Difference between revisions of "Z-DNA"
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| − | '''Z-DNA''' is a form of DNA in which the double helix winds to the left in a zig-zag pattern (instead of to the right, like the more common B-DNA form). | + | '''Z-DNA''' is a left-handed helical form of DNA in which the double helix winds to the left in a zig-zag pattern (instead of to the right, like the more common B-DNA form). |
| − | Z-DNA was the first crystal structure of a DNA molecule to be solved (see: x-ray crystallography). It was solved by [[Alexander Rich]] and co-workers in 1979 at | + | Z-DNA was the first crystal structure of a DNA molecule to be solved (see: x-ray crystallography). It was solved by [[Dr. Alex Rich Laboratory|Alexander Rich]] and co-workers in 1979 at Massachusetts Institute of Technology<ref name=Wang1979>Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, and Rich A (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. ''Nature (London), 282:680-686''.</ref>. |
| − | Z-DNA is quite different from the right-handed forms. Z-DNA is often compared against B-DNA in order to illustrate the major differences. This unique type of DNA | + | Z-DNA is quite different from the right-handed forms. In fact, Z-DNA is often compared against B-DNA in order to illustrate the major differences. This unique type of DNA forms under sequence-dependent conditions that require an alternating purine-pyrimidine sequence. Other chemical environmental factors favor the formation of Z-DNA such as high salt, the presence of some cations, and DNA supercoiling. |
| − | + | While no definitive biological significance of Z-DNA has been found, it is commonly believed to provide torsional strain relief while DNA transcription occurs. | |
| − | After 26 years of attempts, Rich ''et al.'' finally | + | An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form, ''[[Z-Hunt]]'', was written by [[Dr. P. Shing Ho Laboratory|Dr. P. Shing Ho]] in 1984 (at MIT). This algorithm was later developed by Tracy Camp, [[P. Christoph Champ]], Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of Z-DNA (with P. Shing Ho as the principal investigator)<ref name=Champ2004>[[Christoph Champ|Champ PC]], Maurice S, Vargason JM, Camp T, and Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. ''[[Nucleic Acids Research]], 32(22):6501-6510''.</ref>. Z-Hunt is available at [http://gac-web.cgrb.oregonstate.edu/zDNA/ Z-Hunt online]. A comparison of regions with a high sequence-dependent, predicted propensity to form Z-DNA in human chromosome 22 with a selected set of known gene transcription sites suggests there is a correlation<ref name=Champ2004>Champ PC, Maurice S, Vargason JM, Camp T, and Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. ''[[Nucleic Acids Research]], 32(22):6501-6510''.</ref>. |
| + | |||
| + | After 26 years of attempts, Rich ''et al.'' finally crystallized the junction box of B- and Z-DNA. Their results were published in an October 2005 ''Nature'' journal<ref name=Ha2005>Ha SC, Lowenhaupt K, Rich A, Kim YG, and Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. ''Nature, 437:1183-1186''.</ref>. Whenever Z-DNA forms, there must be two junction boxes that allow the flip back to the canonical B-form of DNA. | ||
| + | |||
| + | ==Abstracts== | ||
| + | |||
| + | <div style="padding: 1em; margin: 10px; border: 2px dotted #18e;"> | ||
| + | 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.<ref>Rich A, Zhang S (2003). Timeline: Z-DNA: the long road to biological function. ''Nat Rev Genet, 4(7):566-72''.</ref> | ||
| + | </div> | ||
| + | |||
| + | <div style="padding: 1em; margin: 10px; border: 2px dotted #18e;"> | ||
