagoev, K.B., Alexandrov, B.S., Goodwin, E.H., and Bishop, A.R. (2006) Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition. DNA Repair, 5, 863-867. 

However, time-resolved optical spectroscopy is perhaps the premier method for learning about the dynamics of a complex system, especially on nanosecond or picosecond time scales. Some DNA dynamics data from NMR spectroscopy are presented in Table 4.3. Time-resolved emission decays, time-resolved fluorescence anisotropy, and time-resolved Stokes shifts measurements of probe molecules in DNA have been described (and see below) and fast components in the time decays assigned to various DNA motions. The dynamics as a function of sequence are incompletely mapped and provide an exciting area for future investigations. 

Thus far, the photophysical probe measurements of DNA dynamics agree on several general points (1) DNA has very fast (subnanosecond) motions, and (2) at least some of these motions are temperature dependent. While examination of different dynamics in bent, kinked, looped, tetraplexed, or other more exotic DNAs has yet to be done, there is still more background time-resolved work that needs to be done as a function of sequence. A recent study used FRET to probe the dynamics of hairpin formation, albeit on a much slower time scale [321 ]. Despite the paucity of data on DNA alone, some groups are pio-... 

Hustedt EJ, Kirchner JJ, Spaltenstein A, Hopkins PB, Robinson BH (1995) Monitoring DNA dynamics using spin-labels with different independent mobilities. Biochemistry-US 34... 

Multiple Field Natural Abundance NMR Studies of DNA Dynamics... 

The first experiments using colloidal templates were performed without the polymerization step, using silica beads with a diameter of 1.04 0.4 jxm [20]. The beads were not well-packed over the entire 0(cm) region, with monocrystalline regimes periodically interspersed by polycrystalline regimes. Electrophoresis experiments with a range of DNA samples essentially confirmed that the DNA dynamics in this array correspond to the predictions of biased reptation [33]—the mobility scales likeA ° ° and the diffusivity scales like A reptation plot [36] of the mobility... 

Polymeric matrices formed from a colloidal template have also been used for DNA separations [22]. In contrast to the case in entropic trapping in this type of matrix [34], the electric field compresses the long A.-DNA into a single pore. As illustrated in Figure 54.13, at weak fields the DNA move slowly between the pores, with the direction of the motion biased by the electric field. As the field increases, rope-over-pulley dynamics are observed, whereas at the highest fields the DNA jumps across multiple pores and then coils up. This behavior can only be observed over limited stretches of the medium, since the DNA dynamics change sharply as it tries to transit from one domain to another at the boundaries [22],... 

FIGURE 54.12 DNA dynamics in a polymer matrix formed from colloidal templating in the absence of an electric field, (a) At a given instance in time, four DNA molecules are localized in different pores, (b) Over time, the DNA explores the local pores, (c) The jumping between pores is random in both direction and the waiting time between jumps. (Reprinted from Nykypanchuk, D., et al.. Science, 297, 987, 2002. With permission.)... 

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