Target-induced structure-switching DNA hairpins for sensitive electrochemical monitoring of mercury (II)

A simple, sensitive and reusable electrochemical sensor was designed for determination of mercury (II) (Hg(2+)) by coupling target-induced conformational switch of DNA hairpins with thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination chemistry. The hairpin probe consisted of a stem of 6 base pairs enclosing a 14 nucleotide (nt) loop and an additional 12 nt sticky end at the 3' end. Each hairpin was labeled with ferrocene (Fc) redox tag in the middle of the loop, which was immobilized on the electrode via self-assembly of the terminal thiol moiety at the 5' end. In the presence of target analyte, Hg(2+)-mediated base pairs induced the conformational change from the sticky end to open the hairpins, resulting in the ferrocene tags close to the electrode for the increasing redox current. The strong coordination reaction of T-Hg(2+)-T resulted in a good repeatability and intermediate precision down to 10%. The dynamic concentration range spanned from 5.0nM to 1.0μM Hg(2+) with a detection limit of 2.5nM at the 3s(blank) level. The strategy afforded exquisite selectivity for Hg(2+) against other environmentally related metal ions. Inspiringly, the developed sensor could be reused by introduction of iodide (I(-)).     

Oligonucleotide probes applied for sensitive enzyme-amplified electrochemical assay of mercury(II) ions

We developed a novel electrochemical sensor for Hg(2+) detection using two mercury-specific oligonucleotide probes and streptavidin-horseradish peroxidase (HRP) enzymatic signal amplification. The two mercury-specific oligonucleotide probes comprised a thiolated capture probe and a biotinated signal probe. The thiolated capture probe was immobilized on a gold electrode. In the presence of Hg(2+), the thymine-Hg(2+)-thymine (T-Hg(2+)-T) interaction between the mismatched T-T base pairs directed the biotinated signal probe hybridizing to the capture probe and yielded a biotin-functioned electrode surface. HRP was then immobilized on the biotin-modified substrate via biotin-streptavidin interaction. The immobilized HRP catalyzed the oxidation of hydroquinone (H(2)Q) to benzoquinone (BQ) by hydrogen peroxide (H(2)O(2)) and the generated BQ was further electrochemically reduced at the modified gold electrode, producing a readout signal for quantitative detection of Hg(2+). The results showed that the enzyme-amplified electrochemical sensor system was highly sensitive to Hg(2+) in the concentration of 0.5 nM to 1 μM with a detection limit of 0.3 nM, and it also demonstrated excellent selectivity against other interferential metal ions.     

A highly sensitive and selective optical sensor for Pb(2+) by using conjugated polymers and label-free oligonucleotides

The detection of Pb(2+) with DNA-based biosensor is usually susceptible to severe interference from Hg(2+) because of the T-Hg(2+)-T interaction between Hg(2+) and T residues. In this study, we developed a rapid, sensitive, selective and label-free sensor for the detection of Pb(2+) in the presence of Hg(2+) based on the Pb(2+)-induced G-quadruplex formation with cationic water-soluble conjugated polymer (PMNT) as a "polymeric stain" to transduce optical signal. We selected a specific sequence oligonucleotide, TBAA (5'-GGAAGGTGTGGAAGG-3'), which can form a G-quadruplex structure upon the addition of Pb(2+). This strategy provided a promising alternative to Pb(2+) determination in the presence of Hg(2+) instead of the universal masking agents of Hg(2+) (such as CN(-), SCN(-)). Based on this observation, a simple "mix-and-detect" optical sensor for the detection of Pb(2+) was proposed due to the distinguishable optical properties of PMNT-ssDNA and PMNT-(G-quadruplex) complexes. By this method, we could identify micromolar Pb(2+) concentrations within 5min even with the naked eye. Furthermore, the detection limit was improved to the nanomolar range by the fluorometric method. We also successfully utilized this biosensor for the determination of Pb(2+) in tap water samples.     

