Abstract
While DNA and RNA helices often adopt the canonical B- or A-conformation, the fluid conformational landscape of nucleic acids allows for many higher energy states to be sampled. One such state is the Z-conformation of nucleic acids, which is unique in that it is left-handed and has a “zigzag” backbone. The Z-conformation is recognized and stabilized by Z-DNA/RNA binding domains called Zα domains. We recently demonstrated that a wide range of RNAs can adopt partial Z-conformations termed “A–Z junctions” upon binding to Zα and that the formation of such conformations may be dependent upon both sequence and context. In this chapter, we present general protocols for characterizing the binding of Zα domains to A–Z junction-forming RNAs for the purpose of determining the affinity and stoichiometry of interactions as well as the extent and location of Z-RNA formation.
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References
D’Ascenzo L, Leonarski F, Vicens Q, Auffinger P (2016) ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response. Nucleic Acids Res. https://doi.org/10.1093/nar/gkw388
Harvey SC (1983) DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition. Nucleic Acids Res 11:4867–4878
Wang AHJ et al (1979) Molecular structure of a left-Handed double helical DNA fragment at atomic resolution. Nature. https://doi.org/10.1038/282680a0
Rich A, Zhang S (2003) Z-DNA: The long road to biological function. Nat Rev Genet. https://doi.org/10.1038/nrg1115
Herbert A (2019) Z-DNA and Z-RNA in human disease. Commun Biol. https://doi.org/10.1038/s42003-018-0237-x
Herbert A, Rich A (1996) The biology of left-handed Z-DNA. J Biol Chem. https://doi.org/10.1074/jbc.271.20.11595
Chiang DC, Li Y, Ng SK (2021) The role of the Z-DNA binding domain in innate immunity and stress granules. Front Immunol. https://doi.org/10.3389/fimmu.2020.625504
Lushnikov AY et al (2004) Interaction of the Zα domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy. Nucleic Acids Res. https://doi.org/10.1093/nar/gkh810
Herbert A et al (1998) The Zα domain from human ADAR1 binds to the Z-DNA conformer of many different sequences. Nucleic Acids Res. https://doi.org/10.1093/nar/26.15.3486
Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A (1999) Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 11(80):1841–1845
Brown BA, Lowenhaupt K, Wilbert CM, Hanlon EB, Rich A (2000) The Zα domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc Natl Acad Sci U S A. https://doi.org/10.1073/pnas.240464097
Placido D, Brown BA, Lowenhaupt K, Rich A, Athanasiadis A (2007) A left-handed RNA double helix bound by the Zα domain of the RNA-editing enzyme ADAR1. Structure. https://doi.org/10.1016/j.str.2007.03.001
Kruse H, Mrazikova K, D’Ascenzo L, Sponer J, Auffinger P (2020) Short but weak: the Z-DNA lone-pair·π conundrum challenges standard Carbon Van der Waals Radii. Angew Chem Int Ed. https://doi.org/10.1002/anie.202004201
Chung H et al (2018) Human ADAR1 prevents endogenous RNA from triggering translational shutdown. Cell. https://doi.org/10.1016/j.cell.2017.12.038
Feng S et al (2011) Alternate rRNA secondary structures as regulators of translation. Nat Struct Mol Biol. https://doi.org/10.1038/nsmb.1962
Dickerson RE et al (1982) The anatomy of A-, B-, and Z-DNA. Science 80. https://doi.org/10.1126/science.7071593
Ha SC et al (2009) The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZαADAR1. Nucleic Acids Res. https://doi.org/10.1093/nar/gkn976
Lee YM et al (2013) NMR investigation on the DNA binding and B-Z transition pathway of the Zα domain of human ADAR1. Biophys Chem. https://doi.org/10.1016/j.bpc.2012.12.002
Lee YM et al (2012) NMR study on the B-Z junction formation of DNA duplexes induced by Z-DNA binding domain of human ADAR1. J Am Chem Soc. https://doi.org/10.1021/ja211581b
Kim D et al (2018) Sequence preference and structural heterogeneity of BZ junctions. Nucleic Acids Res. https://doi.org/10.1093/nar/gky784
Sung CH, Lowenhaupt K, Rich A, Kim YG, Kyeong KK (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature. https://doi.org/10.1038/nature04088
Kim D et al (2009) Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA. Nucleic Acids Res. https://doi.org/10.1093/nar/gkp364
