B-Z transition in DNA

The thermodynamic parameters for the temperature dependent B-Z transitions in DNA polymers obtained from van t Hoff analysis (indicated by an index vH) of spectroscopic data and of some directly obtained calorimetric data are presented in Table 4. 

It was also demonstrated that ring breathing SERS bands of nucleic acids bases are conformation sensitive for B Z transitions in DNA. ... 

One well-established observation is that, under conditions where single-stranded polynucleotides give rise to a d.c. polarographic reduction wave, both native DNA and other double-helical natural and synthetic polynucleotides are inactive 22 23,46-47, 58,59,61) Tjjjs js rea(ji]y interpretable in that, in such helical structures, the adenine and cytosine residues are located in the interior of the helix, and hydrogen bonded in complementary base pairs (see below). Z-DNA, in which cytosine residues are at the surface of the helix, is of obvious interest in this regard, and the B - Z transition in the synthetic poly(dG dC) has been investigated with the aid of differential pulse polarography and UV spectroscopy 60). 

In addition to the G-quadruplex other motifs that have been solved include the i-motif, a pH-dependent poly dA helix which forms the basis of a molecular switch, the HIV-1 TAR DNA hairpin, and the B-Z transition in a GC-rich DNA sequence. There are also many protein/ peptide structures that have been solved that have DNA as part of the recognition domain, including a zinc sensor, MetJ repressor, lac repressor, Lambda integrase protein, protection of telomers (Potl)... 

The parameters of the mononucleotide model have been determined for specific ionic conditions, the so-called TBE buffer (90 mM Trisborate, 2.5 mM NajEDTA, pH 8.3). All data refer to DNA. Although RNA may exist in the Z-form, the B-Z transition in RNA has not yet been studied in detail. Other solvents used TA (40 mM Tris, 20 mM acetic acid, 5 mM sodium acetate, 1 mM EDTA) [83H1] TFE (trifluoro ethanol). 

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 ... 

The left-handed Z-DNA structure of poly[d(A-T)] poly[d(A-T)] as well as poly[d(A-C)] poly[d(G-T)] in the presence of Ni ions leads to characteristic IR and Raman spectra. Markers for these particular double-helical secondary structures are Raman frequency (phos-phodiester chain vibration at 746 and 815 cm syn geometry of the purines evidenced by a breathing mode coupled to the deoxyribose vibration at 622 cm a characteristic profile in the 1300-1400 cm region with a shift of the 1374 cm purine line lo lower wavenumbers correlated with the antijsyn reorientation of the nucleosides under the B - Z transition. " ... 

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. 

The B - Z transition is Na -dependent and the endpoint corresponds to 2 positive charges per phosphodiester group. The ability to induce this transition is remarkable in view of the fact that normal methods of induction involve high concentrations of salt (2.5M Na ) or ethanol (60% vol/vol). The complex is now used routinely to induce the Z-conformation and as a probe for DNA structure. 

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. 

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