Editing Z-DNA (section)

=== Pathway of formation of Z-DNA from B-DNA ===

Since the discovery and crystallization of Z-DNA in 1979, the configuration has left scientists puzzled about the pathway and mechanism from the B-DNA configuration to the Z-DNA configuration.<ref>{{Cite journal|last1=Wang|first1=Andrew H.-J.|last2=Quigley|first2=Gary J.|last3=Kolpak|first3=Francis J.|last4=Crawford|first4=James L.|last5=van Boom|first5=Jacques H.|last6=van der Marel|first6=Gijs|last7=Rich|first7=Alexander|date=December 1979|title=Molecular structure of a left-handed double helical DNA fragment at atomic resolution|journal=Nature|volume=282|issue=5740|pages=680–686|doi=10.1038/282680a0|issn=0028-0836|pmid=514347|bibcode=1979Natur.282..680W|s2cid=4337955}}</ref> The conformational change from B-DNA to the Z-DNA structure was unknown at the atomic level, but in 2010, computer simulations conducted by Lee et al. were able to computationally determine that the step-wise propagation of a B-to-Z transition would provide a lower [[activation energy|energy barrier]] than the previously hypothesized concerted mechanism.<ref name=":0">{{Cite journal|last1=Lee|first1=Juyong|last2=Kim|first2=Yang-Gyun|last3=Kim|first3=Kyeong Kyu|last4=Seok|first4=Chaok|date=2010-08-05|title=Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation|journal=The Journal of Physical Chemistry B|volume=114|issue=30|pages=9872–9881|doi=10.1021/jp103419t|pmid=20666528|issn=1520-6106|citeseerx=10.1.1.610.1717}}</ref> Since this was computationally proven, the pathway would still need to be tested experimentally in the lab for further confirmation and validity, in which Lee et al. specifically states in their journal article, "The current [computational] result could be tested by [[Single-molecule FRET]] (smFRET) experiments in the future."<ref name=":0" /> In 2018, the pathway from B-DNA to Z-DNA was experimentally proven using smFRET assays.<ref name=":3">{{Cite journal|last1=Kim|first1=Sook Ho|last2=Lim|first2=So-Hee|last3=Lee|first3=Ae-Ree|last4=Kwon|first4=Do Hoon|last5=Song|first5=Hyun Kyu|last6=Lee|first6=Joon-Hwa|last7=Cho|first7=Minhaeng|last8=Johner|first8=Albert|last9=Lee|first9=Nam-Kyung|date=2018-03-23|title=Unveiling the pathway to Z-DNA in the protein-induced B–Z transition|journal=Nucleic Acids Research|volume=46|issue=8|pages=4129–4137|doi=10.1093/nar/gky200|issn=0305-1048|pmc=5934635|pmid=29584891}}</ref> This was performed by measuring the intensity values between the donor and acceptor fluorescent dyes, also known as [[Fluorophore]]s, in relation to each other as they exchange electrons, while tagged onto a DNA molecule.<ref>{{Cite journal|last1=Cooper|first1=David|last2=Uhm|first2=Heui|last3=Tauzin|first3=Lawrence J.|last4=Poddar|first4=Nitesh|last5=Landes|first5=Christy F.|date=2013-06-03|title=Photobleaching Lifetimes of Cyanine Fluorophores Used for Single-Molecule Förster Resonance Energy Transfer in the Presence of Various Photoprotection Systems|journal=ChemBioChem|volume=14|issue=9|pages=1075–1080|doi=10.1002/cbic.201300030|pmc=3871170|issn=1439-4227|pmid=23733413}}</ref><ref>{{Cite journal|last=Didenko|first=Vladimir V.|date=November 2001|title=DNA Probes Using Fluorescence Resonance Energy Transfer (FRET): Designs and Applications|journal=BioTechniques|volume=31|issue=5|pages=1106–1121|doi=10.2144/01315rv02|issn=0736-6205|pmc=1941713|pmid=11730017}}</ref> The distances between the fluorophores could be used to quantitatively calculate the changes in proximity of the dyes and conformational changes in the DNA. A Z-DNA high affinity [[DNA-binding protein|binding protein]], hZαADAR1,<ref>{{Cite journal|last1=Herbert|first1=A.|last2=Alfken|first2=J.|last3=Kim|first3=Y.-G.|last4=Mian|first4=I. S.|last5=Nishikura|first5=K.|last6=Rich|first6=A.|date=1997-08-05|title=A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase|journal=Proceedings of the National Academy of Sciences|volume=94|issue=16|pages=8421–8426|doi=10.1073/pnas.94.16.8421|issn=0027-8424|pmc=22942|pmid=9237992|bibcode=1997PNAS...94.8421H|doi-access=free}}</ref> was used at varying concentrations to induce the transformation from B-DNA to Z-DNA.<ref name=":3" /> The smFRET assays revealed a B* transition state, which formed as the binding of hZαADAR1 accumulated on the B-DNA structure and stabilized it.<ref name=":3" /> This step occurs to avoid high junction energy, in which the B-DNA structure is allowed to undergo a conformational change to the Z-DNA structure without a major, disruptive change in energy. This result coincides with the computational results of Lee et al. proving the mechanism to be step-wise and its purpose being that it provides a lower energy barrier for the conformational change from the B-DNA to Z-DNA configuration.<ref name=":0" /> Contrary to the previous notion, the binding proteins do not actually stabilize the Z-DNA conformation after it is formed, but instead they actually promote the formation of the Z-DNA directly from the B* conformation, which is formed by the B-DNA structure being bound by high affinity proteins.<ref name=":3" />