Journal of Molecular Evolution

, Volume 81, Issue 5–6, pp 225–234 | Cite as

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

Original Article

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.

Keywords

DNAzyme (deoxyribozyme) In vitro selection Sodium Lanthanides Functional motif 

Notes

Acknowledgments

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

References

  1. Aiba Y, Komiyama M (2012) Artificial site-selective DNA cutters to manipulate single-stranded DNA. Polym J 44:929CrossRefGoogle Scholar
  2. 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 48:3512CrossRefPubMedGoogle Scholar
  3. Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Biol 1:223CrossRefPubMedGoogle Scholar
  4. Brown AK, Li J, Pavot CM, Lu Y (2003) A lead-dependent DNAzyme with a two-step mechanism. Biochemistry 42:7152CrossRefPubMedGoogle Scholar
  5. Carrigan MA, Ricardo A, Ang DN, Benner SA (2004) Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry 43:11446CrossRefPubMedGoogle Scholar
  6. Chu CC, Wong OY, Silverman SK (2014) A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation. ChemBioChem 15:1905PubMedCentralCrossRefPubMedGoogle Scholar
  7. Cruz RP, Withers JB, Li Y (2004) Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem Biol 11:57CrossRefPubMedGoogle Scholar
  8. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818CrossRefPubMedGoogle Scholar
  9. Faulhammer D, Famulok M (1996) The Ca2+ Ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew Chem Int Ed Engl 35:2837CrossRefGoogle Scholar
  10. 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 269:188CrossRefPubMedGoogle Scholar
  11. Franzen S (2010) Expanding the catalytic repertoire of ribozymes and deoxyribozymes beyond RNA substrates. Curr Opin Mol Ther 12:223PubMedGoogle Scholar
  12. Geyer CR, Sen D (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem Biol 4:579CrossRefPubMedGoogle Scholar
  13. Harris DC (2010) Quantitative chemical analysis. Macmillan, New YorkGoogle Scholar
  14. 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 52:11734CrossRefPubMedGoogle Scholar
  15. Hollenstein M, Hipolito C, Lam C, Dietrich D, Perrin DM (2008) A highly selective DNAzyme sensor for mercuric ions. Angew Chem Int Ed Engl 47:4346CrossRefPubMedGoogle Scholar
  16. 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 10:1988CrossRefPubMedGoogle Scholar
  17. 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 15:174CrossRefPubMedGoogle Scholar
  18. Huang PJ, Lin J, Cao J, Vazin M, Liu J (2014a) Ultrasensitive DNAzyme beacon for lanthanides and metal speciation. Anal Chem 86:1816CrossRefPubMedGoogle Scholar
  19. Huang PJ, Vazin M, Liu J (2014b) In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal Chem 86:9993CrossRefPubMedGoogle Scholar
  20. 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 285:25850PubMedCentralCrossRefPubMedGoogle Scholar
  21. Ihms HE, Lu Y (2012) In vitro selection of metal ion-selective DNAzymes. Methods Mol Biol 848:297PubMedCentralCrossRefPubMedGoogle Scholar
  22. Jiang D, Xu J, Sheng Y, Sun Y, Zhang J (2010) An allosteric DNAzyme with dual RNA-cleaving and DNA-cleaving activities. FEBS J 277:2543CrossRefPubMedGoogle Scholar
  23. Johns GC, Joyce GF (2005) The promise and peril of continuous in vitro evolution. J Mol Evol 61:253CrossRefPubMedGoogle Scholar
  24. Jose AM, Soukup GA, Breaker RR (2001) Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 29:1631PubMedCentralCrossRefPubMedGoogle Scholar
  25. Joyce GF (2004) Directed evolution of nucleic acid enzymes. Annu Rev Biochem 73:791CrossRefPubMedGoogle Scholar
  26. Knitt DS, Herschlag D (1996) pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa. Biochemistry 35:1560CrossRefPubMedGoogle Scholar
  27. 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 6:1062CrossRefPubMedGoogle Scholar
  28. Kuhns S, Joyce G (2003) Perfectly complementary nucleic acid enzymes. J Mol Evol 56:711CrossRefPubMedGoogle Scholar
  29. Levy M, Ellington AD (2002) ATP-dependent allosteric DNA enzymes. Chem Biol 9:417CrossRefPubMedGoogle Scholar
  30. Li Y, Breaker RR (2001) In vitro selection of kinase and ligase deoxyribozymes. Methods 23:179CrossRefPubMedGoogle Scholar
  31. Li J, Lu Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J Am Chem Soc 122:10466CrossRefGoogle Scholar
