DNAzyme-Based Sensing for Metal Ions in Ocean Platform

Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

The ocean contains a number of metal ions that are either beneficial or detrimental to marine lives or ecology. Developing sensors for on-site and real-time detection of these metal ions plays an important role in our understanding the ocean as well as its protection. DNAzymes, DNA molecules with enzymatic functions, have emerged as a new class of sensing molecules for metal ions, because DNAzymes with high affinity and specificity for almost any metal ions at a specific oxidation state can be obtained through in vitro selection. By integrating the DNAzyme with different signal transduction molecules, such as fluorophores or nanoparticles, DNAzyme-based sensors for a broad range of metal ions with high sensitivity (with limit of detection down to ppt) and selectivity (with over a million fold) have been reported. In this chapter, we summarize recent progress in DNAzyme-based sensors for metal ions and describe detailed protocols in designing fluorescent and colorimetric sensors for uranium and mercury. The diverse range of metal ions it can detect as well as its excellent sensing properties makes DNAzyme an excellent choice for ocean sensing.

Key words

DNAzyme Sensing Seawater Uranium Mercury Colorimetric sensor Fluorescent ­sensor Fluorophores Nanoparticles Ocean 

Notes

Acknowledgements

The authors acknowledge the financial support from the US National Institutes of Health (ES016865), Department of Energy (DE-FG02-08-ER64568), National Science Foundation (CTS-0120978, DMR-0117792, and DMI-0328162).