| + | Forty-nine years ago Watson and Crick proposed a double-stranded (ds-) model for DNA. This double helix has become an icon of molecular biology. Twenty-six years later, Rich accidently discovered Z-DNA, an exotic left-handed nucleic acid. For many years thereafter, this left-handed DNA was thought to be an artifact. DNA is no longer looked upon as a static molecule but rather an extremely dynamic structure in which different conformations are in equilibrium with each other. Many researchers have spent the last two decades characterizing this novel left-handed DNA structure. Now many investigators are beginning to accept the possibility that this novel ds-DNA conformation may play a significant ''in vivo'' role within eukaryotic and prokaryotic cells. However, more research needs to be performed before it is absolutely accepted by all in the scientific community.<ref>Gagna CE, Lambert WC (2003). The halting arrival of left-handed Z-DNA. ''Med Hypotheses, 60(3):418-23''.</ref> | ||
| + | </div> | ||
| + | <div style="padding: 1em; margin: 10px; border: 2px dotted #18e;"> | ||
| + | Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near the promoter region stimulates transcription. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA. Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These have been examined extensively, but their structure was unknown. Here we describe the structure of a B-Z junction as revealed by X-ray crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification.<ref name=ha>Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. ''Nature, 437:1183-1186''.</ref> | ||
| + | </div> | ||
| + | <div style="padding: 1em; margin: 10px; border: 2px dotted #18e;"> | ||
| + | The mammalian genome contains tens of thousands of CG and TG repeat sequences that have high potential to form the nonclassical left-handed double-helical Z-DNA structure. Previously we showed that activation of the colony-stimulating factor 1 (CSF1) gene by the chromatin remodeling enzyme, BRG1, results in formation of Z-DNA at the TG repeat sequence located within the promoter. In this report, we show that the TG repeats are assembled in a positioned nucleosome in the silent CSF1 promoter and that activation by BRG1 disrupts this nucleosome and results in Z-DNA formation. Active transcription is not required for the formation of Z-DNA but does result in an expanded region of Z-DNA. Formation of sequences by both BRG1 and the Z-DNA is required for effective chromatin remodeling of the CSF1 promoter. We propose the Z-DNA formation induced by BRG1 promotes a transition from a transient and partial remodeling to a more extensive disruption of the canonical nucleosomal structure. The data presented in this report establish that Z-DNA formation is an important mechanism in modulating chromatin structure, in similarity to the activities of ATP-dependent remodelers and posttranslational histone modifications.<ref name=Liu>Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. ''Mol Cell Biol, 26(7):2550-9''.</ref> | ||
| + | </div> | ||
==Representation of various forms of DNA== | ==Representation of various forms of DNA== | ||
| Line 46: | Line 64: | ||
==References== | ==References== | ||
| − | * Champ PC, Maurice S, Vargason JM, Camp T, | + | <small><references/></small> |
| − | * | + | ;General references |
| − | * | + | * Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". ''Methods, [Epub ahead of print]''. PMID: 18848994. |
| − | * Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, | + | *Zhang H, Yu H, Ren J, Qu X (2006). "[http://www.biophysj.org/cgi/content/full/90/9/3203 Reversible B/Z-DNA Transition under the Low Salt Condition and Non-B-Form PolydApolydT Selectivity by a Cubane-Like Europium-L-Aspartic Acid Complex]". ''Biophysical Journal 90:3203-3207''. {{doi|10.1529/biophysj.105.07840}} |
| + | * Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. ''Nature, 437:1183-1186''. | ||
| + | * [[Christoph Champ|Champ PC]], Maurice S, Vargason JM, Camp T, Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. ''Nucleic Acids Research, 32(22):6501-6510''. | ||
| + | * Eichman BF, Schroth GP, Basham BE, Ho PS (1999). The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. ''Nucleic Acids Res, 27(2):543-550''. | ||
| + | *Sinden RR, Pearson CE, Potaman VN, Ussery DW (1998). "DNA: Structure and Function". ''In Advances in Genome Biology. V R.D., ed.''. | ||
| + | * Ho PS (1994). The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. ''Proc Natl Acad Sci USA, 91(20):9549-9553''. | ||
| + | * Sinden RR (1994). DNA structure and function. ''Academic Press, 179-216''. | ||
