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

Journal of Molecular Evolution

Volumn 81, Issue 5-6, 2015, Pages 225-234

  Torabi, Seyed Fakhreddin ^a   Lu, Yi ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

DNAzyme (deoxyribozyme); Functional motif; In vitro selection; Lanthanides; Sodium

Indexed keywords

DEOXYRIBOZYME; MONOVALENT CATION; RIBONUCLEASE; SODIUM;

CONFORMATION; METABOLISM; NUCLEOTIDE MOTIF; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE;

CATIONS, MONOVALENT; DNA, CATALYTIC; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; RIBONUCLEASES; SELEX APTAMER TECHNIQUE; SODIUM;

EID: 84948382395     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-015-9715-7     Document Type: Article

References (64)

1. Aiba Y, Komiyama M (2012) Artificial site-selective DNA cutters to manipulate single-stranded DNA. Polym J 44:929
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 48:3512
3. Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Biol 1:223
4. Brown AK, Li J, Pavot CM, Lu Y (2003) A lead-dependent DNAzyme with a two-step mechanism. Biochemistry 42:7152
5. Carrigan MA, Ricardo A, Ang DN, Benner SA (2004) Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry 43:11446
6. Chu CC, Wong OY, Silverman SK (2014) A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation. ChemBioChem 15:1905
7. Cruz RP, Withers JB, Li Y (2004) Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem Biol 11:57
8. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818
9. 2+ Ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew Chem Int Ed Engl 35:2837
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 269:188
11. Franzen S (2010) Expanding the catalytic repertoire of ribozymes and deoxyribozymes beyond RNA substrates. Curr Opin Mol Ther 12:223
12. Geyer CR, Sen D (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem Biol 4:579
13. Harris DC (2010) Quantitative chemical analysis. Macmillan, New York
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 52:11734
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 47:4346
16. 2+-independent RNA cleavage. ChemBioChem 10:1988
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 15:174
18. Huang PJ, Lin J, Cao J, Vazin M, Liu J (2014a) Ultrasensitive DNAzyme beacon for lanthanides and metal speciation. Anal Chem 86:1816
19. Huang PJ, Vazin M, Liu J (2014b) In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal Chem 86:9993
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 285:25850
21. Ihms HE, Lu Y (2012) In vitro selection of metal ion-selective DNAzymes. Methods Mol Biol 848:297
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 277:2543
23. Johns GC, Joyce GF (2005) The promise and peril of continuous in vitro evolution. J Mol Evol 61:253
24. Jose AM, Soukup GA, Breaker RR (2001) Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 29:1631
25. Joyce GF (2004) Directed evolution of nucleic acid enzymes. Annu Rev Biochem 73:791
26. Knitt DS, Herschlag D (1996) pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa. Biochemistry 35:1560
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 6:1062
28. Kuhns S, Joyce G (2003) Perfectly complementary nucleic acid enzymes. J Mol Evol 56:711
29. Levy M, Ellington AD (2002) ATP-dependent allosteric DNA enzymes. Chem Biol 9:417
30. Li Y, Breaker RR (2001) In vitro selection of kinase and ligase deoxyribozymes. Methods 23:179
31. Li J, Lu Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J Am Chem Soc 122:10466
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 28:481
33. Liu J (2015) Lanthanide-dependent RNA-cleaving DNAzymes as metal biosensors. Can J Chem 93:273
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 46:7587
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 104:2056
36. Liu J, Cao Z, Lu Y (2009) Functional nucleic acid sensors. Chem Rev 109:1948
37. Lu Y (2002) New transition-metal-dependent DNAzymes as efficient endonucleases and as selective metal biosensors. Chemistry 8:4588
38. Lu Y, Liu J (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr Opin Biotechnol 17:580
39. Martell AE, Calvin M (1952) Chemistry of the metal chelate compounds. Prentice-Hall, New York
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 131:5506
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 131:2657
42. 2+-dependent DNAzymes. J Mol Evol 61:216
43. Roth A, Breaker RR (1998) An amino acid as a cofactor for a catalytic polynucleotide. Proc Natl Acad Sci USA 95:6027
44. Santoro SW, Joyce GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94:4262
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 61:192
46. Schlosser K, Li Y (2009) Biologically inspired synthetic enzymes made from DNA. Chem Biol 16:311
47. Schlosser K, Li Y (2010) A versatile endoribonuclease mimic made of DNA: characteristics and applications of the 8-17 RNA-cleaving DNAzyme. ChemBioChem 11:866
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 36:4768
49. Sen D, Geyer CR (1998) DNA enzymes. Curr Opin Chem Biol 2:680
50. Sreedhara A, Cowan JA (2002) Structural and catalytic roles for divalent magnesium in nucleic acid biochemistry. Biometals 15:211
51. Tang J, Breaker RR (1997) Rational design of allosteric ribozymes. Chem Biol 4:453
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 35:7572
53. Torabi SF, Lu Y (2014) Functional DNA nanomaterials for sensing and imaging in living cells. Curr Opin Biotechnol 28:88
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 112:5903
55. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505
56. Vazin M, Huang PJ, Matuszek Z, Liu J (2015) Biochemical characterization of a lanthanide-dependent DNAzyme with normal and phosphorothioate-modified substrates. Biochemistry 54:6132
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 318:33
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 114:2881
59. Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611
60. Xiang Y, Lu Y (2014) DNA as sensors and imaging agents for metal ions. Inorg Chem 53:1925
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:e53
62. 3+-mediated bridging between dopa-containing protein films in water. Proc Natl Acad Sci USA 107:12850
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 189:7991
64. Zivarts M, Liu Y, Breaker RR (2005) Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res 33:622