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Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure 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 thought to be one of three biologically active double helical structures along with A- and B-DNA.
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 MIT. The crystallisation of a B- to Z-DNA junction in 2005 provided a better understanding of the potential role Z-DNA plays in cells. 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.
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. The Z-DNA helix is left handed and has a structure that repeats every 2 base pairs. The major and minor grooves, unlike A- and B-DNA, show little difference in width. Formation of this structure is generally unfavourable, although certain conditions can promote it; such as alternating purine-pyrimidine sequence, DNA supercoiling or high salt and some cations. Z-DNA can form a junction with B-DNA in a structure which involves the extrusion of a base pair.
Predicting Z-DNA structure
It is possible to predict the likelihood of a DNA sequence forming a Z-DNA structure. An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form, ZHunt, 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). Z-Hunt is available at Z-Hunt online.
While no definitive biological significance of Z-DNA has been found, it is commonly believed to provide torsional strain relief (supercoiling) while DNA transcription occurs. The potential to form a Z-DNA structure also correlates with regions of active transcription. 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.
Z-DNA formed after transcription initiation in some cases may be bound by RNA modifying enzymes which then alter the sequence of the newly-formed RNA .
Comparison Geometries of Some DNA Forms
|Nucleobases:||Purine (Adenine, Guanine) | Pyrimidine (Uracil, Thymine, Cytosine)|
|Nucleosides:||Adenosine/Deoxyadenosine | Guanosine/Deoxyguanosine | Uridine | Thymidine | Cytidine/Deoxycytidine|
|Nucleotides:||monophosphates (AMP, GMP, UMP, CMP) | diphosphates (ADP, GDP, UDP, CDP) | triphosphates (ATP, GTP, UTP, CTP) | cyclic (cAMP, cGMP, cADPR)|
|Deoxynucleotides:||monophosphates (dAMP, dGMP, TMP, dCMP) | diphosphates (dADP, dGDP, TDP, dCDP) | triphosphates (dATP, dGTP, TTP, dCTP)|
|Ribonucleic acids:||RNA | mRNA (pre-mRNA/hnRNA) | tRNA | rRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA|
|Deoxyribonucleic acids:||DNA | cDNA | gDNA | msDNA | mtDNA|
|Nucleic acid analogues:||GNA | LNA | PNA | TNA | morpholino|
|Cloning vectors:||phagemid | plasmid | lambda phage | cosmid | P1 phage | fosmid | BAC | YAC | HAC|