This page has been archived and is no longer updated
Z-DNA: the long road to biological function
Author: A. Rich
Keywords
Keywords for this Article
Add keywords to your Content
Save
|
Cancel
Share
|
Cancel
Revoke
|
Cancel
Rate & Certify
Rate Me...
Rate Me
!
Comment
Save
|
Cancel
Flag Inappropriate
The Content is
Objectionable
Explicit
Offensive
Inaccurate
Comment
Flag Content
|
Cancel
Delete Content
Reason
Delete
|
Cancel
Close
Full Screen
"� 2003 Nature Publishing Group 566 | JULY 2003 | VOLUME 4 www.nature.com/reviews/genetics PERSPECTIVES 48. Gould, S. J. & Lewontin, R. C. The Spandrels of San- Marco and the Panglossian paradigm ? a critique of the adaptationist program. Proc. Royal Soc. London B 205, 581?598 (1979). 49. Iltis, H. H. From teosinte to maize: the catastrophic sexual transmutation. Science 222, 886?894 (1983). 50. Iltis, H. H. Homeotic sexual translocations and the origin of maize (Zea mays, Poaceae): a new look at an old problem. Econ. Bot. 54, 7?42 (2000). 51. Lauter, N. & Doebley, J. Genetic variation for phenotypically invariant traits detected in teosinte: implications for the evolution of novel forms. Genetics 160, 333?342 (2002). 52. Gibson, G. Developmental evolution: going beyond the ?just so?. Curr. Biol. 9, 942?945 (1999). Acknowledgements I would like to thank E. Meyerowitz, in whose laboratory this work began, J. Trager of Huntington Gardens, San Marino, California, and L. Song of the University of California, Fullerton, for Welwitschia materials, and two anonymous reviewers. This work is supported by a National Science Foundation grant. Online Links DATABASES The following terms in this article are linked online to: MaizeGDB: http://www.maizegdb.org rolled leaf 1 TAIR: http://www.arabidopsis.org INO | LFY | STM FURTHER INFORMATION Floral Genome Project: http://fgp.bio.psu.edu/fgp/index.html Access to this interactive links box is free online. protein and is required for proper development and pigmentation of the seed coat. Plant Cell 14, 2463?2479 (2002). 36. Bowe, L. M. et al. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales? closest relatives are conifers. Proc. Natl Acad. Sci. USA 97, 4092?4097 (2000). 37. Chaw, S. M. et al. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl Acad. Sci. USA 97, 4086?4091 (2000). 38. Qiu, Y.-L. et al. Phylogeny of basal angiosperms: analyses of five genes from three genomes. Int. J. Plant Sci. 161, 3?27 (2000). 39. Mathews, S. & Donoghue, M. J. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. J. Plant Sci. 161, 41?55 (2000). 40. Soltis, D. E. et al. Missing links: the genetic architecture of flower and floral diversification. Trends Plant Sci. 7, 22?31 (2002). 41. Lanfranchi, G. et al. Identification of 4370 expressed sequence tags from a 3?-end-specific cDNA library of human skeletal muscle by DNA sequencing and filter hybridization. Genome Res. 6, 35?42 (1996). 42. Albert, V. A. et al. Pleiotropy, redundancy and the evolution of flowers. Trends Plant Sci. 7, 297?301 (2002). 43. Theissen, G. et al. in Developmental Genetics and Plant Evolution: Systematics Association Special Volume Series 65 (eds Cronk, Q. C. B. et al.) 173?206 (Taylor and Francis, London, 2002). 44. Lamark, J. B. Zoological Philosophy (1809) 122 (Univ. Chicago Press, Chicago, 1984) (Translated by H. Elliot). 45. Mayr, E. The Growth of Biological Thought (Belknap, Cambridge, Massachusetts, 1982). 46. Frohlich, M. W. MADS about Gnetales. Proc. Natl Acad. Sci. USA 96, 8811?8813 (1999). 47. Gould, S. J. Sociobiology: the art of storytelling. New Sci. 80, 530?533 (1978). 7. Frohlich, M. W. & Parker, D. S. The Mostly Male theory of flower evolutionary origins: from genes to fossils. Syst. Bot. 25, 155?170 (2000). 8. Frohlich, M. W. in Beyond Heterochrony: The Evolution of Development (ed. Zelditch, M. L.) 59?106 (John Wiley, New York, 2001). 9. Frohlich, M. W. in Developmental Genetics and Plant Evolution: Systematics Association Special Volume Series 65 (eds Cronk, Q. C. B. et al.) 85?108 (Taylor and Francis, London, 2002). 10. Doyle, J. A. Seed plant phylogeny and the relationships of Gnetales. Int. J. Plant Sci. 157, 3?39 (1996). 11. Frohlich M. W. & Meyerowitz, E. M. The search for flower homeotic gene homologs in basal angiosperms and gnetales: a potential new source of data on the evolutionary origin of flowers. Int. J. Plant Sci. 158, 131?142 (1997). 12. Baum, D. A. The evolution of plant development. Curr. Opin. Plant Biol. 1, 79?86 (1998). 13. Lohmann, J. U. & Weigel, D. Building beauty: the genetic control of floral patterning. Dev. Cell 2, 135?142 (2002). 14. Donoghue, M. J. & Doyle, J. A. Seed plant phylogeny: demise of the anthophyte hypothesis? Curr. Biol. 10, 106?109 (2000). 15. Frohlich, M. W. & Estabrook, G. F. Wilkinson support calculated with exact probabilities: an example using Floricaula/LEAFY amino acid sequences that compares three hypotheses involving gene gain/loss in seed plants. Mol. Biol. Evol. 17, 1914?1925 (2000). 16. Mouradov, A. et al. NEEDLY, a Pinus radiata ortholog of FLORICAULA/LEAFY genes, expressed in both reproductive and vegetative meristems. Proc. Natl Acad. Sci. USA 95, 6537?6542 (1998). 17. Mellerowicz, E. J. et al. PRFLL a Pinus radiata homologue of FLORICAULA and LEAFY is expressed in buds containing vegetative shoot and undifferentiated male cone primordia. Planta 206, 619?629 (1998). 18. Colombo, L. et al. The Petunia MADS box gene FBP11 determines ovule identity. Plant Cell 7, 1859?1868 (1995). 19. Decraene, L. P. R. & Smets, E. F. Notes on the evolution of androecial organisation in the Magnoliophytina (angiosperms). Bot. Acta 111, 77?86 (1998). 20. Hufford, L. The morphology and evolution of male reproductive structures of Gnetales Int. J. Plant Sci. 157, 95?112 (1996). 21. Endress, P. K. Structure and function of female and bisexual organ complexes in Gnetales. Int. J. Plant Sci. 157, 113?125 (1996). 22. Yao, X. et al. The Corystosperm pollen organ Pteruchus from the Triassic of Antarctica. Amer. J. Bot. 82, 535?546 (1995). 23. Klavins, S. D. et al. Anatomy of Umkomasia (Corystospermales) from the Triassic of Antarctica. Amer. J. Bot. 89, 664?676 (2002). 24. Shindo, S. et al. Characterization of a FLORICAULA/LEAFY homologue of Gnetum parvifolium and its implications for the evolution of reproductive organs in seed plants. Int. J. Plant Sci. 162, 1199?1209 (2001). 25. Long, J. A. et al. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 379, 66?69 (1996). 26. Brown, R. C. & Mogensen, H. L. Late ovule and early embryo development in Quercus gambelii. Amer. J. Bot. 59, 311?316 (1972). 27. Bowman, J. L. et al. Establishment of polarity in angiosperm lateral organs. Trends Genet. 18, 134?141 (2002). 28. Svoma, E. Seed development and function in Artabotrys hexapetalus (Annonaceae). Plant Syst. Evol. 207, 205?223 (1997). 