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RNA-Processing DNAzymes

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RNA Structure and Function

Part of the book series: RNA Technologies ((RNATECHN,volume 14))

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Abstract

The great potential of nucleic acids as therapeutics has been recognized for a while but has experienced a tremendous attention with the recent development of RNA vaccines. In contrast to protein-targeting strategies, nucleic acid-based approaches often have the advantage that the required target selectivity is not realized via matching a specific structure, but plainly via the primary sequence of the applied RNA or DNA construct. This sequence is then either directly processed or comprises an additional unit capable of processing a target molecule. The latter is true for a number of DNA sequences, called DNAzymes, that are capable of both binding and processing a target with a high selectivity. While the mRNA technology has the inherent strength of bringing something into the system, RNA-processing DNA catalysts such as RNA-cleaving DNAzymes have the inherent strength of taking something out of the system. Consequently, the DNAzyme technology has the potential to emerge as counterpart to the mRNA technology. However, and in line with the endeavors that were required for the success of the mRNA technology, specific improvements need to be realized to unravel the full potential of RNA-processing DNAzymes. This review provides an overview of recent findings and remaining limitations.

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References

  • Appaiahgari MB, Vrati S (2007) DNAzyme-mediated Inhibition of Japanese encephalitis virus replication in mouse brain. Mol Ther 15:1593–1599

    Article  CAS  PubMed  Google Scholar 

  • Baum DA, Silverman SK (2008) Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell Mol Life Sci 65:2156–2174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Borggräfe J, Gertzen CGW, Viegas A et al (2022a) The architecture of the 10–23 DNAzyme and its implications for DNA-mediated catalysis. FEBS J in Press: https://doi.org/10.1111/febs.16698

    Article  Google Scholar 

  • Borggräfe J, Victor J, Rosenbach H et al (2022b) Time-resolved structural analysis of an RNA-cleaving DNA catalyst. Nature 601:144–149

    Article  PubMed  Google Scholar 

  • Breaker RR (1997) DNA enzymes. Nat Biotechnol 15:427–431

    Article  CAS  PubMed  Google Scholar 

  • Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Biol 1:223–229

    Article  CAS  PubMed  Google Scholar 

  • Cai H, Santiago FS, Prado-Lourenco L et al. (2012) DNAzyme targeting c-jun suppresses skin cancer growth. Sci Transl Med 4:139ra82

    Google Scholar 

  • Cairns MJ, Sun L-Q (2004) Target-site selection for the 10–23 DNAzyme. Methods Mol Biol 252:267–277

    CAS  PubMed  Google Scholar 

  • Cao Y, Yang L, Jiang W et al (2014) Therapeutic evaluation of Epstein-barr virus-encoded latent membrane protein-1 targeted DNAzyme for treating of nasopharyngeal carcinomas. Mol Ther 22:371–377

    Article  CAS  PubMed  Google Scholar 

  • Chandra M, Sachdeva A, Silverman SK (2009) DNA-catalyzed sequence-specific hydrolysis of DNA. Nat Chem Biol 5:718–720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chandrasekar J, Silverman SK (2013) Catalytic DNA with phosphatase activity. Proc Natl Acad Sci USA 110:5315–5320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chandrasekar J, Wylder AC, Silverman SK (2015) Phosphoserine lyase deoxyribozymes: DNA-catalyzed formation of dehydroalanine residues in peptides. J Am Chem Soc 137:9575–9578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chinnapen DJF, Sen D (2004) A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc Natl Acad Sci USA 101:65–69

    Article  CAS  PubMed  Google Scholar 

  • Cho EA, Moloney FJ, Cai H et al (2013) Safety and tolerability of an intratumorally injected DNAzyme, Dz13, in patients with nodular basal-cell carcinoma: A phase 1 first-in-human trial (DISCOVER). Lancet 381:1835–1843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chu C-C, Wong OY, Silverman SK (2014) A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation. ChemBioChem 15:1905–1910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cuchillo CM, Nogués MV, Raines RT (2011) Bovine pancreatic ribonuclease: Fifty years of the first enzymatic reaction mechanism. Biochemistry 50:7835–7841

