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Z-DNA

Bailey Meyer

The Consequences of Z-DNA Binding to Vaccinia E3L Protein

As Z-DNA has been researched more thoroughly, it has been discovered that the structure of Z-DNA can bind to Z-DNA binding proteins through london dispersion and hydrogen bonding [1]. One example of a Z-DNA binding protein is the vaccinia E3L protein, which is a product of the E3L gene and mimics a mammalian protein that binds Z-DNA.[25][26]. Not only does the E3L protein have affinity to Z-DNA, it has also been found to play a role in the level of severity of virulence in mice caused by vaccinia virus, a type of poxvirus. Two critical components to the E3L protein that determine virulence are the N-terminus and the C-terminus. The N-terminus is made of up a sequence similar to that of the Zα domain, also called Adenosine deaminase z-alpha domain, while the C-terminus is composed of a double stranded RNA binding motif [1]. Through research done by Kim, Y. et al. at the Massachusetts Institute of Technology, it was shown that replacing the N-terminus of the E3L gene with a Zα domain sequence, containing 14 similar Z-DNA binding residues, had little to no effect on the virulence of the gene [1]. In Contrast, Kim, Y. et al. also found that deleting all 83 residues of the E3L N-terminus resulted in decreased virulence. This supports their claim that the N-terminus containing the Z-DNA binding residues is necessary for virulence. [1]. Overall, these findings show that the similar Z-DNA binding residues within the N-terminus of the E3L protein and the Zα domain are the most important factors determining virulence caused by the vaccinia virus, while amino acid residues not involved in Z-DNA binding have little to no effect. A future implication of these findings includes reducing Z-DNA binding of E3L in vaccines containing the vaccinia virus so negative reactions to the virus can be minimized in humans.

Furthermore, Alexander Rich and Jin-Ah Kwon found that E3L acts as a transactivator for human IL-6, NF-AT, and p53 genes. Their results show that HeLa cells containing E3L had increased expression of human IL-6, NF-AT, and p53 genes and point mutations or deletions of certain Z-DNA binding amino acid residues decreased that expression [2]. Specifically, mutations in Tyr 48 and Pro 63 were found to reduce transactivation of the previously mentioned genes, as a result of loss of hydrogen bonding and london dispersion forces between E3L and the Z-DNA. Overall, these results show that decreasing the bonds and interactions between Z-DNA and Z-DNA binding proteins decreases both virulence, gene regulation, and expression and therefore, strong bonds between Z-DNA and the E3L binding protein is for these functions.

Bailey-Raye (talk) 00:36, 18 November 2018 (UTC)

Citations

[1]. Kim, S. H.; Lim, S.; Lee, A.; Kwon, D, H.; Song, H. K.; Lee, J.; Cho, M.; Johner, A.; Lee, N.; Hong, S. “A Role for Z-DNA binding in vaccinia virus pathogenesis”. Nucleic Acids Research, 2018, 46,8 4129–4137.

[2]. Kwon, J.; Rich, A. Biological function of the vaccinia virus Z-DNA binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells. PNAS, 2005, 102, 36, 12759–12764.

Haley White

Biological Significance While it is unknown whether Z-DNA is directly responsible for the formation of any biological conditions, it has been linked to both Alzheimer's disease and Systemic lupus erythematosus. A study was conducted on the DNA found in the hippocampus of brains that were normal, moderately affected with Alzheimer’s disease, and severely affected with Alzheimer’s disease. Through the use of Circular dichroism, this study showed the presence of Z-DNA in the DNA of those severely affected [1]. In this study it was also found that major portions of the moderately affected DNA was in the B-Z intermediate conformation. This is significant because from these findings it was concluded that the transition from B-DNA to Z-DNA is dependent on the progression of Alzheimer's Disease [1]. Additionally, Z-DNA is associated with systemic Lupus Erythematosus (SLE) through the presence of naturally occurring antibodies. Significant amounts of anti Z-DNA antibodies were found in SLE patients and were not present in other rheumatic diseases [2]. There are two types of these antibodies, one interacts with the bases exposed on the surface of Z-DNA and denatured DNA, while the other exclusively interacts with the zig-zag backbone of only Z-DNA. Similar to that found in Alzheimer's Disease, the antibodies vary depending on the stage of the disease with maximal antibodies in the most active stages of SLE.

Citations

[1]. Suram, A.; Rao, J.; Latha, K. S.; Viswamitra, M. A. Evidence to Show the Topological Change of DNA from B-DNA to Z-DNA Conformation in the Hippocampus of Alzheimer's Brain. NeuroMolecular Medicine, 2002, 02, 289-297.

[2]. Lafer, E. M.; Valle, R. P. C.; Möller, A.; Nordheim, A.; Schur, P. H.; Rich, A.; Stollar, B. D. Z-DNA-specific Antibodies in Human Systemic Lupus Erythematosus. J. Clin. Invest., 1983, 71, 314-321.

Mauro Gracia

Pathway 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. 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 energy barrier than the previously hypothesized concerted mechanism. 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." In 2018, the pathway from B-DNA to Z-DNA was experimentally proven using smFRET assays. 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. 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 binding protein, hZαADAR1, was used at varying concentrations to induce the transformation from B-DNA to Z-DNA. The smFRET assays revealed a B* transition state, which formed as the binding of hZαADAR1 accumulated on the B-DNA structure and stabilized it. 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. 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.

Sources:

[1] Andrew, H.J.W., Quigley, G.J., Koplack, F.J., et. al. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979. 282. 680-686.

[2] Lee, J., Kim, Y.G., Kim, K.K. et. al. Transition between B-DNA and Z-DNA: Free Energy Landscape for the B-Z Junction Propagation. J. Phys. Chem. 2010. 114. 9872-9881.

[3] Kim, S.H., Lim, S., Lee, A.R., et. al. Unveiling the pathway to Z-DNA in the protein-induced B–Z transition. Nucleic Acids Research. 2018. 8. 4129–4137.

[4] Cooper, D., Uhm, H., Tauzin, L., et. al. Photobleaching Lifetimes of Cyanine Fluorophores Used for Single-Molecule Fçrster Resonance Energy Transfer in the Presence of Various Photoprotection Systems. ChemBioChem. 2013. 14. 1075 – 1080.

[5] Didenko, V. DNA Probes Using Fluorescence Resonance Energy Transfer (FRET): Designs and Applications. Biotechniques. 2001. 31. 1106–1121.

[6] Herbert, A., Alfken, J., Kim, Y., et. al. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl. Acad. Sci. 1997. 94. 8421–8426.  — Preceding unsigned comment added by 76.78.10.37 (talk) 03:44, 12 November 2018 (UTC) 76.78.10.37 (talk) 04:15, 12 November 2018 (UTC)