29. Taylor, T. N. et al. Permineralized seed fern cupules from the Triassic of Antarctica ? implications for cupule and carpel evolution. Amer. J. Bot. 81, 666?677 (1994). 30. Griffith, M. E. et al. PETAL LOSS gene regulates initiation and orientation of second whorl organs in the Arabidopsis flower. Development 126, 5635?5644 (1999). 31. Nelson, J. M. et al. Expression of a mutant maize gene in the ventral leaf epidermis is sufficient to signal a switch of the leaf?s dorsoventral axis. Development 129, 4581?4589 (2002). 32. Gro�-Hardt, R. et al. WUSCHEL signaling functions in interregional communication during Arabidopsis ovule development. Genes Dev. 16, 1129?1138 (2002). 33. Winter, K. U. et al. Evolution of class B floral homeotic proteins: obligate heterodimerization originated from homodimerization. Mol. Biol. Evol. 19, 587?596 (2002). 34. Becker, A. et al. A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes. Mol. Genet. Genomics 266, 942?950 (2002). 35. Nesi, N. et al. The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain Z-DNA: the long road to biological function Alexander Rich and Shuguang Zhang TIMELINE Biologists were puzzled by the discovery of left-handed Z-DNA because it seemed unnecessary. Z-DNA was stabilized by the negative supercoiling generated by transcription, which indicated a transient localized conformational change. Few laboratories worked on the biology of Z-DNA. However, the discovery that certain classes of proteins bound to Z-DNA with high affinity and great specificity indicated a biological role. The most recent data show that some of these proteins participate in the pathology of poxviruses. When Watson and Crick proposed their model for the right-handed double helical structure of DNA (B-DNA) in 1953, it was compatible with the only experimen- tal data on the structure at that time: DNA FIBRE X-RAY DIFFRACTION analysis. However, fibre diffraction yielded too little data to ?prove? the structure. It was not until the late 1970s, when DNA synthesis was developed, that it became possible to carry out SINGLE-CRYSTAL X-RAY DIFFRACTION on spe- cific molecules to define the structure. Amazingly, the familiar right-handed B-DNA double helix that had been the focus of molecular biology for the preceding 25 years did not appear in this first atomic- resolution view of the double helix. Instead, the first single-crystal X-ray structure of a DNA fragment ? a self-complementary DNA hexamer d(CG) 3 ? showed a left- handed double helix with two anti-parallel chains that were held together by Watson?Crick base pairs 1 (see TIMELINE). The alternative structure pointed to an unusual function for this form of DNA. The organization of the molecule was completely different from that which had � 2003 Nature Publishing Group PERSPECTIVES NATURE REVIEWS | GENETICS VOLUME 4 | JULY 2003 | 567 be a part of biological systems, which indi- cated a connection between this alternative conformation and biological phenomena. Early experiments showed that the negative supercoiling of plasmids in prokaryotes would stabilize Z-DNA 10 . Many in vitro experiments were carried out to determine the energy that was required for a supercoiled plasmid with a particular sequence to flip from the B form to the Z form. The energetics of these conformations was studied for several different sequences 11 .This ultimately led Ho et al.to devise a computer program that made it possible to calculate the relative energy required to flip any sequence from the B form to the Z form 12 . Workers in several laboratories deter- mined crystal and solution structures of DNA sequences in the Z conformation. These pro- vided a great deal of detailed information about the Z conformation and, at the same time, many chemists discovered ways in which the Z conformation could be stabilized relative to the B conformation. Nonetheless, work on the biology of Z-DNA progressed slowly. By the mid-1980s, after several years of research, nothing definitive had emerged about Z-DNA function. During this period, although some notable studies supported a functional role for Z-DNA in transcription (see later), others showed that the influence of Z-DNA on transcription was dependent on the gene that was examined, which increased scepticism and decreased enthusiasm for studying the biological role of Z-DNA. Many people felt that Z-DNA was a non-functional been anticipated. Instead of all the residues having bases organized in the ANTI-CONFORMA- TION,in this molecule every other base rotated around the glycosyl bonds so that the bases alternated in anti- and SYN-CONFORMATIONS along the chain. Also, there was a zigzag arrangement of the backbone of the molecule (hence, the name Z-DNA) that looked differ- ent from the smooth continuous coil seen in models of B-DNA (FIG. 1).Instead of having a helix with a major and minor groove, the base pairs were set off to the side, away from the axis, and only one groove was found that was analogous to the minor groove of B-DNA. The bases that form the major groove in B-DNA were reorganized in Z-DNA to form the convex outer surface. The general response to this unusual structure was amazement, coupled with scepticism. However, after a brief period of excitement, the biological community largely ignored Z-DNA, as it did not seem to be required to explain anything. Recent research on this alternative conformation of the dou- ble helix has begun to show that Z-DNA has important biological functions. Conformation and stability The relationship between Z-DNA and the more familiar B-DNA was indicated by the earlier work of Pohl and Jovin 2 ,who showed that the ultraviolet CIRCULAR DICHROISM of poly(dG-dC) was nearly inverted in 4 M sodium chloride solution. The suspicion that this was the result of a conversion from B-DNA to Z-DNA was confirmed by examin- ing the RAMAN SPECTRA of these solutions and the Z-DNA crystals 3 .The conversion of B- DNA to Z-DNA was associated with a ?flip- ping over? of the base pairs so that they had an upside down orientation relative to that of B-DNA. This flipping over resulted both in the production of a syn-conformation in every other base and a change in the deoxyribose-ring pucker in alternate bases. The net result of this reorganization was that the phosphate groups were closer together in Z-DNA than in B-DNA. Hence, under stan- dard cellular conditions, the electrostatic repulsion of these charged phosphate groups would push the molecule into the B-DNA conformation. In the presence of a high-salt solution, the electrostatic repulsion of the phosphate residues is vastly decreased, and Z-DNA becomes the stable conformation. Several studies quickly showed that chemi- cal modification, including