References

  1. 1.
    Butler A (1998) Acquisition and utilization of transition metal ions by marine organisms. Science 281(5374):207–210PubMedCrossRefGoogle Scholar
  2. 2.
    Ardini F, Magi E, Grotti M (2011) Determination of ultratrace levels of dissolved metals in seawater by reaction cell inductively coupled plasma mass spectrometry after ammonia induced magnesium hydroxide coprecipitation. Anal Chim Acta 706(1):84–88PubMedCrossRefGoogle Scholar
  3. 3.
    Moore TS, Mullaugh KM, Holyoke RR, Madison ANS, Yucel M, Luther GW (2009) Marine chemical technology and sensors for marine waters: potentials and limits. Ann Rev Mar Sci 1:91–115PubMedCrossRefGoogle Scholar
  4. 4.
    Achterberg EP, Holland TW, Bowie AR, Fauzi R, Mantoura C, Worsfold PJ (2001) Determination of iron in seawater. Anal Chim Acta 442(1):1–14CrossRefGoogle Scholar
  5. 5.
    Takata H, Zheng J, Tagami K, Aono T, Uchida S (2011) Determination of 232 Th in seawater by ICP-MS after preconcentration and separation using a chelating resin. Talanta 85(4):1772–1777PubMedCrossRefGoogle Scholar
  6. 6.
    Colbert D, Johnson KS, Coale KH (1998) Determination of cadmium in seawater using automated on-line preconcentration and direct injection graphite furnace atomic absorption spectrometry. Anal Chim Acta 377(2–3): 255–262CrossRefGoogle Scholar
  7. 7.
    Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. ChemBiol 1(4):223–229Google Scholar
  8. 8.
    Li J, Lu Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J Am Chem Soc 122(42):10466–10467CrossRefGoogle Scholar
  9. 9.
    Cuenoud B, Szostak JW (1995) A DNA metalloenzyme with DNA ligase activity. Nature 375(6532):611–614PubMedCrossRefGoogle Scholar
  10. 10.
    Carmi N, Shultz LA, Breaker RR (1996) In vitro selection of self-cleaving DNAs. Chem Biol 3(12):1039–1046PubMedCrossRefGoogle Scholar
  11. 11.
    Wang W, Billen LP, Li Y (2002) Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem Biol 9(4):507–517PubMedCrossRefGoogle Scholar
  12. 12.
    Santoro SW, Joyce GF, Sakthivel K, Gramatikova S, Barbas CF III (2000) RNA cleavage by a DNA enzyme with extended chemical functionality. J Am Chem Soc 122(11):2433–2439PubMedCrossRefGoogle Scholar
  13. 13.
    Mei SHJ, Liu Z, Brennan JD, Li Y (2003) An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling. J Am Chem Soc 125(2):412–420PubMedCrossRefGoogle Scholar
  14. 14.
    Bruesehoff PJ, Li J, Augustine AJ, Lu Y (2002) Improving metal ion specificity during in vitro selection of catalytic DNA. Comb Chem High Throughput Screen 5(4):327–335PubMedGoogle Scholar
  15. 15.
    Wang Y, Silverman SK (2003) Deoxyribozymes that synthesize branched and lariat RNA. J Am Chem Soc 125(23):6880–6881PubMedCrossRefGoogle Scholar
  16. 16.
    Hollenstein M, Hipolito C, Lam C, Dietrich D, Perrin DM (2008) A highly selective DNAzyme sensor for mercuric ions. Angew Chem-Int Ed 47(23):4346–4350CrossRefGoogle Scholar
  17. 17.
    Liu J, Brown AK, Meng X, Cropek DM, Istok JD, Watson DB et al (2007) A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity. Proc Natl Acad Sci U S A 104(7):2056–2061PubMedCrossRefGoogle Scholar
  18. 18.
    He Q-C, Zhou J-M, Zhou D-M, Nakamatsu Y, Baba T, Taira K (2002) Comparison of metal-ion-dependent cleavages of RNA by a DNA enzyme and a hammerhead ribozyme. Biomacromolecules 3(1):69–83PubMedCrossRefGoogle Scholar
  19. 19.
    Liu J, Lu Y (2004) Accelerated color change of gold nanoparticles assembled by DNAzymes for simple and fast colorimetric Pb2+ detection. J Am Chem Soc 126(39):12298–12305PubMedCrossRefGoogle Scholar
  20. 20.
    Khachigian LM (2005) DNAzymes targeting immediate-early genes as inhibitors of angiogenesis and restenosis. In: Khachigian LM (ed) Synthetic nucleic acids as inhibitors of gene expression. CRC, New York, pp 153–159Google Scholar
  21. 21.
    Liu J, Lu Y (2006) Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons. Methods in molecular biology, Totowa, NJ, p 335 (Fluorescent energy transfer nucleic acid probes, pp 275–288)Google Scholar
  22. 22.
    Cheglakov Z, Weizmann Y, Beissenhirtz MK, Willner I (2006) Ultrasensitive detection of DNA by the PCR-induced generation of DNAzymes: the DNAzyme primer approach. Chem Commun 30:3205–3207CrossRefGoogle Scholar
  23. 23.
    Cheglakov Z, Weizmann Y, Basnar B, Willner I (2007) Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes. Org Biomol Chem 5(2):223–225PubMedCrossRefGoogle Scholar
  24. 24.
    Liu J, Lu Y (2007) A DNAzyme catalytic beacon sensor for paramagnetic Cu2+ ions in aqueous solution with high sensitivity and selectivity. J Am Chem Soc 129(32):9838–9839PubMedCrossRefGoogle Scholar
  25. 25.
    Liu J, Lu Y (2007) Colorimetric Cu2+ detection with a ligation DNAzyme and nanoparticles. Chem Commun 46:4872–4874CrossRefGoogle Scholar
