Skip to main content
Log in

Identification of the Same Na+-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions

  • Original Article
  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na+ and reported to be highly selective for Na+ over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce4+ and found to be active with trivalent lanthanides, Y3+ and Pb2+. Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60 % sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na+ is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na+. Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na+ and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na+-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Aiba Y, Komiyama M (2012) Artificial site-selective DNA cutters to manipulate single-stranded DNA. Polym J 44:929

    Article  CAS  Google Scholar 

  • Ali MM, Li Y (2009) Colorimetric sensing by using allosteric-DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe. Angew Chem Int Ed Engl 48:3512

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Brown AK, Li J, Pavot CM, Lu Y (2003) A lead-dependent DNAzyme with a two-step mechanism. Biochemistry 42:7152

    Article  CAS  PubMed  Google Scholar 

  • Carrigan MA, Ricardo A, Ang DN, Benner SA (2004) Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry 43:11446

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cruz RP, Withers JB, Li Y (2004) Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem Biol 11:57

    Article  CAS  PubMed  Google Scholar 

  • Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818

    Article  CAS  PubMed  Google Scholar 

  • Faulhammer D, Famulok M (1996) The Ca2+ Ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew Chem Int Ed Engl 35:2837

    Article  CAS  Google Scholar 

  • Faulhammer D, Famulok M (1997) Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides. J Mol Biol 269:188

    Article  CAS  PubMed  Google Scholar 

  • Franzen S (2010) Expanding the catalytic repertoire of ribozymes and deoxyribozymes beyond RNA substrates. Curr Opin Mol Ther 12:223

    CAS  PubMed  Google Scholar 

  • Geyer CR, Sen D (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem Biol 4:579

    Article  CAS  PubMed  Google Scholar 

  • Harris DC (2010) Quantitative chemical analysis. Macmillan, New York

    Google Scholar 

  • Hennig C, Ikeda-Ohno A, Kraus W, Weiss S, Pattison P, Emerich H, Abdala PM, Scheinost AC (2013) Crystal structure and solution species of Ce(III) and Ce(IV) formates: from mononuclear to hexanuclear complexes. Inorg Chem 52:11734

    Article  CAS  PubMed  Google Scholar 

  • Hollenstein M, Hipolito C, Lam C, Dietrich D, Perrin DM (2008) A highly selective DNAzyme sensor for mercuric ions. Angew Chem Int Ed Engl 47:4346

    Article  CAS  PubMed  Google Scholar 

  • Hollenstein M, Hipolito CJ, Lam CH, Perrin DM (2009) A DNAzyme with three protein-like functional groups: enhancing catalytic efficiency of M2+-independent RNA cleavage. ChemBioChem 10:1988

    Article  CAS  PubMed  Google Scholar 

  • Hollenstein M, Hipolito CJ, Lam CH, Perrin DM (2013) Toward the combinatorial selection of chemically modified DNAzyme RNase A mimics active against all-RNA substrates. ACS Comb Sci 15:174

    Article  CAS  PubMed  Google Scholar 

  • Huang PJ, Lin J, Cao J, Vazin M, Liu J (2014a) Ultrasensitive DNAzyme beacon for lanthanides and metal speciation. Anal Chem 86:1816

    Article  CAS  PubMed  Google Scholar 

  • Huang PJ, Vazin M, Liu J (2014b) In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal Chem 86:9993

    Article  CAS  PubMed  Google Scholar 

  • Hwang DS, Zeng H, Masic A, Harrington MJ, Israelachvili JN, Waite JH (2010) Protein- and metal-dependent interactions of a prominent protein in mussel adhesive plaques. J Biol Chem 285:25850

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ihms HE, Lu Y (2012) In vitro selection of metal ion-selective DNAzymes. Methods Mol Biol 848:297

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jiang D, Xu J, Sheng Y, Sun Y, Zhang J (2010) An allosteric DNAzyme with dual RNA-cleaving and DNA-cleaving activities. FEBS J 277:2543

    Article  CAS  PubMed  Google Scholar 

  • Johns GC, Joyce GF (2005) The promise and peril of continuous in vitro evolution. J Mol Evol 61:253

    Article  CAS  PubMed  Google Scholar 

  • Jose AM, Soukup GA, Breaker RR (2001) Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 29:1631

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Joyce GF (2004) Directed evolution of nucleic acid enzymes. Annu Rev Biochem 73:791

    Article  CAS  PubMed  Google Scholar 

  • Knitt DS, Herschlag D (1996) pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa. Biochemistry 35:1560

    Article  CAS  PubMed  Google Scholar 

  • Koizumi M, Soukup GA, Kerr JN, Breaker RR (1999) Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat Struct Biol 6:1062

    Article  CAS  PubMed  Google Scholar 

  • Kuhns S, Joyce G (2003) Perfectly complementary nucleic acid enzymes. J Mol Evol 56:711

    Article  CAS  PubMed  Google Scholar 

  • Levy M, Ellington AD (2002) ATP-dependent allosteric DNA enzymes. Chem Biol 9:417

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Breaker RR (2001) In vitro selection of kinase and ligase deoxyribozymes. Methods 23:179

    Article  CAS  PubMed  Google Scholar 

  • Li J, Lu Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J Am Chem Soc 122:10466

    Article  CAS  Google Scholar 

  • Li J, Zheng W, Kwon AH, Lu Y (2000) In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res 28:481

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Liu J (2015) Lanthanide-dependent RNA-cleaving DNAzymes as metal biosensors. Can J Chem 93:273