cytosine methyla- tion and many other cations, such as spermine and spermidine, would stabilize the Z confor- mation 4 .It emerged that the lowest energy- level ground state of DNA in a physiological solution was B-DNA, and that the Z confor- mation was a higher energy state. Because purines can form the syn-conformation with- out an energy penalty, it became apparent that the specific sequence of the base pairs was important in determining the energy that was required to change B-DNA to Z-DNA 5 .The sequences that most readily converted had alterations of purines and pyrimidines, espe- cially alternations of C and G. This change also occurred easily with alternations of CA on one strand and TG on the other 6,7 .However,many other sequences were shown to be capable of forming Z-DNA 8 . This discovery stimulated a burst of research from chemists who were interested in studying DNA conformational changes. Although the ionic conditions that were suitable for stabilizing Z-DNA in most experiments were different from those pre- sent in a cell, spermine, spermidine and cytosine methylation, which also stabilize Z-DNA 4 ,are found in vivo.Furthermore, the discovery that negative supercoiling would stabilize Z-DNA indicated biological involvement 9 .Negative supercoiling req- uires energy and tends to unwind B-DNA. For example, in a plasmid with three nega- tive supercoils, if one turn of the DNA helix changed from right-handed to left-handed, two negative supercoils would disappear and the energy of negative supercoiling would then stabilize a small segment of Z-DNA (FIG. 2).Supercoiling was known to Figure 1 | Discovery of Z-DNA. Cover of Nature, showing the discovery of left-handed Z-DNA in side and end views, with the right-handed B-DNA in the enclosed box 1 . The shaded guanine residues in Z-DNA are near the outside of the helix in the end view, compared with their central location in B-DNA. Z-DNA segment (one turn) ? = ? 3 ? = ?1 Figure 2 | Negative supercoiling stabilizes Z-DNA. A double helical plasmid with three negative supercoils (?) is shown on the left. The energy of supercoiling is proportional to the square of the number of supercoils. On the right, one turn switches the DNA from right- to left-handed, and two negative supercoils are removed. The change of negative supercoiling energy stabilizes Z-DNA formation. � 2003 Nature Publishing Group 568 | JULY 2003 | VOLUME 4 www.nature.com/reviews/genetics PERSPECTIVES 22 and estimated that ~80% of its genes have sequences that favour Z-DNA forma- tion near the transcription start site (P. S. Ho,personal communication). As these were not present in many pseudogenes, Z-DNA-forming sequences near the tran- scription start site might have a functional role. To study the association between Z-DNA and transcription more directly, Rich collabo- rated with Wittig and colleagues to use a tech- nique developed by Cook at Oxford University. Mammalian cells were encapsulated in agarose microbeads and mild detergent treatment lysed the cytoplasmic membrane and perme- abilized the nuclear membrane, but left the nucleus otherwise intact. The resulting ?entrapped? nuclei replicated DNA at nearly the in vivo rate and were able to carry out tran- scription 23 .Using biotinylated monoclonal antibodies against Z-DNA, the level of Z-DNA was determined in these nuclei, and was shown to be regulated by torsional strain 24 .Moreover, an increase in the transcriptional activity of the embedded nuclei resulted in a parallel increase in the amount of bound Z-DNA 25 . Using a short ultraviolet (UV) laser pulse for protein?DNA cross linking, they linked the biotinylated anti-Z-DNA antibodies to DNA. This made it possible to isolate DNA restric- tion fragments that were bound to the antibody and probe them for specific nucleotide sequences. They found that three regions near the promoters of the C-MYC gene formed Z-DNA when C-MYC was expressed (FIG. 3), and the Z-DNA-forming nucleotides were identified. However, these regions quickly reverted to B-DNA if C-MYC trans- cription was switched off 26,27 .Nonetheless, especially in systemic lupus erythematosus 16 . Antibodies to Z-DNA also provided a useful tool for characterizing chromosome organi- zation. They bound specifically to the inter- band regions of the Drosophila polytene chromosomes, and this binding was particu- larly strong in the puff regions, which are the sites of enhanced transcriptional activity 17 . Others found the same staining patterns in unfixed POLYTENE CHROMOSOMES 18 .However, some studies have shown antibody binding outside these regions 19 . Further studies in protozoa also indicated a link to transcription. Ciliated protozoa have two nuclei: the macronucleus, which is the site of transcription, and the micronucleus, which contains DNA that is involved in sexual repro- duction. Anti-Z-DNA antibodies stained the macronucleus of the ciliated protozoan Stylonychia,but not its micronucleus 20 . A real breakthrough came with the work of Liu and Wang 21 , in 1987, on the interaction of the RNA polymerase complex with the DNA duplex during transcription. They suggested that the complex does not rotate around the helical DNA, but instead plows straight through. Because the ends of the DNA mole- cule are fixed, the DNA behind the moving polymerase is unwound and subjected to nega- tive torsional strain, which is known to stabilize Z-DNA. In front of the moving polymerase, positive torsional strain develops. Further evidence came from the work of Ho and colleagues, who first studied the distri- bution of sequences that favoured Z-DNA formation in 137 human genes. They found a high concentration of these sequences near the transcription start site 22 .In more recent exper- iments, Ho scanned human chromosome conformational phenomenon and this atti- tude became relatively widespread 13 .So, although chemists continued to find Z-DNA interesting, by the end of the 1980s the biol- ogy of Z-DNA was not receiving attention from researchers, and its study had largely disappeared, except in the Rich laboratory. Transcription and Z-DNA In fact, the groundwork towards showing a biological role for Z-DNA came from immunological research that was carried out years before the downturn of interest in this area. Unlike B-DNA, Z-DNA is highly anti- genic; both polyclonal 14 and monoclonal 15 antibodies can be raised to Z-DNA molecules. The characterization of these antibodies led to the discovery that Z-DNA-specific antibodies are found in human autoimmune diseases, Pohl and Jovin find that the CD spectrum of poly(dG-dC) nearly inverts in 4 M NaCl. Antibodies to Z-DNA bind strongly to Drosophila polytene chromosomes in transcriptionally active regions. The first single-crystal structure of a DNA