  26. 26.
    Lee JH, Wang ZD, Liu JW, Lu Y (2008) Highly sensitive and selective colorimetric sensors for Uranyl (UO22+): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems. J Am Chem Soc 130(43):14217–14226CrossRefGoogle Scholar
  27. 27.
    Wang Z, Lee JH, Lu Y (2008) Label free colorimetric detection of metal ions using gold nanoparticles and DNAzyme with 3 nM detection limit and tunable dynamic range. Adv Mater 20:3263–3267CrossRefGoogle Scholar
  28. 28.
    Lan T, Furuya K, Lu Y (2010) A highly selective lead sensor based on a classic lead DNAzyme. Chem Commun 46(22):3896–3898CrossRefGoogle Scholar
  29. 29.
    Hung YL, Hsiung TM, Chen YY, Huang YF, Huang CC (2010) Colorimetric detection of heavy metal ions using label-free gold nanoparticles and alkanethiols. J Phys Chem C 114(39):16329–16334CrossRefGoogle Scholar
  30. 30.
    Kong RM, Zhang XB, Chen Z, Meng HM, Song ZL, Tan WH et al (2011) Unimolecular catalytic DNA biosensor for amplified detection of l-histidine via an enzymatic recycling cleavage strategy. Anal Chem 83(20): 7603–7607CrossRefGoogle Scholar
  31. 31.
    Zhang XB, Kong RM, Lu Y (2011) Metal ion sensors based on DNAzymes and related DNA molecules. In: Cooks RG, Yeung ES (eds) Annual review of analytical chemistry, vol 4. Annual Reviews, Palo Alto, CA, pp 105–128Google Scholar
  32. 32.
    Liu JW, Cao ZH, Lu Y (2009) Functional nucleic acid sensors. Chem Rev 109(5):1948–1998CrossRefGoogle Scholar
  33. 33.
    Brown AK, Liu J, He Y, Lu Y (2009) Biochemical characterization of a uranyl ­ion-specific DNAzyme. ChemBioChem 10(3): 486–492PubMedCrossRefGoogle Scholar
  34. 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 46(40): 7587–7590CrossRefGoogle Scholar
  35. 35.
    Wang ZD, Lee JH, Lu Y (2008) Highly sensitive “turn-on” fluorescent sensor for Hg2+ in aqueous solution based on structure-switching DNA. Chem Commun 45:6005–6007CrossRefGoogle Scholar
  36. 36.
    Lee JH, Yigit MV, Mazumdar D, Lu Y (2010) Molecular diagnostic and drug delivery agents based on aptamer-nanomaterial conjugates. Adv Drug Deliv Rev 62(6):592–605CrossRefGoogle Scholar
  37. 37.
    Liu J, Lu Y (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J Am Chem Soc 125(22): 6642–6643PubMedCrossRefGoogle Scholar
  38. 38.
    Mirkin CA, Letsinger RL, Mucic RC, Storhoff JJ (1996) A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382(6592):607–609CrossRefGoogle Scholar
  39. 39.
    Liu J, Lu Y (2005) Stimuli-responsive disassembly of nanoparticle aggregates for light-up colorimetric sensing. J Am Chem Soc 127(36): 12677–12683PubMedCrossRefGoogle Scholar
  40. 40.
    Li H, Rothberg L (2004) Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc Natl Acad Sci U S A 101(39): 14036–14039PubMedCrossRefGoogle Scholar
  41. 41.
    Wernette DP, Swearingen CB, Cropek DM, Lu Y, Sweedler JV, Bohn PW (2006) Incorporation of a DNAzyme into Au-coated nanocapillary array membranes with an internal standard for Pb(II) sensing. Analyst 131(1):41CrossRefGoogle Scholar
  42. 42.
    Dalavoy TS, Wernette DP, Gong M, Sweedler JV, Lu Y, Flachsbart BR et al (2008) Immobilization of DNAzyme catalytic beacons on PMMA for Pb2+ detection. Lab Chip 8(5):786–793PubMedCrossRefGoogle Scholar
  43. 43.
    Mazumdar D, Liu JW, Lu G, Zhou JZ, Lu Y (2010) Easy-to-use dipstick tests for detection of lead in paints using non-cross-linked gold nanoparticle-DNAzyme conjugates. Chem Commun 46(9):1416–1418CrossRefGoogle Scholar
  44. 44.
    Liu J, Mazumdar D, Lu Y (2006) A simple and sensitive “dipstick” test in serum based on lateral flow separation of aptamer-linked nanostructures. Angew Chem Int Ed 45(47):7955–7959CrossRefGoogle Scholar
  45. 45.
    Prants SV, Uleysky MY, Budyansky MV (2011) Numerical simulation of propagation of radioactive pollution in the ocean from the Fukushima Dai-ichi nuclear power plant. Doklady Earth Sci 439(2):1179–1182CrossRefGoogle Scholar
  46. 46.
    Kinoshita N, Sueki K, Sasa K, Kitagawa J, Ikarashi S, Nishimura T et al (2011) Assessment of individual radionuclide distributions from the Fukushima nuclear accident covering central-east Japan. Proc Natl Acad Sci U S A 108(49):19526–19529PubMedCrossRefGoogle Scholar
  47. 47.
    Takeuchi T (1980) Extraction of lithium from sea-water with metallic aluminum. J Nucl Sci Technol 17(12):922–928CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Department of Materials Science and EngineeringUniversity of IllinoisUrbanaUSA
  2. 2.School of Advanced Materials Science and EngineeringSungkyunkwan University (SKKU)SuwonSouth Korea
  3. 3.Department of ChemistryUniversity of IllinoisUrbanaUSA

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