    Article  CAS  PubMed  Google Scholar 

  • Cuenoud B, Szostak JW (1995) A DNA metalloenzyme with DNA ligase activity. Nature 375:611–614

    Article  CAS  PubMed  Google Scholar 

  • Culbertson MC, Temburnikar KW, Sau SP et al (2016) Evaluating TNA stability under simulated physiological conditions. Bioorg Med Chem Lett 26:2418–2421

    Article  CAS  PubMed  Google Scholar 

  • Dicke T, Pali-Schöll I, Kaufmann A et al (2012) Absence of unspecific innate immune cell activation by GATA-3-specific DNAzymes. Nucleic Acid Ther 22:117–126

    Article  CAS  PubMed  Google Scholar 

  • Dunham CM, Murray JB, Scott WG (2003) A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme. J Mol Biol 332:327–336

    Article  CAS  PubMed  Google Scholar 

  • Flynn-Charlebois A, Wang Y, Prior TK et al (2003) Deoxyribozymes with 2′-5′ RNA ligase activity. J Am Chem Soc 125:2444–2454

    Article  CAS  PubMed  Google Scholar 

  • Fratini AV, Kopka ML, Drew HR et al (1982) Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem 257:14686–14707

    Article  CAS  PubMed  Google Scholar 

  • Freund N, Taylor AI, Arangundy-Franklin S et al (2022) A two-residue nascent-strand steric gate controls synthesis of 2′-O-methyl- and 2′-O-(2-methoxyethyl)-RNA. Nat Chem in Press. https://doi.org/10.1038/s41557-022-01050-8

    Article  Google Scholar 

  • Gerber PP, Donde MJ, Matheson NJ et al (2022) XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun 13:6716

    Article  PubMed  PubMed Central  Google Scholar 

  • Gu H, Furukawa K, Weinberg Z et al (2013) Small, highly active DNAs that hydrolyze DNA. J Am Chem Soc 135:9121–9129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hadjiolov AA, Venkov PV, Tsanev RG (1966) Ribonucleic acids fractionation by density-gradient centrifugation and by agar gel electrophoresis: A comparison. Anal Biochem 17:263–267

    Article  CAS  PubMed  Google Scholar 

  • Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952

    Article  CAS  PubMed  Google Scholar 

  • Hervey JRD, Freund N, Houlihan G et al (2022) Efficient synthesis and replication of diverse sequence libraries composed of biostable nucleic acid analogues. RSC Chem Biol 3:1209–1215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hoagland MB, Stephenson ML, Scott JF et al (1958) A soluble ribonucleic acid intermediate in protein synthesis. J Biol Chem 231:241–257

    Article  CAS  PubMed  Google Scholar 

  • Hollenstein M (2015) DNA catalysis: The chemical repertoire of DNAzymes. Molecules 20:20777–20804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Homburg U, Turowska A, Kuhlmann J et al (2013) Safety profile and pharmacokinetics of SB010, an inhaled GATA-3-specific DNAzyme, in phase I clinical trials in healthy and asthmatic subjects. Eur Respir J 42:4858

    Google Scholar 

  • Huang P-JJ, Liu J (2015) Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing. Nucleic Acids Res 43:6125–6133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jakobsen MR, Haasnoot J, Wengel J et al (2007) Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites. Retrovirology 4:29

    Article  PubMed  PubMed Central  Google Scholar 

  • Kruger K, Grabowski PJ, Zaug AJ et al (1982) Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell 31:147–157

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  CAS  PubMed  Google Scholar 

  • Littlefield JW, Keller EB, Gross J et al (1955) Studies of cytoplamsic ribonucleoprotein particles from the liver of the rat. J Biol Chem 217:111–124