fragment unexpectedly reveals a left-handed double helix, named as Z-DNA. Z-DNA is found to be stabilized by negative supercoiling. Z-DNA antibodies are found to stain transcriptionally active macronuclei, but not the inactive micronuclei, of ciliated protozoa. Z-DNA is shown to exist in vivo. The level of Z-DNA in metabolically active permeabilized mammalian cell nuclei is shown to be regulated by torsional strain. Liu and Wang recognize that negative supercoiling is produced behind a moving RNA polymerase during transcription. The transcription of human C-MYC is correlated with Z-DNA formation near its promoter in permeabilized nuclei. The Z-DNA-binding domain from the ADAR1 editing enzyme is isolated, and a Z-DNA-specific restriction endonuclease is constructed. It is shown that the Z-DNA- binding domain of ADAR1 binds Z-RNA as well as Z-DNA. The editing enzyme double-stranded RNA adenosine deaminase (ADAR1) is found to bind tightly and specifically to Z-DNA. The co-crystal structure of Z-DNA bound to the ADAR1 Z-DNA binding domain is solved. Z-DNA formation is correlated with the level of RNA synthesis in permeabilized nuclei. 1972 1979 1981 1982 1983 1987 1989 1991 1992 1995 1997 1999 2000 Timeline | From Z-DNA structure to function A method is developed to identify high-affinity Z-DNA-binding proteins. Exon 1 Exon 2 Exon 3 PO P1 P3 P1 Z1 Z2 Z3 275 336 245 C-MYC Figure 3 | Transcription stabilizes Z-DNA. Metabolically active permeabilized nuclei were used to show that C-MYC transcription is associated with the formation of Z-DNA in three restriction fragments, which are labelled Z1?Z3 (numbers above the boxes show the size of the fragments). These are all found near the C-MYC promoters, which are labelled P0?P3 (REF. 26). When transcription is turned off, the continued action of topoisomerases relaxes the Z-DNA, which disappears entirely after ~15 minutes. Therefore, Z-DNA is formed transiently in association with transcription. � 2003 Nature Publishing Group PERSPECTIVES of a Z-DNA-binding nuclear-RNA-editing enzyme 32 called double-stranded RNA adenosine deaminase (ADAR1). ADAR1 acts on double-stranded segments that are formed in pre-mRNA, binding to the duplex and selectively deaminating adenosine to yield inosine. Ribosomes interpret inosine as guanine, so it can alter the amino-acid sequence of a DNA-encoded protein. A typi- cal substrate of this enzyme is an RNA duplex in which an exon is paired with a region of an intron. The deaminase edits several pre- mRNAs, including a glutamate receptor that is expressed in the central nervous system (CNS) 33 .The receptor is an ion channel, and a glutamine residue near the centre of the channel is changed through editing to argi- nine; its positive charge restricts the entry of calcium ions, a change that is essential for CNS function. Another substrate is the sero- tonin receptor 33 .In all of these cases, the functional properties of the edited protein (with the amino-acid alteration) are detectably different from those of the unedited protein. The editing enzyme is found in all metazoa and acts to increase the functional diversity of proteins that are transcribed from a given locus. the constitutively expressed actin control retained its Z-DNA at all times. This showed a correlation between transcription and Z-DNA conformation, which has also been found in other genes 28 . So, the negative torsional strain induced by the movement of RNA polymerase 21 sta- bilized Z-DNA formation near the transcrip- tion start site. Although topoisomerases tried to relax the DNA, the continued movement of RNA polymerases generated more nega- tive torsional strain than the topoisomerases could relax. However, on the cessation of transcription, topoisomerase action rapidly converted the DNA back to the B conforma- tion. So, Z-DNA was seen as a metastable conformation that formed and disappeared depending on physiological activities. How is Z-DNA formation initiated in transcription? One answer was afforded by the recent work of Liu et al. who studied the chromatin remodelling system SWI/SNF 29 . This complex of proteins helps to turn on genes by unwrapping DNA from nucleo- somes. Liu et al. studied the human colony stimulating factor 1 gene (CSF1), which is turned on by this system. Unwrapping the nucleosome leaves the DNA negatively supercoiled as a result of the way in which it is wrapped around the nucleosome. Liu et al. discovered that the released DNA was in the Z conformation. It had been known for sev- eral years that Z-DNA could not form nucle- osomes 30 .So, the nucleosome cannot reform and the site is kept open, which allows the accumulation of other transcription factors and the initiation of transcription by RNA polymerase. They showed that transcription was triggered by Z-DNA formation. Given the prevalence of sequences that favour Z-DNA formation near transcription sites, it is possible that this mechanism is widespread 22 . Proteins that bind Z-DNA Identifying binding proteins. If Z-DNA were to have biological functions, it seemed highly likely that there would be a class of proteins that would bind specifically to it. Several attempts were made to isolate such proteins, using columns and other techniques. Early attempts met with limited success but did result in the important and serendipitous dis- covery that is described in BOX 1. The problem with Z-DNA-binding pro- teins was devising a method that would make it possible to isolate proteins that bound selectively to Z-DNA with high affin- ity. Herbert developed a powerful technique for identifying Z-DNA-binding proteins with the exclusion of proteins that could bind to B-DNA 31 .The method used a gel- shift assay with radioactive-labelled chemi- cally stabilized Z-DNA in the presence of a ~20,000-fold excess of B-DNA and single- stranded DNA. This technique detected proteins that bound specifically and tightly to Z-DNA and led to the isolation, in 1995, NATURE REVIEWS | GENETICS VOLUME 4 | JULY 2003 | 569 A yeast one-hybrid system shows that Z-DNA-binding proteins can act as potent effectors of gene expression in vivo. The co-crystal structure of the DLM-1 Z-DNA-binding domain complexed to Z-DNA is solved. Nucleosome remodelling of the human CSF1 gene shown to produce Z-DNA in the promoter region that is necessary for transcription. E3L, a protein produced by vaccinia virus that is necessary for the mortality of infected mice, is found to be a Z-DNA-binding protein. 2001 2002 2003 Box 1 | Discovery of self-assembling peptides from the study of zuotin Zhang developed a simple gel- retardation assay using stabilized methylated Z-DNA [d(5mCG)n] to purify the first naturally occurring left- handed Z-DNA-binding protein. A yeast protein called zuotin was found to bind Z-DNA in the presence of a 400-fold molar excess of right-handed B-DNA 46 .Zuotin had an interesting repetitive sequence motif ? AEAEAKAKAEAEAKAK ? which has been extensively developed by Zhang to create a class of simple ?