Abstract
Catalytic DNAs (DNAzymes) with peroxidase-like activity have great potential in bioanalytical chemistry [1], owing to numerous advantages that DNA enzymes offer over conventional protein enzymes, including structural simplicity, low cost, thermal stability, and straightforward handling and preparation. Maximizing the efficiency of the peroxidase activity of such DNAzymes is a subject in need of review. In this chapter, we discuss the optimal experimental conditions for the peroxidase activity of these DNAzymes and describe general procedures for their utilization.
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References
Kosman J, Juskowiak B (2011) Peroxidase-mimicking DNAzymes for biosensing applications: a review. Anal Chim Acta 707(1-2):7–17. https://doi.org/10.1016/j.aca.2011.08.050
Veitch NC (2004) Horseradish peroxidase: a modern view of a classic enzyme. Phytochemistry 65(3):249–259
Travascio P, Li Y, Sen D (1998) DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chem Biol 5(9):505–517
Li Y, Geyer CR, Sen D (1996) Recognition of anionic porphyrins by DNA aptamers. Biochemistry 35(21):6911–6922. https://doi.org/10.1021/bi960038h
Travascio P, Bennet AJ, Wang DY, Sen D (1999) A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites. Chem Biol 6(11):779–787
Travascio P, Witting PK, Mauk AG, Sen D (2001) The peroxidase activity of a hemin--DNA oligonucleotide complex: free radical damage to specific guanine bases of the DNA. J Am Chem Soc 123(7):1337–1348
Travascio P, Sen D, Bennet AJ (2006) DNA and RNA enzymes with peroxidase activity. An investigation into the mechanism of action. Can J Chem 84(4):613–619. https://doi.org/10.1139/v06-057
Furtmuller PG, Zederbauer M, Jantschko W, Helm J, Bogner M, Jakopitsch C, Obinger C (2006) Active site structure and catalytic mechanisms of human peroxidases. Arch Biochem Biophys 445(2):199–213. https://doi.org/10.1016/j.abb.2005.09.017
Li W, Li Y, Liu Z, Lin B, Yi H, Xu F, Nie Z, Yao S (2016) Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity. Nucleic Acids Res 44(15):7373–7384. https://doi.org/10.1093/nar/gkw634
Chang T, Gong H, Ding P, Liu X, Li W, Bing T, Cao Z, Shangguan D (2016) Activity enhancement of G-quadruplex/hemin DNAzyme by flanking d(CCC). Chem Eur J 22(12):4015–4021. https://doi.org/10.1002/chem.201504797
Cheng M, Zhou J, Jia G, Ai X, Mergny J-L, Li C (2017) Relations between the loop transposition of DNA G-quadruplex and the catalytic function of DNAzyme. Biochim Biophys Acta Gen Subj 1861(8):1913–1920. https://doi.org/10.1016/j.bbagen.2017.05.016
Nakayama S, Sintim HO (2012) Investigating the interactions between cations, peroxidation substrates and G-quadruplex topology in DNAzyme peroxidation reactions using statistical testing. Anal Chim Acta 747:1–6. https://doi.org/10.1016/j.aca.2012.08.008
Saito K, Tai H, Hemmi H, Kobayashi N, Yamamoto Y (2012) Interaction between the heme and a G-quartet in a heme-DNA complex. Inorg Chem 51(15):8168–8176. https://doi.org/10.1021/ic3005739
Shibata T, Nakayama Y, Katahira Y, Tai H, Moritaka Y, Nakano Y, Yamamoto Y (2017) Characterization of the interaction between heme and a parallel G-quadruplex DNA formed from d(TTGAGG). Biochim Biophys Acta 1861(5 Pt B):1264–1270. https://doi.org/10.1016/j.bbagen.2016.11.005
Cheng X, Liu X, Bing T, Cao Z, Shangguan D (2009) General peroxidase activity of G-quadruplex-hemin complexes and its application in ligand screening. Biochemistry 48(33):7817–7823. https://doi.org/10.1021/bi9006786