  32. 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 28:481PubMedCentralCrossRefPubMedGoogle Scholar
  33. Liu J (2015) Lanthanide-dependent RNA-cleaving DNAzymes as metal biosensors. Can J Chem 93:273CrossRefGoogle Scholar
  34. 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 46:7587CrossRefPubMedGoogle Scholar
  35. 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 104:2056PubMedCentralCrossRefPubMedGoogle Scholar
  36. Liu J, Cao Z, Lu Y (2009) Functional nucleic acid sensors. Chem Rev 109:1948PubMedCentralCrossRefPubMedGoogle Scholar
  37. Lu Y (2002) New transition-metal-dependent DNAzymes as efficient endonucleases and as selective metal biosensors. Chemistry 8:4588CrossRefPubMedGoogle Scholar
  38. Lu Y, Liu J (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr Opin Biotechnol 17:580CrossRefPubMedGoogle Scholar
  39. Martell AE, Calvin M (1952) Chemistry of the metal chelate compounds. Prentice-Hall, New YorkGoogle Scholar
  40. 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 131:5506PubMedCentralCrossRefPubMedGoogle Scholar
  41. 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 131:2657CrossRefPubMedGoogle Scholar
  42. Nelson K, Bruesehoff P, Lu Y (2005) In vitro selection of high temperature Zn2+-dependent DNAzymes. J Mol Evol 61:216CrossRefPubMedGoogle Scholar
  43. Roth A, Breaker RR (1998) An amino acid as a cofactor for a catalytic polynucleotide. Proc Natl Acad Sci USA 95:6027PubMedCentralCrossRefPubMedGoogle Scholar
  44. Santoro SW, Joyce GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94:4262PubMedCentralCrossRefPubMedGoogle Scholar
  45. 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 61:192CrossRefPubMedGoogle Scholar
  46. Schlosser K, Li Y (2009) Biologically inspired synthetic enzymes made from DNA. Chem Biol 16:311CrossRefPubMedGoogle Scholar
  47. Schlosser K, Li Y (2010) A versatile endoribonuclease mimic made of DNA: characteristics and applications of the 8-17 RNA-cleaving DNAzyme. ChemBioChem 11:866CrossRefPubMedGoogle Scholar
  48. 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 36:4768PubMedCentralCrossRefPubMedGoogle Scholar
  49. Sen D, Geyer CR (1998) DNA enzymes. Curr Opin Chem Biol 2:680CrossRefPubMedGoogle Scholar
  50. Sreedhara A, Cowan JA (2002) Structural and catalytic roles for divalent magnesium in nucleic acid biochemistry. Biometals 15:211CrossRefPubMedGoogle Scholar
  51. Tang J, Breaker RR (1997) Rational design of allosteric ribozymes. Chem Biol 4:453CrossRefPubMedGoogle Scholar
  52. 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 35:7572CrossRefGoogle Scholar
  53. Torabi SF, Lu Y (2014) Functional DNA nanomaterials for sensing and imaging in living cells. Curr Opin Biotechnol 28:88CrossRefPubMedGoogle Scholar
  54. 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 112:5903PubMedCentralCrossRefPubMedGoogle Scholar
  55. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505CrossRefPubMedGoogle Scholar
  56. Vazin M, Huang PJ, Matuszek Z, Liu J (2015) Biochemical characterization of a lanthanide-dependent DNAzyme with normal and phosphorothioate-modified substrates. Biochemistry 54:6132CrossRefPubMedGoogle Scholar
  57. Wang DY, Lai BH, Sen D (2002) A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J Mol Biol 318:33CrossRefPubMedGoogle Scholar
  58. 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 114:2881CrossRefPubMedGoogle Scholar
  59. Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611CrossRefPubMedGoogle Scholar
  60. Xiang Y, Lu Y (2014) DNA as sensors and imaging agents for metal ions. Inorg Chem 53:1925PubMedCentralCrossRefPubMedGoogle Scholar
  61. 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:e53PubMedCentralCrossRefPubMedGoogle Scholar
  62. 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 107:12850PubMedCentralCrossRefPubMedGoogle Scholar
  63. 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 189:7991PubMedCentralCrossRefPubMedGoogle Scholar
  64. Zivarts M, Liu Y, Breaker RR (2005) Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res 33:622PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of BiochemistryUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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