-sheet peptides that are self-complementary as a result of the presence of both positive and negative side chains on one side of the ?-sheet and hydrophobic side chains on the other 47 . This serendipitous discovery of a self-complementary peptide inspired Zhang to design several new members of this peptide class, which form 3-dimensional (3D) nanofibre scaffolds that can be used in 3D cell culture 48?50 .The four self-complementary peptides shown here ? RDA16-I, RAD16-II, EAK-I and EAK16-II (the segment from yeast zuotin) ? form stable ?-sheet structures in water and undergo spontaneous assembly to form nanofibre scaffolds. These nanofibre scaffolds hold large volumes of water (>99.5% water content). Tissue cells can be embedded in a 3D nanofibre scaffold in which they can establish molecular gradients that often mimic the in vivo environment. Other related self-assembling peptide systems have also been designed, which range from ?molecular switch? peptides that undergo marked conformational changes 51 to ?molecular carpet? peptides for surface engineering to peptide nanotubes and nanovesicles 52?55 ,all ofwhich originated with the Z-DNA-binding zuotin discovery. RAD16-I RAD16-II EAK16-I EAK16-II from zuotin � 2003 Nature Publishing Group 570 | JULY 2003 | VOLUME 4 www.nature.com/reviews/genetics PERSPECTIVES The 70-amino-acid binding domain was found to adopt a helix?turn?helix ?-sheet motif (winged helix) in which the recognition helix and the ?-sheet were bound to five successive phosphate groups in the zigzag backbone of Z-DNA. Also, it recognized the syn-conformation of guanine. So, the Z? ADAR1 domain is designed to specifically recognize the structural features of Z-DNA ? it is spe- cific for the conformation, not the sequence. The winged-helix protein motif is also widely present in sequence-specific DNA-recognition proteins, which bind to the bases in the major groove of B-DNA. The use of this domain for binding to the Z-DNA conformation shows an interesting adaptation of a widely used DNA-binding tertiary-protein fold. It is likely that the Z-DNA-binding domain of ADAR1 targets the Z-DNA-forming regions of certain transcriptionally active genes, as only they have Z-DNA. The use of an exon?intron duplex in the editing process means that edit- ing has to be rapid, as the introns are rapidly removed by the splicing apparatus. Z? ADAR1 seems to be active in vivo in the editing of cer- tain transcripts in which it might target the gene 41 ;however, its role in double-stranded RNA (dsRNA) editing is not resolved. Interestingly, dsRNA can also adopt a Z-RNA conformation, which might be a substrate for ADAR1 (BOX 2). Other Z-DNA-binding proteins The co-crystal structure of Z? ADAR1 and Z-DNA made it possible to identify those amino acids that are important for Z-DNA recognition. A computer search rapidly dis- covered other proteins with similar sequence motifs, such as DLM1,which is upregulated in tissues that are in contact with tumours as well as during the inter- feron response 42 .The co-crystal structure of the Z-DNA-binding domain of DLM1 (Z? DLM1 ) and d(CG) 3 was solved at a resolu- tion of 1.85 �, and showed that this second protein domain recognizes Z-DNA in a manner similar to that of Z? ADAR1 (REF. 43). Another Z-DNA-binding protein is E3L, which is found in poxviruses, including the vaccinia virus. These large DNA viruses reside in the cytoplasm of cells and produce several proteins that help to abort the interferon response of the host cell. E3L is a small protein that is necessary for pathogenicity 44 .Ifvaccinia virus is given to a mouse, the mouse dies within one week. However, a virus that has a mutated or missing E3L is no longer pathogenic for the mouse, even though the virus can still reproduce in cell culture 44 . The protein has an N-terminal domain with a sequence that is characteristic of Z-DNA d(CG) 6 segment was inserted between two longer segments with sequences that would not easily form Z-DNA 38 .In such cases, the Z? ADAR1 would bind to the central region, hold- ing it in the Z conformation, whereas the flank- ing regions remained in the B conformation. Therefore, the binding energy was great enough to hold a small segment of DNA in the Z conformation and also provided enough energy to stabilize the two B?Z junctions. Oh and Kim developed a yeast one-hybrid system to study Z-DNA-binding proteins in vivo 39 .They discovered that when Z? ADAR1 that has been fused to an activation domain binds to Z-DNA near a promoter, it enhances the transcription of the reporter gene. However, even without the activation domain, a level of transcriptional activation remains. These find- ings are consistent with the suggestion of Liu et al. 29 that Z-DNA formation near the promoter would stimulate transcription. Schwartz et al. discovered that the purified Z? ADAR1 domain from ADAR1 could be co- crystallized with d(CG) 3 .The crystal struc- ture, solved at a resolution of 2.1 � (REF. 40), showed that the DNA was identical in form to that seen in the first crystal of Z-DNA 1 . A Z-DNA-binding domain Proteolytic dissection of the editing enzyme ADAR1 made it possible to isolate a domain from the N-terminus, called Z? ADAR1 ,which contains all the Z-DNA-binding properties that are associated with the editing enzyme 34 . This domain was used by Kim et al.to create a conformationally specific restriction endonu- clease that would only cut Z-DNA 35,36 . Several experiments were carried out to illustrate the interaction of the Z? ADAR1 domain with DNA in solution. If the dode- camer d(CG) 6 was put in solution, it produced the typical circular-dichroism spectrum of B-DNA. As Z? ADAR1 was added to the physio- logical solution, the spectrum gradually changed, which reflected conversion to the Z form 37 .This showed that the Z? domain of ADAR1 was capable of stabilizing the dode- camer in the Z conformation, which was prob- ably generated by BROWNIAN MOTION that twisted the dodecamer fragment. After flipping into the Z-DNA conformation, the Z? ADAR1 domain binds to the DNA and prevents it returning to the B conformation. In later experiments, a similar phenomenon was shown in a longer DNA molecule in which the Box 2 | Z-RNA The discovery of the structure of left-handed Z-DNA naturally led to the question of whether RNA could also form this conformation. In 1982, chemically modified oligoribonucleotides indicated that this was a possibility 56 , and further nuclear magnetic resonance, circular dichroism and absorption spectroscopy studies strongly