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Yu X, Chen Y et al (2017) Crystal structure of an RNA-cleaving DNAzyme. Nat Commun 8:2006

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma L, Liu J (2020) Catalytic nucleic acids: biochemistry, chemical biology, biosensors, and nanotechnology. iScience 23:100815

    Google Scholar 

  • McQuillen K, Roberts RB, Britten RJ (1959) Synthesis of nascent protein by ribosomes in Escherichia Coli. Proc Natl Acad Sci USA 45:1437–1447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Micura R, Höbartner C (2020) Fundamental studies of functional nucleic acids: Aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 49:7331–7353

    Article  CAS  PubMed  Google Scholar 

  • Mohammadi-Arani R, Javadi-Zarnaghi F, Boccaletto P et al (2022) DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. Nucleic Acids Res 50:W261–W265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morrison D, Rothenbroker M, Li Y (2018) DNAzymes: Selected for applications. Small Methods 2:1700319

    Article  Google Scholar 

  • Nguyen K, Wang Y, England WE et al (2021) Allele-specific RNA knockdown with a biologically stable and catalytically efficient XNAzyme. J Am Chem Soc 143:4519–4523

    Article  CAS  PubMed  Google Scholar 

  • Nowakowski J, Shim PJ, Prasad GS, a. (1999) Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10–23 DNA enzyme. Nat Struct Biol 6:151–156

    Article  CAS  PubMed  Google Scholar 

  • Pechlaner M, Sigel RKO (2012) Characterization of metal ion-nucleic acid interactions in solution. Metal Ions in Life Sciences, pp 1–42

    Google Scholar 

  • Ponce-Salvatierra A, Wawrzyniak-Turek K, Steuerwald U et al (2016) Crystal structure of a DNA catalyst. Nature 529:231–234

    Article  CAS  PubMed  Google Scholar 

  • Pradeepkumar PI, Höbartner C, Baum DA et al (2008) DNA-catalyzed formation of nucleopeptide linkages. Angew Chemie - Int Ed 47:1753–1757

    Article  CAS  Google Scholar 

  • Pradeepkumar PI, Höbartner C (2012) RNA-cleaving DNA enzymes and their potential therapeutic applications as antibacterial and antiviral agents. From Nucleic Acids Sequences to Molecular Medicine Berlin, Heidelberg: Springer Berlin Heidelberg. pp 371–410

    Google Scholar 

  • Pyle AM, Chu VT, Jankowsky E et al (2000) Using DNAzylnes to cut, process, and map RNA molecules for structural studies or modification. Methods Enzymol 317:140–146

    Article  CAS  PubMed  Google Scholar 

  • Record MT, Lohman TM, de Haseth P (1976) Ion effects on ligand–nucleic acid interactions. J Mol Biol 107:145–158

    Article  CAS  PubMed  Google Scholar 

  • Rivas E, Eddy SR (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 16:583–605

    Article  CAS  PubMed  Google Scholar 

  • Roberts RB (1958) Microsomal particles and protein synthesis; papers presented at the First Symposium of the Biophysical Society, at the Massachusetts Institute of Technology, Cambridge, February 5, 6, and 8, 1958. New York: Published on behalf of the Washington Academy of Sciences, Washington, D.C., by Pergamon Press

    Google Scholar 

  • Rosenbach H, Borggräfe J, Victor J et al (2020a) Influence of monovalent metal ions on metal binding and catalytic activity of the 10–23 DNAzyme. Biol Chem 402:99–111

    Article  PubMed  Google Scholar 

  • Rosenbach H, Victor J, Etzkorn M et al (2020b) Molecular features and metal ions that influence 10–23 DNAzyme activity. Molecules 25:3100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruvkun G (2001) Glimpses of a tiny RNA world. Science 294:797–799

    Article  CAS  PubMed  Google Scholar 

  • Santoro SW, Joyce GF (1997a) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94:4262–4266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santoro SW, Joyce GF (1997b) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94:4262–4266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schöning K-U, Scholz P, Guntha S et al (2000) Chemical etiology of nucleic acid structure: The α-threofuranosyl-(3′→2′) oligonucleotide system. Science 290:1347–1351

