Aqueous lead speciation determined using DNAzyme GR5
Gaganprit K. Gill A , Juewen Liu B , Heather M. Gaebler A , Ian Hamilton A and D. Scott Smith
A
B
Abstract
The on-site and real-time detection of metal ions is important for environmental monitoring and risk assessment. For appropriate management decisions, it is necessary to specifically sense the labile fraction of metal rather than total metal. This study provides a proof-of-principle that the DNAzyme GR5 can be used to sense labile lead in natural waters containing dissolved organic matter.
DNAzyme-based sensors are a promising technology for possible labile metal monitoring that have not yet been fully tested in real waters. In clean, buffered, laboratory waters specific DNAzymes interact with specific metal ions and produce a signal (e.g. fluorescence). In more complex natural solutions the free ion concentration is reduced by complexation (e.g. to dissolved organic matter, DOM) and the signal would not be proportional to total metal, but hypothetically proportional to the labile fraction of total metal; i.e. the fraction of metal available to interact with the DNA.
Here, an existing metal specific RNA-cleaving DNAzyme for Pb2+ (GR5) is used to test waters representative of natural solutions. Samples were prepared with ionic strengths from 25 to 100 mM using sodium acetate, sodium chloride and sodium bicarbonate. In addition, pH values of 6.5, 7.5 and 8.5 were tested for the different electrolytes, with and without added dissolved organic carbon, at 2, 5 and 8 mg C L–1. Lead additions were performed at toxicologically relevant levels (less than or equal to 1 µM of added lead).
The GR5 response was found to be dependent on ionic strength, including identity of the background electrolyte, where high ionic strength slowed the reaction and chloride media increased reaction speed. Reproducible responses of GR5 are possible at conditions similar to natural waters, except responses were too fast for high pH (8.5 or higher), low DOC (less than 2 mg C L–1) and low ionic strength (25 mM). It is found that GR5 responds to three lead species, PbOH+, PbCl+ and Pb2+, with relative sensitivities in the same order. GR5 does not respond to lead complexed with acetate, carbonate or DOM. It is possible to use the measured first-order rate constant for lead induced fluorescence of GR5 to calculate ionic lead that agrees within a factor of two with respect to Windermere Humic Aqueous Model predictions. Thus, GR5 may represent a labile lead probe, although further work is necessary to test this.
Keywords: dissolved organic matter, DNAzyme, fluorescence spectroscopy, free lead cation, kinetic-based analytical method, metal bioavailability, metal complexations, metal speciation.
References
Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chemistry & Biology 1(4), 223-229.
| Crossref | Google Scholar | PubMed |
Brown AK, Li J, Pavot CMB, Lu Y (2003) A lead-dependent DNAzyme with a two-step mechanism. Biochemistry 42(23), 7152-7161.
| Crossref | Google Scholar | PubMed |
Bryan SE, Tipping E, Hamilton-Taylor J (2002) Comparison of measured and modelled copper binding by natural organic matter in freshwaters. Comparative Biochemistry and Physiology – C. Toxicology & Pharmacology 133(1–2), 37-49.
| Crossref | Google Scholar | PubMed |
Chen W, Guéguen C, Smith DS, Galceran J, Puy J, Companys E (2018) Metal (Pb, Cd, and Zn) binding to diverse organic matter samples and implications for speciation modeling. Environmental Science & Technology 52(7), 4163-4172.
| Crossref | Google Scholar | PubMed |
de Paiva Magalhãaes D, da Costa Marques MR, Baptista DF, Buss DF (2015) Metal bioavailability and toxicity in freshwaters. Environmental Chemistry Letters 13(1), 69-87.
| Crossref | Google Scholar |
Di Toro DM, Allen HE, Bergman HL, Meyer JS, Paquin PR, Santore RC (2001) Biotic ligand model of the acute toxicity of metals. 1. Technical basis. Environmental Toxicology and Chemistry 20, 2383-2396.
| Crossref | Google Scholar | PubMed |
Florence TM (1986) Electrochemical approaches to trace element speciation in waters. A review. The Analyst 111(5), 489-505.