indicated that Z-RNA could be formed in high- ionic-strength solutions 57,58 .More detailed structural information was obtained from X-ray crystallographic studies with chimeric hexamers that were made of alternating CG residues in which the two central CG residues were ribonucleotides, whereas the flanking pair of nucleotides were deoxyribonucleotides. These and other structural studies showed that the conformation of Z-RNA was similar to that of Z-DNA 59,60 .Z-RNA was also found to be immunogenic and, although Z-RNA specific antibodies could be isolated 61 ,some antibodies recognized both Z-RNA and Z-DNA. Staining experiments with Z-RNA-specific antibodies showed that the antibody bound to fixed protozoan cells that were visualized by immunofluorescence microscopy. The antibodies were mostly found in the cytoplasm, which indicated that some cytoplasmic sequences in fixed cells existed as Z-RNA 62 .Cytoplasmic microinjection of anti-Z-RNA antibodies was found to inhibit cell multiplication 63 . The experiments on Z-RNA were mostly carried out in the late 1980s, and since 1990 there have been no further publications. However, a possible physiological role for Z-RNA was suggested recently by Brown, and Lowenhaupt et al., who found that the Z-DNA-binding domain of the editing enzyme double-stranded RNA adenosine deaminase (ADAR1) could bind to Z-RNA and Z-DNA 64 with similar affinity. It had been known for some time that certain RNA viruses that replicate in the cytoplasm undergo considerable changes in sequence, which were probably the consequence of hyper-editing by ADAR1. Sequence analysis of the virus found in measles encephalitis showed that the RNA undergoes many edits: adenines are replaced by guanines, and uracils by cytosines. So, this virus has been extensively hyper-edited by the editing enzyme 64 .Full length ADAR1 that contains the Z-DNA-binding domain is upregulated by the interferon response of the cell, which is triggered by the measles virus. Furthermore, ADAR1 accumulates in the cytoplasm in which the measles virus replicates. So, it is possible that the Z? ADAR1 binds to negatively torsionally strained double-stranded RNA, which might form during viral replication, targeting the editing enzyme to this site. The Z-DNA/Z-RNA-binding domain might have a role in the attempts of cells to inactivate the invading virus. More experimental data are needed to test this hypothesis. � 2003 Nature Publishing Group PERSPECTIVES vaccinia virus, it might also be active in humans. This molecule could be developed to eliminate the harmful side-effects of vac- cination. More importantly, the E3L protein of the closely related variola virus, which is the agent of smallpox, is almost identical to the vaccinia E3L 45 .So, small molecule drugs that bind to E3L might make it possible to develop a therapy for smallpox. This is the first example in which a Z-DNA-binding protein has been found to be involved in viral pathogenesis. If other viruses use a similar mechanism to downregulate the host response, then these proteins might be potential targets for anti-viral drugs. Conclusions The Z-DNA conformation has been difficult to study because it does not exist as a stable feature of the double helix. Instead, it is a transient structure that is occasionally induced by biological activity and then quickly disappears. The discovery and bio- logical activity of Z-DNA-specific binding proteins point the way to a broader under- standing of its biological roles. One active area of research will be the comparison of the occurrence of Z-DNA-forming sequences and Z-DNA-binding proteins between prokaryotes and eukaryotes; already, there are indications that sequences that form Z-DNA are less frequent in prokaryotes (P. S. Ho, per- sonal communication). What we have seen so far is just the beginning, but it has provided insights that are likely to stimulate more research into this unusual left-handed version of the DNA double helix. binding (Z E3L ) and a C-terminal domain that has a dsRNA-binding motif. In infected cells, E3L is exported to the nucleus where it accumulates. Viral pathogenicity To investigate the pathogenicity of the vac- cinia virus in the mouse, and its relationship to the possible Z-DNA-binding activities of E3L, a collaboration was set up between the Rich laboratory and the Jacobs laboratory. Chimeric viruses were created in which the N-terminal domain of vaccinia E3L (Z E3L ) was removed. Z E3L has sequence similarities to Z? ADAR1 and Z? DLM1 .Two chimeric viruses were created in which the two known Z-DNA-binding domains were substituted for Z E3L .In carrying out these domain swaps, a little more than a dozen amino acids in the domain remained unchanged; these were the residues that were known to bind Z-DNA in the co-crystals. However, more than 50 other residues were changed. The chimeric viruses were as pathogenic as the wild type 45 ;how- ever, when the N-terminal residues of vac- cinia E3L were deleted, the mice survived (FIG. 4).Other experiments were carried out in which mutations were introduced into both chimeric and wild-type viruses; if Z-DNA binding was weakened by these mutations, viral pathogenicity was reduced 45 . It was postulated that the Z E3L domain in the nucleus of the infected cell might bind to the Z-DNA that formed near the transcription start site of certain genes, which would impair the ability of the host cell to carry out transcription and so inhibit the anti-viral response 45 . It is likely that a small molecule or drug can be made that will bind to the Z-DNA-binding pocket of the E3L molecule. If such a mole- cule rescued mice that were infected with NATURE REVIEWS | GENETICS VOLUME 4 | JULY 2003 | 571 % Survival 0 20 40 60 80 100 Days post-infection 48101220 6 WT (Z E3L ) E3L (?1? 