Electrically contacted enzyme based on dual hairpin DNA structure and its application for amplified detection of Hg2+

In the present study, based on a dual hairpin DNA structure, a novel system of electrically contacted enzyme and its signal amplification for ultrasensitive detection of Hg(2+) was demonstrated. In the presence of Hg(2+), with the interaction of thymine-Hg(2+)-thymine (T-Hg(2+)-T), DNA sequence dully labeled with ferrocene (Fc) at 5' end and horseradish peroxidase (HRP) at 3' end, hybridized to the capture probe and formed the dual hairpin structure on the electrode. Fc unit acts as a relay that electrically contacts HRP with the electrode and activates the bioelectrocatalyzed reduction of H(2)O(2). And based on the bioelectrocatalyzed signal amplification of the presented system, Hg(2+) could be quantitatively detected in the range of 10(-10)-10(-6)M with a low detection limit of 52 pM. And it also demonstrated excellent selectivity against other interferential metal ions.     

Reusable evanescent wave DNA biosensor for rapid, highly sensitive, and selective detection of mercury ions

Mercury ions (Hg(2+)) are a highly toxic and ubiquitous pollutants requiring rapid and sensitive on-site detection methods in the environment and foods. Herein, we report an envanescent wave DNA-based biosensor for rapid and very sensitive Hg(2+) detection based on a direct structure-competitive detection mode. In this system, a DNA probe covalently immobilized onto a fiber optic sensor contains a short common oligonucleotide sequences that can hybidize with a fluorescently labeled complementary DNA. The DNA probe also comprises a sequence of T-T mismatch pairs that binds with Hg(2+) to form a T-Hg(2+)-T complex by folding of the DNA segments into a hairpin structure. With a structure-competitive mode, a higher concentration of Hg(2+) leads to less fluorescence-labeled cDNA bound to the sensor surface and thus to lower fluorescence signal. The total analysis time for a single sample, including the measurement and surface regeneration, was under 6 min with a Hg(2+) detection limit of 2.1 nM. The high specificity of the sensor was demonstrated by evaluating its response to a number of potentially interfering metal ions. The sensor's surface can be regenerated with a 0.5% SDS solution (pH 1.9) over 100 times with no significant deterioration of performance. This platform is potentially applicable to detect other heavy metal ions or small-molecule analytes for which DNA/aptamers can be used as specific sensing probes.     

Oligonucleotide-based fluorogenic sensor for simultaneous detection of heavy metal ions

In this study, we report a new fluorogenic sensor based on fluorescence resonance energy transfer (FRET) for detection of heavy metal ions in aqueous solution. The method showed the advantage of being simple, highly sensitive and selective, and rapid. The donor (CdTe QDs) and acceptor (TAMRA or Cy5) are brought into close proximity to one another due to Hg(2+) and Ag(+) form strong and stable T-Hg(2+)-T complexes and C-Ag(+)-C complexes, which quenches the fluorescent intensity of CdTe QDs and enables the energy transfer from donor to acceptor. This sensor showed high sensitivity and selectivity when only one kind of ion (Ag(+) or Hg(2+)) exists. Furthermore, the assay can also simultaneously detect Ag(+) and Hg(2+) in water media with the limit of detection (LOD) of 2.5 and 1.8 nM, separately, which satisfactorily meets the sensitivity demands of Environmental Protection Agency (EPA) and World Health Organization (WHO). This assay also exhibits excellent selectivity toward Ag(+) and Hg(2+). Therefore, this method is of great practical and theoretical importance for detecting heavy metal ions in aqueous solution.     

A Simple and Rapid Resonance Scattering Spectral Method for Detection of Trace Hg<Superscript>2+</Superscript> Using Aptamer-Nanogold as Probe

Single-strand deoxyribonucleic acid (ssDNA) were used to modified nanogold particle to obtain a aptamer-nanogold probe (NGssDNA) for Hg(II). The probe is not aggregated in high concentration of NaCl. In the pH 7.0 Na₂HPO₄-NaH₂PO₄ buffer solution and in the presence of high concentration of NaCl, NGssDNA interact with Hg(II) to form stable double-strand T-Hg(II)-T mismatches and to release nanogold particles from the probe. The released nanogold particles aggregated to form bigger clusters which leaded the resonance scattering (RS) intensity at 540 nm enhanced linearly with the concentration of Hg²⁺ in the range of 0.39–1666.7 nM, with detection of 0.1 nM. This simple, rapid, and sensitive aptamer-nanogold RS assay was applied to determination of Hg²⁺ in wastewater, with satisfactory results.     