    Article  PubMed  Google Scholar 

  • Schubert S, Gül DC, Grunert H-P et al (2003) RNA cleaving “10–23” DNAzymes with enhanced stability and activity. Nucleic Acids Res 31:5982–5992

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sednev MV, Liaqat A, Höbartner C (2022) High-throughput activity profiling of RNA-cleaving DNA catalysts by deoxyribozyme sequencing (DZ-seq). J Am Chem Soc 144:2090–2094

    Article  CAS  PubMed  Google Scholar 

  • Silverman SK (2009) Deoxyribozymes: Selection design and serendipity in the development of DNA catalysts. Acc Chem Res 42:1521–1531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Silverman SK (2015) Pursuing DNA catalysts for protein modification. Acc Chem Res 48:1369–1379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Silverman SK (2016) Catalytic DNA: Scope, applications, and biochemistry of deoxyribozymes. Trends Biochem Sci 41:595–609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spitale RC, Chaput JC (2022) Reply to: On gene silencing by the X10–23 DNAzyme. Nat Chem 14:859–861

    Article  CAS  PubMed  Google Scholar 

  • Steffen FD, Khier M, Kowerko D et al (2020) Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts. Nat Commun 11:104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steger G, Victor J (2022) Design of a DNAzyme. Methods Mol Biol, DNAzymes: 47–63

    Google Scholar 

  • Taylor AI, Holliger P (2022) On gene silencing by the X10–23 DNAzyme. Nat Chem 14:855–858

    Article  CAS  PubMed  Google Scholar 

  • Taylor AI, Wan CJK, Donde MJ et al (2022) A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat Chem 14:1295–1305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Travascio P, Li Y, Sen D (1998) DNA-enhanced peroxidase activity of a DNA aptamer–hemin complex. Chem Biol 5:505–517

    Article  CAS  PubMed  Google Scholar 

  • Vester B, Lundberg LB, Sørensen MD et al (2002) LNAzymes: Incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage. J Am Chem Soc 124:13682–13683

    Article  CAS  PubMed  Google Scholar 

  • Victor J, Steger G, Riesner D (2018) Inability of DNAzymes to cleave RNA in vivo is due to limited Mg2+ concentration in cells. Eur Biophys J 47:333–343

    Article  CAS  PubMed  Google Scholar 

  • Walsh SM, Sachdeva A, Silverman SK (2013) DNA catalysts with tyrosine kinase activity. J Am Chem Soc 135:14928–14931

    Article  CAS  PubMed  Google Scholar 

  • Walsh SM, Konecki SN, Silverman SK (2015) Identification of sequence-selective tyrosine kinase deoxyribozymes. J Mol Evol 81:218–224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Nguyen K, Spitale RC et al (2021) A biologically stable DNAzyme that efficiently silences gene expression in cells. Nat Chem 13:319–326

    Article  CAS  PubMed  Google Scholar 

  • Wong OY, Pradeepkumar PI, Silverman SK (2011) DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates. Biochemistry 50:4741–4749

    Article  CAS  PubMed  Google Scholar 

  • Workman C, Krogh A (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 27:4816–4822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zacchia M, Abategiovanni ML, Stratigis S et al (2016) Potassium: From physiology to clinical implications. Kidney Dis 2:72–79

    Article  Google Scholar 

  • Zhang J (2018) RNA-cleaving DNAzymes: Old catalysts with new tricks for intracellular and in vivo applications. Catalysts 8:550

    Article  Google Scholar 

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Span, I., Etzkorn, M. (2023). RNA-Processing DNAzymes. In: Barciszewski, J. (eds) RNA Structure and Function. RNA Technologies, vol 14. Springer, Cham. https://doi.org/10.1007/978-3-031-36390-0_28

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