83) Z? DLM1 Z? ADAR1 Figure 4 | The lethality of mice following intracerebral inoculation of 100 viral plaque-forming units of vaccinia virus constructs 45 . No lethality is associated with the deletion of the 83 N-terminal residues of the E3L protein (?1?83). However, the wild-type (WT) virus and the two chimeric viruses in which the wild- type E3L N-terminal domain has been substituted by either Z? DLM1 or Z? ADAR1 are all equally pathogenic. The wild type and the two chimeric E3L molecules have residues in common, which are important in binding Z-DNA in the two co-crystal structures that have been solved. Reproduced with permission from REF. 45. Glossary ADAR1 The editing enzyme double-stranded RNA adenosine deaminase, which converts adenine to inosine in pre-mRNA. This enzyme has an N-terminal domain that binds tightly to Z-DNA. ANTI- AND SYN-CONFORMATIONS Nucleic-acid bases can rotate about the glycosyl bond. The Watson?Crick hydrogen-bonding atoms point away from the sugar in the anti-conformation (as in B-DNA), and have the opposite orientation in the syn-conformation. Purines can form the syn-conformation more easily than pyrimidines. BROWNIAN MOTION The random kinetic thermal motion of molecules. DNA FIBRE X-RAY DIFFRACTION ANALYSIS X-rays are scattered by electrons and if a molecule has regular periodicities, they will be detected by the diffraction pattern. In this technique, DNA molecules are orientated so that their long axes are parallel. Although the diffraction pattern can provide some information about the molecule, the conclusions are often tentative because the number of reflections is relatively small. CIRCULAR DICHROISM This method measures the difference in absorption of right and left circularly polarized light as it passes through a solution containing molecules that absorb at that wavelength. The circular-dichroism spectrum is plotted as a function of wavelength. POLYTENE CHROMOSOME A chromosome that has duplicated many times and has remained laterally associated so that it is visible, as seen in Drosophila salivary glands. RAMAN SPECTRUM Measures the vibrations of molecules that are usually influenced by the conformation of a molecule. This can be obtained from crystalline materials as well as materials in solution. SINGLE-CRYSTAL X-RAY DIFFRACTION In this technique, a molecule is crystallized to produce many repetitions that are organized in a regular three- dimensional array. This produces X-ray diffraction with a large number of reflections. Solution of the crystal structure can establish the conformation of the molecule because large amounts of redundant data are collected. � 2003 Nature Publishing Group 572 | JULY 2003 | VOLUME 4 www.nature.com/reviews/genetics PERSPECTIVES 46. Zhang, S., Lockshin, C., Herbert, A., Winter, E. & Rich, A. Zuotin, a putative Z-DNA binding protein in Saccharomyces cerevisiae. EMBO J. 11, 3787?3796 (1992). 47. Zhang, S., Holmes, T., Lockshin, C. & Rich, A. Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane. Proc. Natl Acad. Sci. USA 90, 3334?3338 (1993). 48. Zhang, S. et al. Self-complementary oligopeptide matrices support mammalian cell attachment. Biomaterials 16, 1385?1393 (1995). 49. Holmes, T., Delacalle, S., Su, X., Rich, A. & Zhang, S. Extensive neurite outgrowth and active neuronal synapses on peptide scaffolds. Proc. Natl Acad. Sci. USA 97, 6728?6733 (2000). 50. Kisiday, J. et al. Self-assembling peptide hydrogel fosters chondrocyte extracellular matrix production and cell division: implications for cartilage tissue repair. Proc. Natl Acad. Sci. USA 99, 9996?10001 (2002). 51. Zhang, S. & Rich, A. Direct conversion of an oligopeptide from a ?-sheet to an ?-helix: a model for amyloid formation. Proc. Natl Acad. Sci. USA 94, 23?28 (1997). 52. Zhang, S. et al. Biological surface engineering: a simple system for cell pattern formation. Biomaterials 20, 1213?1220 (1999). 53. Vauthey, S., Santoso, S., Gong, H., Watson, N. & Zhang, S. Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles. Proc. Natl Acad. Sci. USA 99, 5355?5360 (2002). 54. von Maltzahn, G., Vauthey, S., Santoso, S. & Zhang, S. Positively charged surfactant-like peptides self- assemble into nanostructures. Langmuir 19, 4332?4337 (2003). 55. Zhang, S. Building from bottom-up. Materials Today 6, 20?27 (2003). 56. Uesugi, W., Shida, T. & Ikehara, M. Synthesis and properties of CpG analogues containing an 8-bromoguanosine residue. Evidence for Z-RNA duplex formation. Biochemistry 21, 3400?3408 (1982). 57. Hall, K., Cruz, P., Tinoko, I., Jovin, T. M. & van de Sande, J. H. ?Z-RNA? ? a left-handed RNA double helix. Nature 311, 584?586 (1984). 58. Davis, P. W., Hall, K., Cruz, P., Tinoco, I. & Neilson, T. The tetraribonucleotide rCpGpCpG forms a left-handed Z-RNA double helix. Nucleic Acids Res. 14, 1279?1291 (1986). 59. Teng, M. K., Liaw, Y. C., van der Marel, G. A., van Boom, J. H. & Wang, A.-H. Effects of the O2? hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)- [Z-DNA]. Biochemistry 28, 4923?4928 (1989). 60. Davis, P. W., Adamiak, R. W. & Tinoco, I. Z-RNA: the solution NMR structure of r(CGCGCG). Biopolymers 29, 109?122 (1990). 61. Hardin, C. C., Zarling, D. A., Wolk, S. K., Ross, W. S. & Tincoc, I. Characterization of anti-Z-RNA polyclonal antibodies: epitope properties and recognition of Z-DNA. Biochemistry 27, 4169?4177 (1988). 62. Zarling, D. A., Calhoun, C. J., Hardin, C. C. & Zarling, A. H. Cytoplasmic Z-RNA. Proc. Natl Acad. Sci. USA 84, 6117?6121 (1987). 63. Zarling, D. A., Calhoun, C. J., Feuerstein, B. G. & Sena, E. P. Cytoplasmic microinjection of immunoglobulin Gs recognizing RNA helices inhibits human cell growth. J. Mol. Biol. 211, 147?160 (1990). 64. Brown, B. A., Lowenhaupt, K., Wilbert, C. M., Hanlon, C. B. & Rich, A. The Za domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc. Natl Acad. Sci. USA 97, 13532?13586 (2000). Online links DATABASES The following terms in this article are linked online to: Entrez: http://www.ncbi.nlm.nih.gov/entrez DLM1 | E3L | zuotin LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink C-MYC | CSF1 OMIM: http://www.ncbi.nlm.nih.gov/Omim systemic lupus erythematosus FURTHER INFORMATION Shuguang Zhang?s laboratory: http://web.mit.edu/lms/www Access to this interactive links box is free online. 23. Jackson, D. A., Yuan, J. & Cook, P. R. A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. J. Cell Sci. 90, 365?378 (1988). 24. Wittig, B., Dorbic, T. & Rich, A. The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain. J. Cell. Biol. 108, 755?764 (1989). 25. Wittig, B., Dorbic, T. & Rich, A. Transcription is associated with Z-DNA formation in metabolically active permeabilized mammalian cell nuclei. Proc. Natl Acad. Sci. USA 88, 2259?2263 (1991). 26. Wittig, B., Wolfl, S., Dorbic, T., Vahrson, W. & Rich, A. Transcription of human C-MYC in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene. EMBO J. 11, 4653?4663 (1992). 27. Wolfl, S., Wittig, B. & Rich, A. Identification of transcriptionally induced Z-DNA segments in the human C-MYC gene. Biochim. Biophys. Acta 1264, 294?302 (1995). 28. Wolfl, S., Martinez, C., Rich, A. & Majzoub, J. A. Transcription of the human corticotropin-releasing hormone gene in NPLC cells is correlated with Z-DNA formation. Proc. Natl Acad. Sci. USA 93, 3664?3668 (1996). 29. Liu, R. et al. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell 106, 309?318 (2001). 30. Garner, M. M. & Felsenfeld, G. Effect of Z-DNA on nucleosome placement. J. Mol. Biol. 196, 581?590 (1987). 31. Herbert, A. G. & Rich, A. A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide. Nucl. Acids Res. 21, 2669?2672 (1993). 32. Herbert, A., Lowenhaupt, K., Spitzner, J. & Rich, A. Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proc. Natl Acad. Sci. USA 92, 7550?7554 (1995). 33. Bass, B. L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817?846 (2002). 34. Herbert, A. et al. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl Acad. Sci. USA 94, 8421?8426 (1997). 35. Kim, Y.-G., Kim, P. S., Herbert, A. & Rich, A. Construction of a Z-DNA-specific restriction endonuclease. Proc. Natl Acad. Sci. USA 94, 12875?12879 (1997). 36. Kim, Y. G., Lowenhaupt, K., Schwartz, T. & Rich, A. The interaction between Z-DNA and the Zab domain of dsRNA adenosine deaminase characterized using fusion nucleases. J. Biol. Chem. 274, 19081?19086 (1999). 37. Berger, I. et al. Spectroscopic characterization of a DNA- binding domain, Z?, from the editing enzyme dsRNA adenosine deaminase: evidence for left-handed Z-DNA in the Z?-DNA complex. Biochemistry 37, 13313?13321 (1998). 38. Kim, Y.-G. et al. The Zab domain of the human RNA editing enzyme ADAR1 recognizes Z-DNA when surrounded by B-DNA. J. Biol. Chem. 275, 26828?26833 (2000). 39. Oh, D.-B., Kim, Y.-G. & Rich, A. Z-DNA-binding proteins can act as potent effectors of gene expression in vivo. Proc. Natl Acad. Sci. USA 99, 16666?16671 (2002). 40. Schwartz, T., Rould, M. A., Lowenhaupt, K., Herbert, A. & Rich, A. Crystal structure of the Z? domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284, 1841?1845 (1999). 41. Herbert, A. & Rich, A. Role of binding domains for dsRNA and Z-DNA in the in vivo editing of minimal substrates by ADAR1. Proc. Natl Acad. Sci. USA 98, 12132?12137 (2001). 42. Fu, Y. et al. Cloning of DLM-1, a novel gene that is up- regulated in activated macrophages, using RNA differential display. Gene 240, 157?163 (1999). 43. Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U. & Rich, A. Structure of the DLM-1?Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nature Struct. Biol. 8, 761?765 (2001). 44. Brandt, T. A. & Jacobs, B. L. Both carboxy- and amino- terminal domains of the vaccinia virus interferon resistance gene, E3L are required for pathogenesis in a mouse model. J. Virol. 75, 850?856 (2001). 45. Kim, Y.-G. et al. A role for Z-DNA binding in vaccinia virus pathogenesis. Proc. Natl Acad. Sci. USA 100, 6974?6979 (2003). Alexander Rich is at the Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 68-233, Cambridge, Massachusetts 02139, USA. Shuguang Zhang is at the Center for Biomedical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room NE47-379, Cambridge, Massachusetts 02139, USA. Correspondence to S.Z. e-mail: shuguang@mit.edu doi:10.1038/nrg1115 1. Wang, A. H. J. et al. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680?686 (1979). 2. Pohl, F. M. & Jovin, T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). J. Mol. Biol. 67, 375?396 (1972). 3. Thamann, T. J., Lord, R. C., Wang, A. H. J. & Rich, A. High salt form of poly(dG-dC)?poly(dG-dC) is left handed Z-DNA: raman spectra of crystals and solutions. Nucl. Acids Res. 9, 5443?5457 (1981). 4. Behe, M. & Felsenfeld, G. Effects of methylation on a synthetic polynucleotide: the B?Z transition in poly(dG?m5dC)?poly(dG?m5dC). Proc. Natl Acad. Sci. USA 78, 1619?1623 (1981). 5. Rich, A., Nordheim, A. & Wang, A. H.-J. The chemistry and biology of left-handed Z-DNA. Ann. Rev. Biochem. 53, 791?846 (1984). 6. Nordheim, A. & Rich, A. The sequence (dC?dA) n ?(dG?dT) n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc. Natl Acad. Sci. USA 80, 1821?1825 (1983). 7. Haniford, D. B. & Pulleyblank, D. E. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature 302, 632?634 (1983). 8. Feigon, J., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H. & Rich, A. Z-DNA forms without an alternating purine?pyrimidine sequence in solution. Science 230, 82?84 (1985). 9. Peck, L. J., Nordheim, A., Rich, A. & Wang, J. C. Flipping of cloned d(pGpG)n?d(pCpG)n DNA sequences from right to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc. Natl Acad. Sci. USA 79, 4560?4564 (1982). 10. Haniford, D. B. & Pulleyblank, D. E. The in vivo occurrence of Z-DNA. J. Biomol. Struct. Dyn. 1, 593?609 (1983). 11. Ellison, M. J., Kelleher, R. J., Wang, A. H.-J., Habener, J. F. & Rich, A. Sequence-dependent energetics of the B?Z transition in supercoiled DNA containing nonalternating purine?pyrimidine sequences. Proc. Natl Acad. Sci. USA 82, 8320?8324 (1985). 12. Ho, P. S., Ellison, M. J., Quigley, G. J. & Rich, A. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J. 5, 2737?2744 (1986). 13. Marx, J. Z-DNA: still searching for a function. Science 230, 794?796 (1985). 14. Lafer, E. M., Moller, A., Nordheim, A., Stollar, B. D. & Rich, A. Antibodies specific for left-handed DNA. Proc. Natl Acad. Sci. USA 78, 3546?3550 (1981). 15. Moller, A. et al. Monoclonal antibodies recognize different parts of Z-DNA. J. Biol. Chem. 257, 12081?12085 (1982). 16. Lafer, E. M. et al. Z-DNA specific antibodies in human systemic lupus erythematosus. J. Clin. Invest. 71, 314?321 (1983). 17. Nordheim, A. et al. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature 294, 417?422 (1981). 18. Lancillotti, F., Lopez, M. C., Arias, P. & Alonso, C. Z-DNA in transcriptionally active chromosomes. Proc. Natl Acad. Sci. USA 84, 1560?1564 (1987). 19. Arndt-Jovin, D. J. et al. Left-handed Z-DNA in bands of acid-fixed polytene chromosomes. Proc. Natl Acad. Sci. USA 80, 4344?4348 (1983). 20. Lipps, H. J. et al. Antibodies against Z-DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate Stylonychia mytilus. Cell 32, 435?441 (1983). 21. Liu, L. F. & Wang, J. C. Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. USA 84, 7024?7027 (1987). 22. Schroth, G. P., Chou, P.-J. & Ho, P. S. Mapping Z-DNA in the human genome: computer aided mapping reveals a non-random distribution of potential Z-DNA forming sequences in human genes. J. Biol. Chem. 267, 11846?11855 (1992). "
Add Content to Group
|
Bookmark
|
Keywords
|
Flag Inappropriate
share
Close
Digg
Facebook
MySpace
Google+
Comments
Close
Please Post Your Comment
*
The Comment you have entered exceeds the maximum length.
Submit
|
Cancel
*
Required
Comments
Please Post Your Comment
No comments yet.
Save Note
Note
View
Public
Private
Friends & Groups
Friends
Groups
Save
|
Cancel
|
Delete
Please provide your notes.
Next
|
Prev
|
Close
|
Edit
|
Delete
Genetics
Gene Inheritance and Transmission
Gene Expression and Regulation
Nucleic Acid Structure and Function
Chromosomes and Cytogenetics
Evolutionary Genetics
Population and Quantitative Genetics
Genomics
Genes and Disease
Genetics and Society
Cell Biology
Cell Origins and Metabolism
Proteins and Gene Expression
Subcellular Compartments
Cell Communication
Cell Cycle and Cell Division
Scientific Communication
Career Planning
Loading ...
Scitable Chat
Register
|
Sign In
Visual Browse
Close
Comments
CloseComments
Please Post Your Comment