| Crossref | Google Scholar |
Galceran J, Huidobro C, Companys E, Alberti G (2007) AGNES: a technique for determining the concentration of free metal ions. The case of Zn(II) in coastal mediterranean seawater. Talanta 71, 1795-1803.
| Crossref | Google Scholar | PubMed |
Gheorghiu C, Smith DS, Al-Reasi HA, McGeer JC, Wilkie MP (2010) Influence of natural organic matter (NOM) quality on Cu–gill binding in the rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology 97(4), 343-352.
| Crossref | Google Scholar | PubMed |
Goedecker S, Teter M, Hutter J (1996) Separable dual-space gaussian pseudopotentials. Physical Review – B. Condensed Matter 54(3), 1703-1710.
| Crossref | Google Scholar | PubMed |
Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. Journal of Computational Chemistry 27(15), 1787-1799.
| Crossref | Google Scholar | PubMed |
Huang PJJ, Liu J (2014) Sensing parts-per-trillion Cd2+, Hg2+, and Pb2+ collectively and individually using phosphorothioate DNAzymes. Analytical Chemistry 86(12), 5999-6005.
| Crossref | Google Scholar | PubMed |
Hutter J, Iannuzzi M, Schiffmann F, VandeVondele J (2013) CP2K Atomistic simulations of condensed matter systems. WIREs Computational Molecular Science 4(1), 15-25.
| Crossref | Google Scholar |
Jansen RAG, van Leeuwen HP, Cleven RFMJ, van den Hoop MAGT (1998) Speciation and lability of zinc(II) in river waters. Environmental Science and Technology 32(24), 3882-3886.
| Crossref | Google Scholar |
Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, et al. (2020) CP2K: an electronic structure and molecular dynamics software package – Quickstep: efficient and accurate electronic structure calculations. The Journal of Chemical Physics 152(19), 194103.
| Crossref | Google Scholar |
Lan T, Furuya K, Lu Y (2010) A highly selective lead sensor based on a classic lead DNAzyme. Chemical Communications 46(22), 3896-3898.
| Crossref | Google Scholar | PubMed |
Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J (2017) Crystal structure of an RNA-cleaving DNAzyme. Nature Communications 8(1), 2006.
| Crossref | Google Scholar | PubMed |
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. Proceedings of the National Academy of Sciences of the United States of America 104(7), 2056-2061.
| Crossref | Google Scholar | PubMed |
Lofts S, Tipping E (2011) Assessing WHAM/Model VII against field measurements of free metal ion concentrations: model performance and the role of uncertainty in parameters and inputs. Environmental Chemistry 8(5), 501-516.
| Crossref | Google Scholar |
Lu Y, Liu J (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current Opinion in Biotechnology 17(6), 580-588.
| Crossref | Google Scholar | PubMed |
Luider CD, Crusius J, Playle RC, Curtis PJ (2004) Influence of natural organic matter source on copper speciation as demonstrated by Cu binding to fish gills, by ion selective electrode, and by DGT gel sampler. Environmental Science & Technology 38(10), 2865-2872.
| Crossref | Google Scholar | PubMed |
Mager EM, Esbaugh AJ, Brix KV, Ryan AC, Grosell M (2011) Influences of water chemistry on the acute toxicity of lead to Pimephales promelas and Ceriodaphnia dubia. Comparative Biochemistry and Physiology – C. Toxicology & Pharmacology 153(1), 82-90.
| Crossref | Google Scholar | PubMed |
Markich SJ, Brown PL, Batley GE, Apte SC, Stauber JL (2001) Incorporating metal speciation and bioavailability into water quality guidelines for protecting aquatic ecosystems. Australasian Society for Ecotoxicology 7, 109-122.
| Google Scholar |
Moon WJ, Huang PJJ, Liu J (2021) Probing metal-dependent phosphate binding for the catalysis of the 17E DNAzyme. Biochemistry 60(24), 1909-1918.
| Crossref | Google Scholar | PubMed |
Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Physical Review Letters 77(18), 3865-3868.
