Left-Handed DNA

Rg. 2. Main reaction catalyzed by reverse gytases ATP-dependent Unking number increase. Sup negatively supercoiled DNA (right-handed superhelix), equivalent to an underwinding of the double helix Sup positively supercoiled DNA (left-handed superhelix), equivalent to a overwinding of the double helix. 

The structure proposed by Watson and Crick was modeled to fit crystallographic data obtained on a sample of the most common form of DNA called B DNA Other forms include A DNA which is similar to but more compact than B DNA and Z DNA which IS a left handed double helix... 

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. 

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

Wang, A.H.-J., et al. Molecular structure of a left-handed DNA fragment at atomic resolution. Nature 282 680-686, 1979. 

Figure 10.19 Heterodimerization of leucine zipper proteins can alter their DNA-binding specificity. Leucine zipper homodimers bind to symmetric DNA sequences, as shown In the left-hand and center drawings. These two proteins recognize different DNA sequences, as indicated by the red and blue regions in the DNA. The two different monomers can combine to form a heterodimer that recognizes a hybrid DNA sequence, composed of one red and one blue region.

FIGURE 12.14 Comparison of the deoxy-guanosine conformation in B- and Z-DNA. In B-DNA, the Cl -N-9 glycosyl bond is always in the anti position (lefi). In contrast, in the left-handed Z-DNA structure, this bond rotates (as shown) to adopt the syn conformation. 

Richmond and collaborators (Figure 12.30). The octamer (Figure 12.29) has surface landmarks that guide the course of the DNA around the octamer 146 bp of B-DNA in a flat, left-handed superhelical conformation make 1.65 turns around the histone core (Figure 12.30), which itself is a protein superhelix consisting of a spiral array of the four histone dimers. Histone 1, a three-domain protein, serves to seal the ends of the DNA turns to the nucleosome core and to organize the additional 40 to 60 bp of DNA that link consecutive nucleo-... 

Rich, A., Nordheim, A., and Wang, A. H.-J., 1984. The chemi.stry and biology of left-handed Z-DNA. Annual Review of Biochemistry 53 791-846. 

The systems reported here are a single turn of B-DNA with G-C, A-T base pair sequence and the left handed Z-DNA with G-C base pair sequence. The B-DNA system is simulated for 4.0 psec and Z-DNA is simulated for 3.5 psec after equilibration. The simulation results are then analyzed for structural and dynamical properties. ... 

Peculiar DNA architecture was demonstrated in 25% aqueous ethanol when DNA was complexed with series of cationic detergents in the presence of poly(glutamic acid) [124]. Electron microscopy and x-ray scattering demonstrated that DNA can pack cetyltrimethylammonium bromide molecules into rodlike micelles, which form a hexagonal lattice. Interestingly, circular dichroism spectroscopy revealed that in these complexes DNA adopts left-handed conformation. 

In the nucleosome, the DNA is supercoiled in a left-handed helix over the surface of the disk-shaped histone octamer (Figure 36-2). The majority of core histone proteins interact with the DNA on the inside of the supercoil without protruding, though the amino terminal tails of all the histones probably protrude outside of this structure and are available for regulatory covalent modifications (see Table 36-1). 

Figure 36-19. Supercoiling of DNA. A left-handed toroidal (solenoidal) supercoil, at left, will convert to a right-handed interwound supercoil, at right, when the cylindric core is removed. Such a transition is analogous to that which occurs when nucleosomes are disrupted by the high salt extraction of histones from chromatin.

Since the discovery of the double hehcal structure of deoxyribonucleic acid (DNA) by Watson and Crick in 1953 [1], there has been considerable belief that the canonical right-handed B-DNA may adopt a wide range of different conformations depending on the nucleotide sequences and environmental conditions. This speculation turned out to be a reahty [2-10]. hi hving systems, the conformational flexibility of DNA resides primarily in the polymorphs of the DNA double hehx (including right-handed and left-handed double hehcal DNA) and occurs under various environmental conditions [4j. The main family of DNA forms identified, based on circular dichroic and... 

Poly(dG-dC) poly(dG-dC) and its methylated analogue structures assume left-handed conformation (Z-DNA) in high molar sodium salt (Na", K" ), in low molar divalent cations (Ca", Mg", Ni ), micromolar concentrations of hexaamine cobalt chloride (Co(NH3)6)Cl3 and in millimolar concentrations of polyamines. In order to analyse the binding of berberine to Z-form DNA, Kumar et al. [186] reported that the Z-DNA structure of poly(dG-dC) poly(dG-dC) prepared in either a high salt concentration (4.0 M) or in 40 mM (Co(NH3)6)Cl3 remained invariant in the presence of berberine up to a nucleotide phosphate/alkaloid molar ratio of 0.8 and suggested that berberine neither bormd to Z-form DNA nor converted the Z-DNA to the... 

The four histone groups that are composed of ho-mogeneous proteins, H2A, H2B, H3, and H4, make up the nucleosome core. Each core consists of two copies of the four histones. The double-stranded DNA is wrapped twice around each core in a left-handed superhelix. A superhelix is the name given to the additional helix made by the double-stranded, helical DNA as it is wrapped around the nucleosome core. A familiar superhelix in everyday life is a twisted spiral telephone cord. The nucleosome core of histones do not recognize specific DNA structures rather, they can bind to any stretch of DNA as long as it is not too close to a neighboring nucleosome. The order of contact of histones to the DNA is as follows ... 

In E. coli cells, DNA replication starts at a specific site called oriC. The oriC locus contains only 245 base pairs. Similar sequences are responsible for initiating the synthesis of plasmid and bacteriophage DNA. The oriC nucleotide sequence binds several units of the tetrameric form of the dnaA protein. This protein is named for the gene that encodes it. The dnaB and dnaC proteins then bind to the complex. As a result of binding these proteins, a portion of the helical DNA is unwound. This forces the rest of the DNA into a left-handed double helix that wraps around the proteins to give a structure... 

Figure 6. Fluorescence decay profiles of trans-7,8-dihydroxy-7,8-dihydro-BP and 8,9,10,11-tetrahydro-BA measured at 23 °C with and without native DNA. Taken from refs. 14 and 15. The upper left-hand corner contains an instrument response profile. Emission and excitation wavelengths, lifetimes, and values of x2 obtained from deconvolution of the lifetime data are also given.

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