Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form.
Proteopedia Z-DNA Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form.
Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form. Z-DNA is thought to be one of three biologically active double-helical structures along with A-DNA and B-DNA.
Whenever a segment of Z-DNA forms, there must be B–Z junctions at its two ends, interfacing it to the B-form of DNA found in the rest of the genome. In 2007, the RNA version of Z-DNA, Z-RNA, was described as a transformed version of an A-RNA double helix into a left-handed helix.
Z-DNA (default scene) is a form of DNA that has a different structure from the more common B-DNA form.It is a left-handed double helix wherein the sugar-phosphate backbone has a zigzag pattern due to the alternate stacking of bases in anti-conformation and syn conformation.
Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form.
Z-DNA usually forms when genes are transcribed and disappears through topoisomerase activity after the gene is no longer transcribed. Every time a stretch of Z-DNA forms, two B–Z junctions are formed at either end. These are associated with the breakage of a base pair (bp) and the extrusion of the bases.
Z-DNA is a left-handed helical form of DNA in which the double helix winds to the left in a zigzag pattern.
Explanation: Thymine is present in DNA. 9. Which of the following is true about Z-DNA helix? It has more base pairs per turn than B-DNA.
Important Differences between B DNA and Z DNA Commonly occurring structural conformations of DNA are – A-DNA, B-DNA and Z-DNA. The key difference between form B DNA and Z DNA is that the B-DNA is right-handed, while the Z-DNA is left-handed.
The main characteristics of Z-DNA is that it is a left-handed double helix. (examine FIGURE 32). It contains ~12-13 base pairs/turn of helix so it is a relatively loosely wound helix. It is called Z-DNA because of the zig-zag pattern of the phosphate back bone.
The lac Z gene is the structural gene encoding the enzyme for metabolizing galactose sugars.
What are the main structural features of DNA found in the Z conformation? There are 12 base-pairs per turn, the bases are tilted relative to the central axis of the molecule, the sugar-phosphate backbone zig-zags slightly, and the helix is left-handed.
A-DNA is favored by low hydration, whereas Z-DNA can be favored by high salt. The second condition is the DNA sequence: A-DNA is favored by certain stretches of purines (or pyrimidines), whereas Z-DNA can be most readily formed by alternating purine-pyrimidine steps.
Z-DNA is a Watson–Crick base-paired, left-handed helix that is distinct from the Watson–Crick right-handed B-DNA (48, 49 ). Z-DNA is thinner (by ∼10%), more extended (by 29%), and has more base pairs per turn than B-DNA (see Fig. 1.12 and Table 1.9). The purine bases of Z-DNA, formed for example with d (CG)3, are rotated into the syn ( C3′-endo) conformation. The pyrimidine bases maintain an anti conformation. Z-DNA is thus characterized by a dinucleotide repeat in which anti and syn conformations of the bases alternate in succession along the chain. The deoxyribose–phosphate backbone follows a zigzag left-handed course rather than the smoothly spiraling right-handed path found in B-DNA. The interphosphate distances also differ from those of B-DNA. There is one deep groove that corresponds to the minor groove in B-DNA. The major groove of B-DNA is replaced in Z-DNA by a convex surface on which purine N-7 and C-8 and the pyrimidine C-5 positions are exposed.
Z-DNA can form in regions of alternating purine–pyrimidine sequence; (GC)n sequences form Z-DNA most easily. (GT) n sequences also form Z-DNA but they require a greater stabilization energy for formation than (GC) n. (AT) n generally does not form Z-DNA since (AT) n easily forms cruciforms. (AT) n can form Z-DNA under two special conditions. First, up to 10 alternating A · T base pairs embedded within a (GC) n or (GT) n region will form Z-DNA ( Klysik et al., 1988 ). Second, conditions of high negative supercoiling, high salt, and the presence of NiCl 2 cause (AT) n to form left-handed DNA ( Nejedly et al., 1989 ).