| + | * Kagawa TF, Howell ML, Tseng K, Ho PS (1993). Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition. ''Nucleic Acids Res, 21(25):5978-5986''. | ||
| + | * Ellison MJ, Fenton MJ, Ho PS, Rich A (1987). Long-range interactions of multiple DNA structural transitions within a common topological domain. ''EMBO J, 6(5):1513-1522''. | ||
| + | * Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. ''EMBO J, 5(10):2737-2744''. | ||
| + | * Kelleher RJ 3rd, Ellison MJ, Ho PS, Rich A (1986). Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA. ''Proc Natl Acad Sci USA, 83(17):6342-6346''. | ||
| + | * Ho PS, Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH, Rich A (1985). G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG). ''EMBO J, 4(13A):3617-3623''. | ||
| + | * Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, Rich A (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. ''Nature (London), 282:680-686''. | ||
| + | |||
| + | ==See also== | ||
| + | *[[wikipedia:Adenosine deaminase]] | ||
| + | **[http://www.genenames.org/data/hgnc_data.php?match=ADAR ADAR1] | ||
| + | *[http://www.ncbi.nlm.nih.gov/sites/entrez/?db=gene&cmd=Retrieve&dopt=summary&list_uids=1435 CSF1: colony stimulating factor 1] | ||
| + | *[[wikipedia:ZBP1]] (Z-DNA binding protein 1) — found in ''Homo sapiens'', ''Mus musculus'', and ''Rattus norvegicus'' (so far) | ||
| + | *[http://amigo.geneontology.org/cgi-bin/amigo/gp-details.cgi?gp=ZFIN:ZDB-GENE-050301-2&session_id=1078amigo1238721938 pkz] (protein kinase containing Z-DNA binding domains) — from ''Danio rerio'' (Zebrafish) | ||
==External links== | ==External links== | ||
| − | * [http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] | + | *[http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] |
| + | *[http://www.cbs.dtu.dk/staff/dave/DNA_coke-1.htm DNA Structural Atlases for Sequenced Genomes] | ||
| + | *[http://humphry.chem.wesleyan.edu:8080/MDDNA/ MDDNA: Structural Bioinformatics of DNA] | ||
| + | *[http://web.mit.edu/newsoffice/1995/zdna-0816.html Rich team finds role for Z-DNA] (1995-08-16) | ||
| + | *[http://books.google.com/books?id=2OD3s17QIAkC&pg=PA94&lpg=PA94&dq=%22z+dna%22&source=web&ots=3GlQ66y6Y4&sig=OKe0fzg9SEiMICwFDX7U471BXSA DNA Conformation And Transcription] (Google Books) | ||
[[Category:Academic Research]] | [[Category:Academic Research]] | ||
Latest revision as of 01:28, 3 April 2009
Z-DNA is a left-handed helical form of DNA in which the double helix winds to the left in a zig-zag pattern (instead of to the right, like the more common B-DNA form).
Z-DNA was the first crystal structure of a DNA molecule to be solved (see: x-ray crystallography). It was solved by Alexander Rich and co-workers in 1979 at Massachusetts Institute of Technology[1].
Z-DNA is quite different from the right-handed forms. In fact, Z-DNA is often compared against B-DNA in order to illustrate the major differences. This unique type of DNA forms under sequence-dependent conditions that require an alternating purine-pyrimidine sequence. Other chemical environmental factors favor the formation of Z-DNA such as high salt, the presence of some cations, and DNA supercoiling.
While no definitive biological significance of Z-DNA has been found, it is commonly believed to provide torsional strain relief while DNA transcription occurs.
An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form, Z-Hunt, was written by Dr. P. Shing Ho in 1984 (at MIT). This algorithm was later developed by Tracy Camp, P. Christoph Champ, Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of Z-DNA (with P. Shing Ho as the principal investigator)[2]. Z-Hunt is available at Z-Hunt online. A comparison of regions with a high sequence-dependent, predicted propensity to form Z-DNA in human chromosome 22 with a selected set of known gene transcription sites suggests there is a correlation[2].
After 26 years of attempts, Rich et al. finally crystallized the junction box of B- and Z-DNA. Their results were published in an October 2005 Nature journal[3]. Whenever Z-DNA forms, there must be two junction boxes that allow the flip back to the canonical B-form of DNA.