Highly sensitive and selective photoelectrochemical DNA sensor for the detection of Hg²⁺ in aqueous solutions

A "turn-on" photoelectrochemical sensor for Hg(2+) detection based on thymine-Hg(2+)-thymine interaction is presented by using a thymine-rich oligonucleotide film and a double-strand DNA intercalator, Ru(bpy)(2)(dppz)(2+) (bpy=2,2'-bipyridine, dppz=dipyrido[3,2-a:2',3'-c]phenazine) as the photocurrent signal reporter. The presence of Hg(2+) induces the formation of a double helical DNA structure which provides binding sites for Ru(bpy)(2)(dppz)(2+). The double helical structure was confirmed by circular dichroism and fluorescence measurements. Under the optimized conditions, a linear relationship between photocurrent and Hg(2+) concentration was obtained over the range of 0.1 nM to 10 nM Hg(2+), with a detection limit of 20 pM. Interference by 10 other metal ions was negligible. Analytical results of Hg(2+) spiked into tap water and lake water by the sensor were in good agreement with mass spectrometry data. With the advantages of high sensitivity and selectivity, simple sensor construction, low instrument cost and low sample volume, this method is potentially suitable for the on-site monitoring of Hg(2+) contamination.     

G-quadruplex DNAzyme-based Hg2+ and cysteine sensors utilizing Hg2+-mediated oligonucleotide switching

A simple and sensitive colorimetric Hg(2+) detection method is reported, based on the Hg(2+)-mediated structural switch of an unlabeled oligonucleotide strand. In the absence of Hg(2+), the oligonucleotide strand forms a stem-loop. A G-rich sequence in the strand is partially caged in the stem-loop structure and cannot fold into a G-quadruplex. In the presence of Hg(2+), T-Hg(2+)-T coordination chemistry leads to the formation of another stem-loop structure and the release of the G-rich sequence. The released sequence folds into a G-quadruplex, which binds hemin to form catalytically active G-quadruplex DNAzymes. This is detected as an absorbance increase in a H(2)O(2)-2,2'-azinobis(3-ethylbenzothiozoline)-6-sulfonic acid (ABTS) reaction system using UV-vis absorption spectroscopy. This simple colorimetric sensor can detect aqueous Hg(2+) at concentrations as low as 9.2 nM with high selectivity. Based on the strong binding interaction between Hg(2+) and the sulfur-containing amino acid cysteine (Cys), and the competition between Cys and a oligonucleotide for Hg(2+), the proposed Hg(2+)-sensing system can be further exploited as a Cys-sensing method. The method has a detection limit for Cys of 19 nM.     

Carbon nanoparticle for highly sensitive and selective fluorescent detection of mercury(II) ion in aqueous solution

In this article, carbon nanoparticles (CNPs) were used as a novel fluorescent sensing platform for highly sensitive and selective Hg(2+) detection. To the best of our knowledge, this is the first example of CNPs obtained from candle soot used in this type of sensor. The general concept used in this approach is based on that adsorption of the fluorescently labeled single-stranded DNA (ssDNA) probe by CNP via π-π stacking interactions between DNA bases and CNP leads to substantial dye fluorescence quenching; however, in the presence of Hg(2+), T-Hg(2+)-T induced hairpin structure does not adsorb on CNP and thus retains the dye fluorescence. A detection limit as low as 10nM was achieved. The present CNP-based biosensor for Hg(2+) detection exhibits remarkable specificity against other possible metal ions. Furthermore, superior selectivity performance was observed when Hg(2+) detection was carried out in the presence of a large amount of other interference ions. Finally, in order to evaluate its potential practical application, Hg(2+) detection was conducted with the use of lake water other than pure buffer and it is believed that it holds great promise for real sample analysis upon further development.     

Visual detection of Hg²⁺ in aqueous solution using gold nanoparticles and thymine-rich hairpin DNA probes

We report a sensitive method for visual detection of mercury ions (II) (Hg2?) in aqueous solution by using gold nanoparticles (Au-NPs) and thymine (T)-rich hairpin DNA probes. The thiolated hairpin DNA probe was immobilized on the Au-NP surface through a self-assembling method. Another thymine-rich, digoxin-labeled DNA probe was introduced to form DNA duplexes on the Au-NP surface with thymine-Hg2?-thymine (T-Hg2?-T) coordination in the presence of Hg2?. The Au-NPs associated with the formed duplexes were captured on the test zone of a lateral flow strip biocomponent (LFSB) by immunoreaction events between the digoxin on the duplexes and anti-digoxin antibodies on the LFSB. The accumulation of Au-NPs produced a characteristic red band on the test zone, enabling visual detection of Hg2? without instrumentation. A detection limit of 0.1 nM was obtained under optimal experimental conditions. This method provides a simple, rapid, sensitive approach for the detection of Hg2? and shows great promise for point-of-care and in-field detection of environmentally toxic mercury.     