The degree of DNA curvature present in the recognition sequence may significantly affect the efficiency of Eco RI cleavage ( 26 ). Among the curvature-altering modifications to the purine functional groups (at C-2 of G and C-6 of A), deletion of the 2-NH 2 group from the G base (which corresponds to the change of dG to dl) most effectively increases the DNA curvature. Although the NH 2 group of the G base is positioned in the minor groove of the helix and is unlikely to contact the protein, its deletion results in an 83% reduction in the efficiency [ kcat/Km) of Eco RI.
The Z-form DNAs are presumed to play a role in various cellular functions such as gene expression and chromosomal recombination ( 49 ). Several lines of evidence point to the presence of at least transient left-handed Z-DNA conformations in vivo. For example, a segment of DNA inserted into a plasmid adopts a left-handed Z-helix in E. coli ( 53 ). Segments of CG tracts as short as 12 bp can readily adopt the Z-form in vivo when they are located in a region of high negative supercoiling ( 54 ). Such sites are often found in the upstream region of promoter sites. In contrast, no Z-DNA is detected even with a 74-bp CG tract when this sequence is located in a region of low negative supercoiling. A DNA target (recognition) site is not methylated by its specific methylase or cleaved by its specific restriction endonuclease ( Bam HI, Eco RI, or Hha I) when the site is in or near a left-handed Z-DNA tract ( 55–57 ).
Z -DNA-binding protein 1 (ZBP1) was initially discovered as the novel gene, DLM-1, associated with anti-tumor host response due to upregulated expression in tumor and surrounding stromal tissue. It was also upregulated in macrophages during stimulation with LPS and IFN-γ, characterizing it as an interferon-inducible gene ( Fu et al., 1999). Structurally, ZBP1 is consisted of two N-terminal Z-DNA binding domains (ZBDs), which has been reported to bind Z-DNA, B-DNA and RNA, followed by two receptor-interacting protein homotypic interaction motifs (RHIM) domains (Fig. 1) ( Ha et al., 2006, 2008; Schwartz et al., 2001). When ZBP1 was found to bind Z-DNA, left-handed dsDNA conformation, through its ZBD it inspired its current name, ZBP1 (Herbert and Rich, 1996; Kuriakose and Kanneganti, 2018). Taniguchi and colleagues discovered ZBP1’s ability to initiate DNA-mediated activation of innate immunity via induction of type I IFNs in association with IRF3 and TBK1 that led them to propose ZBP1 as a cytosolic DNA sensor with a proposed name of DNA-dependent activator of IFN-regulatory factors (DAI) (Herbert and Rich, 1996; Takaoka et al., 2007). More recently, studies have focused on the two RHIM domains which allow interactions with TIR-domain-containing adapter-inducing interferon-β (TRIF), receptor-interacting serine/threonine-protein kinase 1 (RIPK1), RIPK3 and other RIP kinases (Kaiser et al., 2008; Sun et al., 2002 ). RHIM-dependent interactions of ZBP1 are essential for the regulation of necroptosis in response to viral infection and inflammation via induction of NF-κB ( Rebsamen et al., 2009; Upton et al., 2012). ZBP1 has also been reported to sense both viral RNA, influenza A virus (IAV), and murine cytomegalovirus (Kuriakose et al., 2016; Sridharan et al., 2017; Thapa et al., 2016). Recognition of IAV by ZBP1 leads to NLRP3 inflammasome activation and induction of cell death (Kuriakose et al., 2016). ZBP-1 induced cell death during IAV infection involves the production of type I IFNs. Since, Type I IFNs are also induced by RIG-I and TLR signaling, Kesavardhana et al. recently investigated the contribution of these pathways in IAV-induced cell death and explored that sensing IAV by RIG-I triggers cell death via ZBP-1 (Kesavardhana et al., 2017). Further biochemical studies revealed that ZBP1 detects viral ribonucleoprotein (vRNP) and undergoes ubiquitination as a part of its involvement in innate immune response and apoptosis during IAV infection (Kesavardhana et al., 2017 ).