Contents
Abstracts
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.[4]
Forty-nine years ago Watson and Crick proposed a double-stranded (ds-) model for DNA. This double helix has become an icon of molecular biology. Twenty-six years later, Rich accidently discovered Z-DNA, an exotic left-handed nucleic acid. For many years thereafter, this left-handed DNA was thought to be an artifact. DNA is no longer looked upon as a static molecule but rather an extremely dynamic structure in which different conformations are in equilibrium with each other. Many researchers have spent the last two decades characterizing this novel left-handed DNA structure. Now many investigators are beginning to accept the possibility that this novel ds-DNA conformation may play a significant in vivo role within eukaryotic and prokaryotic cells. However, more research needs to be performed before it is absolutely accepted by all in the scientific community.[5]
Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near the promoter region stimulates transcription. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA. Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These have been examined extensively, but their structure was unknown. Here we describe the structure of a B-Z junction as revealed by X-ray crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification.[6]
The mammalian genome contains tens of thousands of CG and TG repeat sequences that have high potential to form the nonclassical left-handed double-helical Z-DNA structure. Previously we showed that activation of the colony-stimulating factor 1 (CSF1) gene by the chromatin remodeling enzyme, BRG1, results in formation of Z-DNA at the TG repeat sequence located within the promoter. In this report, we show that the TG repeats are assembled in a positioned nucleosome in the silent CSF1 promoter and that activation by BRG1 disrupts this nucleosome and results in Z-DNA formation. Active transcription is not required for the formation of Z-DNA but does result in an expanded region of Z-DNA. Formation of sequences by both BRG1 and the Z-DNA is required for effective chromatin remodeling of the CSF1 promoter. We propose the Z-DNA formation induced by BRG1 promotes a transition from a transient and partial remodeling to a more extensive disruption of the canonical nucleosomal structure. The data presented in this report establish that Z-DNA formation is an important mechanism in modulating chromatin structure, in similarity to the activities of ATP-dependent remodelers and posttranslational histone modifications.[7]
Representation of various forms of DNA
Comparison Geometries of Some DNA Forms
| Geometry attribute | A-form | B-form | Z-form |
|---|---|---|---|
| Helix sense | right-handed | right-handed | left-handed |
| Repeating unit | 1 bp | 1 bp | 2 bp |
| Rotation/bp | 33.6° | 35.9° | 60°/2 |
| Mean bp/turn | 10.7 | 10.0 | 12 |
| Inclination of bp to axis | +19° | -1.2° | -9° |
| Rise/bp along axis | 2.3Å | 3.32Å | 3.8Å |
| Pitch/turn of helix | 24.6Å | 33.2Å | 45.6Å |
| Mean propeller twist | +18° | +16° | 0° |
| Glycosyl angle | anti | anti | C: anti, G: syn |
| Sugar pucker | C3'-endo | C2'-endo | C: C2'-endo, G: C2'-exo |
| Diameter | 26Å | 20Å | 18Å |
References
- ↑ Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, and Rich A (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature (London), 282:680-686.
- ↑ 2.0 2.1 Champ PC, Maurice S, Vargason JM, Camp T, and Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510.
- ↑ Ha SC, Lowenhaupt K, Rich A, Kim YG, and Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437:1183-1186.
- ↑ Rich A, Zhang S (2003). Timeline: Z-DNA: the long road to biological function. Nat Rev Genet, 4(7):566-72.
- ↑ Gagna CE, Lambert WC (2003). The halting arrival of left-handed Z-DNA. Med Hypotheses, 60(3):418-23.
- ↑ Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437:1183-1186.
- ↑ Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Mol Cell Biol, 26(7):2550-9.
- General references
- Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". Methods, [Epub ahead of print]. PMID: 18848994.
- Zhang H, Yu H, Ren J, Qu X (2006). "Reversible B/Z-DNA Transition under the Low Salt Condition and Non-B-Form PolydApolydT Selectivity by a Cubane-Like Europium-L-Aspartic Acid Complex". Biophysical Journal 90:3203-3207. DOI:10.1529/biophysj.105.07840
- Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437:1183-1186.
- Champ PC, Maurice S, Vargason JM, Camp T, Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510.
- Eichman BF, Schroth GP, Basham BE, Ho PS (1999). The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. Nucleic Acids Res, 27(2):543-550.
- Sinden RR, Pearson CE, Potaman VN, Ussery DW (1998). "DNA: Structure and Function". In Advances in Genome Biology. V R.D., ed..
- Ho PS (1994). The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc Natl Acad Sci USA, 91(20):9549-9553.
- Sinden RR (1994). DNA structure and function. Academic Press, 179-216.
- Kagawa TF, Howell ML, Tseng K, Ho PS (1993). Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition. Nucleic Acids Res, 21(25):5978-5986.
- Ellison MJ, Fenton MJ, Ho PS, Rich A (1987). Long-range interactions of multiple DNA structural transitions within a common topological domain. EMBO J, 6(5):1513-1522.
- Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J, 5(10):2737-2744.
- Kelleher RJ 3rd, Ellison MJ, Ho PS, Rich A (1986). Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA. Proc Natl Acad Sci USA, 83(17):6342-6346.
- Ho PS, Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH, Rich A (1985). G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG). EMBO J, 4(13A):3617-3623.
- Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, Rich A (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature (London), 282:680-686.
See also
- wikipedia:Adenosine deaminase
- CSF1: colony stimulating factor 1
- wikipedia:ZBP1 (Z-DNA binding protein 1) — found in Homo sapiens, Mus musculus, and Rattus norvegicus (so far)
- pkz (protein kinase containing Z-DNA binding domains) — from Danio rerio (Zebrafish)
