B-Z DNA transition

SDEL was also used to study the coil-helix transition of an alanine-rich peptide [68], the conformational transition of sugar puckering in deoxyadenosine [69], polymerase P [70], and the B-Z DNA transition [71,72]. The coil to helix study [68] demonstrated several properties of SDEL trajectories, like the filtering of high frequency modes and the preservation of thermodynamic properties from slow degrees of freedom when the trajectory resolution is decreased. 

Moradi M, Babin V, Roland C, Sagui C. Reaction path ensemble of the B-Z-DNA transition a comprehensive atomistic study. Nucleic Acids Res. 2013 41 33 3. 

Fig. 1. Configuration of a microtiter plate used to study the induction of B-DNAtx> Z-DNA transition in poly(dG-m dC).poly(dG-m dC) by spermidine. The concentration of spermidine added to the polynucleotide (designated a to h and j inside the plate) is described in Table 1. Column 2 (DNA) contains poly(dG-m dC).poly(dG-m dC) similar to column 3. However, these wells will not be treated with the monoclonal antibody.

CD has been used extensively for following conformational transitions in DNA, such as denaturation and transitions from B A and B — Z DNA. In addition, the CD of DNA triplexes has features which are distinct from those of the duplex. Some of these important applications of CD to the study of DNA have been described by Gray et in this volume. 

Clearly this test of environmental influence requires a well chosen test case. The limited conformational sampling seen in RNA simulations rules this system out as a candidate. In a similar manner, any conformational change which requires overcoming a significant conformational barrier, such as a B-DNA to Z-DNA transition, cannot reasonably be represented in nanosecond length simulations without methods applied to artificially boost the conformational sampling. Since we were able to see spontaneous B-DNA to A-DNA transitions within a nanosecond time period, since the DNA is very flexible and dynamic, and since the equilibrium between A-DNA to B-DNA is very strongly influenced by the environment, this seemed like a reasonable test case. 

The molecule with the charge distribution (73) can be considered as a model for a B-DNA hehx charges on the strands represent the phosphates and the cylinder charge corresponds to adsorbed cations, smeared on the DNA surface (for B-DNA, a 10 A, B 0.4 H [182]). Note that (74) could also be used for the description of electrostatically induced conformational changes of DNA, e.g., for the B- to Z-DNA transition at high salt concentrations [183]. Moreover, the exact theory of electrostatic interaction between two DNA duplexes predicts an attraction between them due to a correlated structure-driven zipper-like charge separation along the molecules [184]. 

Difference Equation to DNA Conformational Transitions A Study of B-Z and B-A DNA Transitions. 

Vibrational spectroscopy and, in particular, Raman scattering have been used to elucidate selected interactions of DNAs. The B Z conformational transition of oligo-DNA duplexes and the interaction of the intercalating dye AO with calf thymus DNA have been explicitly analyzed in the preceding sections. 

Short segments of poly(dG—dC) incorporated within plasmids, or citcular DNA, adopt the Z-conformation under negative superhehcal stress. This left-handed DNA may be important in genetic control. On the other hand, the stmctural alteration of the helix requited in a B-to-Z transition within a plasmid is radical, and would involve either a multistep mechanism or the complete melting and reformation of helix. The improbability of such transitions has led to questions concerning the feasibility of a biological role for Z-DNA. 

Identification of proteins that bind to Z-DNA added one further step to the establishment of the presence of Z-DNA in vivo and its possible biological role. Herbert and Rich [22] demonstrated an in vitro assay system where one type of double-stranded RNA adenosine deaminase, called DRAD-binding Z-DNA. There are evidences that topoisomerase II from Drosophila, hiunan and calf thymus recognizes a number of DNA shapes, including Z-DNA [34,35]. Bloomfield and coworkers [36] have found that the condensation of plasmids is enhanced by Z-DNA conformation in d(CG)n repeats. The information related to B-Z transition [31], the effect of ligands on it [28,29] and X-ray crystal structure data [37,38] appear to suggest that the possible biological role of this polymorphic form of DNA will be soon established. 

Suppose one double helical turn of a superhelical DNA molecule changes from a B conformation to the Z conformation. Calculate the approximate changes in (1) the linking AL/c, (2) the writhe AWr, and (3) the twist A Tw of the DNA as a result of this transition. Show your calculations and explain your answers. For this problem assume that the B form of DNA has 10.4 bp per turn. Why is the B—> Z transition favored in naturally occurring supercoiled DNA ... 

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