Several non-B forms of DNA (bent DNA, cruciforms, Z-DNA, and intramolecular triplex DNA ) were described in previous chapters. There are many other alternative conformations of DNA. Some represent a slight variation of the B-DNA helix whereas others involve the formation of more elaborate structures. The conceptual organization of certain alternative helical forms to an “others” chapter by no means implies that the alternative conformations discussed here are less interesting or less important than those discussed separately in previous chapters. In fact, in the case of the DNA unwinding element, the importance in biology is very clearly understood. In time, our understanding of and appreciation for the structures included here will grow. No doubt other alternative conformations of DNA, in addition to those currently identified, will add to the list presented in this chapter.
Z-DNA is formed by alternating purine–pyrimidine (RY·RY) sequences (where R indicates a purine, A or G, and Y indicates a pyrimidine, C or T; the dot designates the complementary strands), such as the repeating (CG·CG)n and (CA·TG) n motifs ( Table I ). Structurally, the Z -DNA helix is slimmer and more elongated than B -DNA, and it lacks a major groove ( Figure 1B ). Z -DNA represents a high-energy state for DNA; in vivo, most energy required for the B to Z transition is supplied by negative supercoiling, a topological state found in chromosomal DNA.
DNA in a cell can normally be compared to spaghetti on one's plate: a large tangle of strands. To be able to divide DNA neatly between the two daughter cells during cell division, the cell organises this tangle into tightly packed chromosomes. A protein complex called condensin has been known to play a key role in this process, but biologists had no idea exactly how this worked. Until February 2018, when scientists from the Kavli Institute at Delft University of Technology, together with colleagues from EMBL Heidelberg, showed in real time how a condensin protein extrudes a loop in the DNA. Now, follow-up research by the same research groups shows that this is by no means the only way condensin packs up DNA. The researchers discovered an entirely new loop structure, which they call the 'Z loop'. They publish this new phenomenon on 4 March in Nature, where they show, for the first time, how condensins mutually interact to fold DNA into a zigzag structure.
Research leader Prof. Cees Dekker explains: 'The creation of a Z-shaped structure begins when one condensin lands on DNA and makes a single loop. Then, a second condensin binds within that loop and starts to make its own loop, creating a loop in a loop. When the two condensins meet during their tug-of-war, something surprising happens: the second condensin hops over the first one and grabs the DNA outside the loop, continuing its way along the DNA. We were very surprised that condensin complexes can pass each other. This is completely at odds with current models, which assume that condensins block each other when they meet.'
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Since bases get more length to spread out in Z-DNA and since the angle of tilt is 60°, they are closer to the axis and hence the diameter of Z-DNA molecule is 18 A, whereas it is 20 Å in B-DNA.
Due to a different arrangement of molecules within Z-DNA polymer , phosphate backbone follows- a zig-zag course, while in B-DNA it is regular (Fig. 25.17).
a twist through 360°, has twelve base pairs or six repeating dinucleotide units (12 base pairs), while in B-DNA, one complete helix has only ten base pairs or ten repeating units.
Because twelve base pairs are accommodated in one helix in Z-DNA, as against ten in B-DNA, the angle of twist per repeating unit (dinucleotide) is 60°, as against 36° in B-DNA.
Fig. 25.17. Side views of Z-DNA and B-DNA. Two views of Z-DNA are 30° apart. Irregularity of backbone in Z-DNA is shown by heavy lines showing the path of phosphate residues, which is quite regular and smooth in B-DNA (redrawn from Nature, Vol. 282, 1979).
Two strands of double helix are antiparallel in both DNAs.
In this sketch, Geis illustrates the left handed Z-form of double stranded deoxyribonucleic acid (DNA). Z-DNA is indicated by the zig-zag like pattern of the two strands in relationship to each other. Geis shows a line of symmetry down the middle of the illustration highlighting the helix axis of the molecule.
Z-DNA is a duplex structure, with the two strands of the molecule coiling in left-handed helices and a pronounced zig-zag pattern in the phosphorous backbone. Z-DNA can form more easily in an alternating purine-pyrimidine sequence , which is what leads to the zig-zag pattern.