Kong DM, Yang W, Wu J, Li CX, Shen HX (2010) Structure-function study of peroxidase-like G-quadruplex-hemin complexes. Analyst 135(2):321–326. https://doi.org/10.1039/b920293e
Phan AT, Patel DJ (2003) Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics. J Am Chem Soc 125(49):15021–15027. https://doi.org/10.1021/ja037616j
Smith FW, Lau FW, Feigon J (1994) d(G3T4G3) forms an asymmetric diagonally looped dimeric quadruplex with guanosine 5′-syn-syn-anti and 5′-syn-anti-anti N-glycosidic conformations. Proc Natl Acad Sci U S A 91(22):10546–10550
Haider SM, Parkinson GN, Neidle S (2003) Structure of a G-quadruplex-ligand complex. J Mol Biol 326(1):117–125
Risitano A, Fox KR (2003) Stability of intramolecular DNA quadruplexes: Comparison with DNA duplexes. Biochemistry 42(21):6507–6513. https://doi.org/10.1021/bi026997v
Sen D, Gilbert W (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344(6265):410–414. https://doi.org/10.1038/344410a0
Venczel EA, Sen D (1993) Parallel and antiparallel G-DNA structures from a complex telomeric sequence. Biochemistry 32(24):6220–6228
Dai J, Carver M, Yang D (2008) Polymorphism of human telomeric quadruplex structures. Biochimie 90(8):1172–1183. https://doi.org/10.1016/j.biochi.2008.02.026
Rojas AM, Gonzalez PA, Antipov E, Klibanov AM (2007) Specificity of a DNA-based (DNAzyme) peroxidative biocatalyst. Biotechnol Lett 29(2):227–232. https://doi.org/10.1007/s10529-006-9228-y
Grigg JC, Shumayrikh N, Sen D (2014) G-quadruplex structures formed by expanded hexanucleotide repeat RNA and DNA from the neurodegenerative disease-linked C9orf72 gene efficiently sequester and activate heme. PLoS One 9(9):e106449. https://doi.org/10.1371/journal.pone.0106449
Nakayama S, Sintim HO (2010) Biomolecule detection with peroxidase-mimicking DNAzymes; expanding detection modality with fluorogenic compounds. Mol BioSyst 6(1):95–97. https://doi.org/10.1039/b916228c
Golub E, Freeman R, Willner I (2011) A hemin/G-quadruplex acts as an NADH oxidase and NADH peroxidase mimicking DNAzyme. Angew Chem Int Ed Engl 50(49):11710–11714
Wang Y, Hamasaki K, Rando RR (1997) Specificity of aminoglycoside binding to RNA constructs derived from the 16S rRNA decoding region and the HIV-RRE activator region. Biochemistry 36(4):768–779. https://doi.org/10.1021/bi962095g
Li Y, Sen D (1996) A catalytic DNA for porphyrin metallation. Nat Struct Biol 3(9):743–747
Li Y, Sen D (1997) Toward an efficient DNAzyme. Biochemistry 36(18):5589–5599. https://doi.org/10.1021/bi962694n
Poon LC-H (2011) Structural and catalytic properties of DNA/RNA-heme complexes. (Thesis) M.Sc. Simon Faser University
Golub E, Albada HB, Liao WC, Biniuri Y, Willner I (2016) Nucleoapzymes: Hemin/G-quadruplex DNAzyme-Aptamer binding site conjugates with superior enzyme-like catalytic functions. J Am Chem Soc 138(1):164–172. https://doi.org/10.1021/jacs.5b09457
Canale TD, Sen D (2016) Hemin-utilizing G-quadruplex DNAzymes are strongly active in organic co-solvents. Biochim Biophys Acta. https://doi.org/10.1016/j.bbagen.2016.11.019
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We acknowledge grant funding from the Natural Sciences and Engineering Research Council of Canada (NSERC).
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Shumayrikh, N., Sen, D. (2019). Heme•G-Quadruplex DNAzymes: Conditions for Maximizing Their Peroxidase Activity. In: Yang, D., Lin, C. (eds) G-Quadruplex Nucleic Acids. Methods in Molecular Biology, vol 2035. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9666-7_22
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DOI: https://doi.org/10.1007/978-1-4939-9666-7_22
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