    Article  CAS  Google Scholar 

  • Liu J, Lu Y (2007) Rational design of “turn-on” allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity. Angew Chem Int Ed Engl 46:7587

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Brown AK, Meng X, Cropek DM, Istok JD, Watson DB, Lu Y (2007) A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity. Proc Natl Acad Sci USA 104:2056

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Liu J, Cao Z, Lu Y (2009) Functional nucleic acid sensors. Chem Rev 109:1948

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lu Y (2002) New transition-metal-dependent DNAzymes as efficient endonucleases and as selective metal biosensors. Chemistry 8:4588

    Article  CAS  PubMed  Google Scholar 

  • Lu Y, Liu J (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr Opin Biotechnol 17:580

    Article  CAS  PubMed  Google Scholar 

  • Martell AE, Calvin M (1952) Chemistry of the metal chelate compounds. Prentice-Hall, New York

    Google Scholar 

  • Mazumdar D, Nagraj N, Kim HK, Meng X, Brown AK, Sun Q, Li W, Lu Y (2009) Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. J Am Chem Soc 131:5506

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Miyajima Y, Ishizuka T, Yamamoto Y, Sumaoka J, Komiyama M (2009) Origin of high fidelity in target-sequence recognition by PNA-Ce(IV)/EDTA combinations as site-selective DNA cutters. J Am Chem Soc 131:2657

    Article  CAS  PubMed  Google Scholar 

  • Nelson K, Bruesehoff P, Lu Y (2005) In vitro selection of high temperature Zn2+-dependent DNAzymes. J Mol Evol 61:216

    Article  CAS  PubMed  Google Scholar 

  • Roth A, Breaker RR (1998) An amino acid as a cofactor for a catalytic polynucleotide. Proc Natl Acad Sci USA 95:6027

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schlosser K, Li Y (2005) Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection. J Mol Evol 61:192

    Article  CAS  PubMed  Google Scholar 

  • Schlosser K, Li Y (2009) Biologically inspired synthetic enzymes made from DNA. Chem Biol 16:311

    Article  CAS  PubMed  Google Scholar 

  • Schlosser K, Li Y (2010) A versatile endoribonuclease mimic made of DNA: characteristics and applications of the 8-17 RNA-cleaving DNAzyme. ChemBioChem 11:866

    Article  CAS  PubMed  Google Scholar 

  • Schlosser K, Gu J, Lam JC, Li Y (2008) In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions. Nucleic Acids Res 36:4768

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sen D, Geyer CR (1998) DNA enzymes. Curr Opin Chem Biol 2:680

    Article  CAS  PubMed  Google Scholar 

  • Sreedhara A, Cowan JA (2002) Structural and catalytic roles for divalent magnesium in nucleic acid biochemistry. Biometals 15:211

    Article  CAS  PubMed  Google Scholar 

  • Tang J, Breaker RR (1997) Rational design of allosteric ribozymes. Chem Biol 4:453

    Article  CAS  PubMed  Google Scholar 

  • Taylor SW, Chase DB, Emptage MH, Nelson MJ, Waite JH (1996) Ferric Ion Complexes of a DOPA-Containing Adhesive Protein from Mytilus edulis. Inorg Chem 35:7572

    Article  CAS  Google Scholar 

  • Torabi SF, Lu Y (2014) Functional DNA nanomaterials for sensing and imaging in living cells. Curr Opin Biotechnol 28:88

    Article  CAS  PubMed  Google Scholar 

  • Torabi SF, Wu P, McGhee CE, Chen L, Hwang K, Zheng N, Cheng J, Lu Y (2015) In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing. Proc Natl Acad Sci USA 112:5903

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505

    Article  CAS  PubMed  Google Scholar 

  • Vazin M, Huang PJ, Matuszek Z, Liu J (2015) Biochemical characterization of a lanthanide-dependent DNAzyme with normal and phosphorothioate-modified substrates. Biochemistry 54:6132

    Article  CAS  PubMed  Google Scholar 

  • Wang DY, Lai BH, Sen D (2002) A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J Mol Biol 318:33

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Lu CH, Willner I (2014) From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 114:2881

    Article  CAS  PubMed  Google Scholar 

  • Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611

    Article  CAS  PubMed  Google Scholar 

  • Xiang Y, Lu Y (2014) DNA as sensors and imaging agents for metal ions. Inorg Chem 53:1925

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yamamoto Y, Mori M, Aiba Y, Tomita T, Chen W, Zhou JM, Uehara A, Ren Y, Kitamura Y, Komiyama M (2007) Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA. Nucleic Acids Res 35:e53

    Article  PubMed Central  PubMed  Google Scholar 

  • Zeng H, Hwang DS, Israelachvili JN, Waite JH (2010) Strong reversible Fe3+-mediated bridging between dopa-containing protein films in water. Proc Natl Acad Sci USA 107:12850

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang H, Herman JP, Bolton H Jr, Zhang Z, Clark S, Xun L (2007) Evidence that bacterial ABC-type transporter imports free EDTA for metabolism. J Bacteriol 189:7991

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zivarts M, Liu Y, Breaker RR (2005) Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res 33:622

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Claire E. McGhee for critical reading of the manuscript. This work was supported by US National Institutes of Health (Grant R01ES016865).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yi Lu.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Torabi, SF., Lu, Y. Identification of the Same Na+-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions. J Mol Evol 81, 225–234 (2015). https://doi.org/10.1007/s00239-015-9715-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-015-9715-7

Keywords

Navigation