Lee EH et al (2010) NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Zα domains of yatapoxvirus E3L. FEBS Lett. https://doi.org/10.1016/j.febslet.2010.10.003
Lee AR et al (2019) NMR dynamics study reveals the Zα domain of human ADAR1 associates with and dissociates from Z-RNA more slowly than Z-DNA. ACS Chem Biol. https://doi.org/10.1021/acschembio.8b00914
Jeong M et al (2014) NMR study of the Z-DNA binding mode and B-Z transition activity of the Zα domain of human ADAR1 when perturbed by mutation on the α3 helix and β-hairpin. Arch Biochem Biophys. https://doi.org/10.1016/j.abb.2014.06.026
Nichols PJ et al (2021) Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat Commun. https://doi.org/10.1038/s41467-021-21039-0
Schwartz T et al (1999) Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1. J Biol Chem. https://doi.org/10.1074/jbc.274.5.2899
Brunelle JL, Green R (2013) In vitro transcription from plasmid or PCR-amplified DNA. Methods Enzymol. https://doi.org/10.1016/B978-0-12-420037-1.00005-1
Scott LG, Hennig M (2008) RNA structure determination by NMR. Methods Mol Biol. https://doi.org/10.1007/978-1-60327-159-2_2
Jeng S, Gardnerq J, Gumport R (1992) Transcription termination in vitro by bacteriophage T7 RNA polymerase. J. Biol, Chem
Beckert B, Masquida B (2011) Synthesis of RNA by in vitro transcription. Methods Mol Biol. https://doi.org/10.1007/978-1-59745-248-9_3
Edwards AL, Garst AD, Batey RT (2009) Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol Biol. https://doi.org/10.1007/978-1-59745-557-2_9
Francis AJ, Resendiz MJE (2017) Protocol for the solid-phase synthesis of oligomers of RNA containing a 2′-o-thiophenylmethyl modification and characterization via circular dichroism. J Vis Exp. https://doi.org/10.3791/56189
Petrov A, Wu T, Puglisi EV, Puglisi JD (2013) RNA purification by preparative polyacrylamide gel electrophoresis. Methods Enzymol. https://doi.org/10.1016/B978-0-12-420037-1.00017-8
Easton LE, Shibata Y, Lukavsky PJ (2010) Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA. https://doi.org/10.1261/rna.1862210
Kim I, Mckenna SA, Puglisi EV, Puglisi JD (2007) Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA. https://doi.org/10.1261/rna.342607
Miyahara T, Nakatsuji H, Sugiyama H (2016) Similarities and differences between RNA and DNA double-helical structures in circular dichroism spectroscopy: a SAC-CI study. J Phys Chem A. https://doi.org/10.1021/acs.jpca.6b08023
Freyer MW, Lewis EA (2008) Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions. Methods Cell Biol. https://doi.org/10.1016/S0091-679X(07)84004-0
Cole JL, Lary JW, Moody P, Laue TM (2008) Analytical ultracentrifugation: sedimentation velocity and sedimentation equilibrium. Methods Cell Biol. https://doi.org/10.1016/S0091-679X(07)84006-4
Balbo A, Zhao H, Brown PH, Schuck P (2010) Assembly, loading, and alignment of an analytical ultracentrifuge sample cell. J Vis Exp. https://doi.org/10.3791/1530
Fürtig B, Richter C, Wöhnert J, Schwalbe H (2003) NMR spectroscopy of RNA. ChemBioChem 4:936–962
Delaglio F et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
Kladwang W, Hum J, Das R (2012) Ultraviolet shadowing of RNA can cause significant chemical damage in seconds. Sci Rep. https://doi.org/10.1038/srep00517
Edelmann FT, Niedner A, Niessing D (2014) Production of pure and functional RNA for in vitro reconstitution experiments. Methods. https://doi.org/10.1016/j.ymeth.2013.08.034
Woodson SA, Koculi E (2009) Analysis of RNA folding by native polyacrylamide gel electrophoresis. Methods Enzymol. https://doi.org/10.1016/s0076-6879(09)69009-1
Klump HH, Jovin TM (1987) Formation of a left-handed RNA double helix: energetics of the A-Z transition of poly[r(G-C)] in concentrated sodium perchlorate solutions. Biochemistry 26:5186–5190
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Nichols, P.J., Bevers, S., Henen, M.A., Kieft, J.S., Vicens, Q., Vögeli, B. (2023). Adoption of A–Z Junctions in RNAs by Binding of Zα Domains. In: Kim, K.K., Subramani, V.K. (eds) Z-DNA. Methods in Molecular Biology, vol 2651. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3084-6_18
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DOI: https://doi.org/10.1007/978-1-0716-3084-6_18
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