User talk:Bailey-Raye/sandbox

Z-DNA

Bailey Meyer

Biological Function of Z-DNA Z-DNA binding has been found to play a role in the severity of virulence caused by the the viral EL3 gene product. Two critical components to the EL3 gene are the N terminus and the C-terminus. The N terminus is made of up a sequence similar to that of the Zα domain, while the C terminus is composed of a double stranded RNA binding motif [1]. Through research done by the department of Biology at Massachusetts Institute of Technology, it was shown that replacing the N-terminus of the EL3 gene with a Zα domain sequence containing Z-DNA binding residues had little to no effect on the virulence of the gene [1]. However, deleting 83 residues of the N-terminus resulted in decreased virulence [1]. This shows that the N-terminus plays an important role in determining the virulence. Furthermore, replacing the N-terminal with different sequences such as ZαADAR1, showed no change due to the fact that residues present in the sequence still bind to Z-DNA [1]. As a result, contact with Z-DNA is an important contributor to the intensity of virulence. Furthermore, Alexander Rich and Jin-Ah Kwon found that EL3, ZαADAR1, and ZαDLM1 can perform similar task, such as the prevention of apoptosis in HeLa cells caused by hygromycin-B [2]. This is also a direct result of having similar sequences and Z-DNA binding capabilities [2]. Overall, EL3 is important in stopping apoptosis due to its ability form dsRNA binding proteins. dsRNA is responsible for the induction of apoptosis whose effects can be hindered through the production of dsRNA binding proteins from EL3[3].

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.

[3]. Kibler, K.V.; Shors, T.; Perkins, K.B.; Zeman, C.C.; Banaszak, M.P.; Biesterfeldt, J.; Langland, J.O.; Jacobs, B.L. Double-Stranded RNA Is a Trigger for Apoptosis in Vaccinia Virus-Infected Cells. J Virol. 1997, 71,3, 1992–2003.

Haley White

Biological Significance While it is unknown whether Z-DNA is directly responsible for the formation of any biological conditions, it's presence has been linked to both Alzheimer's Disease and Systemic Lupus Erythematosus. A study conducted on normal, moderately affected with Alzheimer’s disease, and severely affected with Alzheimer's Disease human brains 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. 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 Alheimer'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 The pathway from B-DNA to Z-DNA was determined using single-molecule Forster Resonance Energy Transfer (smFRET) assays. [1] This was performed by measuring the intensity values between the donor and acceptor fluorescent dyes, also known as fluorophores, 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. [2,3] A Z-DNA high affinity binding protein, hZαADAR1, [4] was used at varying concentrations to induce the transformation from B-DNA to Z-DNA. [1] The smFRET assays revealed a B* transition state, which formed as the binding of hZαADAR1 accumulated on the B-DNA structure and stabilized it. [1] 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. 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*-DNA conformation, which is formed by the B-DNA structure being bound by high affinity proteins. [1]

Sources:

[1] 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.

[2] 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.

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

[4] 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)