| Crossref | Google Scholar | PubMed |
Pesavento M, Alberti G, Biesuz R (2009) Analytical methods for determination of free metal ion concentration, labile species fraction and metal complexation capacity of environmental waters: a review. Analytica Chimica Acta 631(2), 129-141.
| Crossref | Google Scholar | PubMed |
Ren W, Huang PJJ, He M, Lyu M, Wang C, Wang S, Liu J (2020) Sensitivity of a classic DNAzyme for Pb2+ modulated by cations, anions and buffers. The Analyst 145(4), 1384-1388.
| Crossref | Google Scholar | PubMed |
Santore RC, DiToro DM, Paquin PR, Allen HE, Meyer JS (2001) Biotic ligand model of the acute toxicity of metals. 2. Application to acute copper toxicity in freshwater fish and Daphnia. Environmental Toxicology and Chemistry 20, 2397-2402.
| Crossref | Google Scholar | PubMed |
Saran R, Liu J (2016) A comparison of two classic Pb2+ dependent RNA-cleaving DNAzymes. Inorganic Chemistry Frontiers 3(4), 494-501.
| Crossref | Google Scholar |
Schwartz ML, Curtis PJ, Playle RC (2004) Influence of natural organic matter source on acute copper, lead, and cadmium toxicity to rainbow trout (Oncorhynchus mykiss). Environmental Toxicology and Chemistry 23, 2889-2899.
| Crossref | Google Scholar | PubMed |
Simonin JP, Verweij W (2022) A simplified mean spherical approximation model for the description of activity coefficients in electrolyte mixtures. Industrial & Engineering Chemistry Research 61(35), 13265-13274.
| Crossref | Google Scholar |
Tait TN, Rabson LM, Diamond RL, Cooper CA, McGeer JC, Smith DS (2016) Determination of cupric ion concentrations in marine waters: an improved procedure and comparison with other speciation methods. Environmental Chemistry 13(1), 140-148.
| Crossref | Google Scholar |
Turner D, Whitfield M, Dickson A (1981) The equilibrium speciation of dissolved components in fresh-water and sea water at 25°C and 1 atm pressure. Geochimica et Cosmochimica Acta 45(6), 855-881.
| Crossref | Google Scholar |
van Leeuwen HP, Town RM, Buffle J, Cleven RFMJ, Davison W, Puy J, van Riemsdijk WH, Sigg L (2005) Dynamic speciation analysis and bioavailability of metals in aquatic systems. Environmental Science & Technology 39(22), 8545-8556.
| Crossref | Google Scholar | PubMed |
Ward WL, Plakos K, DeRose VJ (2014) Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chemical Reviews 114(8), 4318-4342.
| Crossref | Google Scholar | PubMed |
Wood CM, Al-Reasi HA, Smith DS (2011) The two faces of DOC. Aquatic Toxicology 105(3–4), 3-8.
| Crossref | Google Scholar | PubMed |
Xiao CQ, Huang Q, Zhang Y, Zhang HQ, Lai L (2020) Binding thermodynamics of divalent metal ions to several biological buffers. Thermochimica Acta 691, 178721.
| Crossref | Google Scholar |
Zhang H, Davison W (2000) Direct in situ measurements of labile inorganic and organically bound metal species in synthetic solutions and natural waters using diffusive gradients in thin films. Analytical Chemistry 72(18), 4447-4457.
| Crossref | Google Scholar | PubMed |
Zhang XB, Kong RM, Lu Y (2011) Metal ion sensors based on DNAzymes and related DNA molecules. Annual Review of Analytical Chemistry 4(1), 105-128.
| Crossref | Google Scholar | PubMed |
Zhou W, Zhang Y, Huang PJJ, Ding J, Liu J (2016) A DNAzyme requiring two different metal ions at two distinct sites. Nucleic Acids Research 44(1), 354-363.
| Crossref | Google Scholar | PubMed |
Zhou W, Saran R, Liu J (2017) Metal sensing by DNA. Chemical Reviews 117(12), 8272-8325.
| Crossref | Google Scholar | PubMed |