Raman spectroscopic detection of the T-Hg II-T base pair and the ionic characteristics of mercury

Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important for designing and fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg(II)-mediated T-T (T-Hg(II)-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of Hg(II). A characteristic Raman marker band at 1586 cm(-1) was observed and assigned to the C4=O4 stretching mode. We confirmed the assignment by the isotopic shift ((18)O-labeling at O4) and density functional theory (DFT) calculations. The unusually low wavenumber of the C4=O4 stretching suggested that the bond order of the C4=O4 bond reduced from its canonical value. This reduction of the bond order can be explained if the enolate-like structure (N3=C4-O4(-)) is involved as a resonance contributor in the thymine ring of the T-Hg(II)-T pair. This resonance includes the N-Hg(II)-bonded state (Hg(II)-N3-C4=O4) and the N-Hg(II)-dissociated state (Hg(II+) N3=C4-O4(-)), and the latter contributor reduced the bond order of N-Hg(II). Consequently, the Hg(II) nucleus in the T-Hg(II)-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.     

Oligonucleotide-functionalized silver nanoparticle extraction and laser-induced fluorescence for ultrasensitive detection of mercury(II) ion

This study describes the development of a simple, sensitive, and selective detection system for Hg(2+) ion by combining nanoparticle extraction, fluorescent dye labeling, and flow injection analysis (FIA) detection. Repeats of 33 thymine nucleotides-functionalized silver nanoparticles (T(33)-AgNPs) specifically capture Hg(2+) from aqueous solution through the coordination between T(33) and Hg(2+). Meanwhile, Hg(2+) ion drives a T(33) conformational change from a random coil to a folded structure. The T(33)-Hg(2+)complexes adsorbed on the NP surface were collected from the initial sample by centrifugation, and they were then detached from the NP surface by addition of H(2)O(2). The T(33)-Hg(2+) complexes preferentially bind to SYBR Green I (SG), enhancing the SG fluorescence. By contrast, SG fluoresces only weakly in the presence of T(33) alone. The extraction efficiency of Hg(2+) was highly dependent on polythymine length, the concentration of T(33)-AgNPs, and the incubaton time of T(33)-AgNPs with Hg(2+). Under optimal extraction and labeling conditions, FIA detection showed the limit of detection (at a signal-to-noise ratio of three) for Hg(2+)of 3 pM. The selectivity of our analytical system is more than 1000-fold for Hg(2+) over any metal ions. We validated the applicability of this system for the determination of Hg(2+) concentrations in tap water.     

Sensitive label-free oligonucleotide-based microfluidic detection of mercury (II) ion by using exonuclease I

Mercury is a highly toxic metal that can cause significant harm to humans and aquatic ecosystems. This paper describes a novel approach for mercury (Hg(2+)) ion detection by using label-free oligonucleotide probes and Escherichia coli exonuclease I (Exo I) in a microfluidic electrophoretic separated platform. Two single-stranded DNAs (ssDNA) TT-21 and TT-44 with 7 Thymine-Thymine mispairs are employed to capture mercury ions. Due to the coordination structure of T-Hg(2+)-T, these ssDNAs are folded into hairpin-like double-stranded DNAs (dsDNA) which are more difficult to be digested by Exo I, as confirmed by polyacrylamide gel electrophoresis (PAGE) analysis. A series of microfluidic capillary electrophoretic separation studies are carried out to investigate the effect of Exo I and mercury ion concentrations on the detected fluorescence intensity. This method has demonstrated a high sensitivity of mercury ion detection with the limit of detection around 15 nM or 3 ppb. An excellent selectivity of the probe for mercury ions over five interference ions Fe(3+), Cd(2+), Pb(2+), Cu(2+) and Ca(2+) is also revealed. This method could potentially be used for mercury ion detection with high sensitivity and reliability.     

Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages

We report Zn(2+)-dependent deoxyribozymes that ligate RNA. The DNA enzymes were identified by in vitro selection and ligate RNA with k(obs) up to 0.5 min(-)(1) at 1 mM Zn(2+) and 23 degrees C, pH 7.9, which is substantially faster than our previously reported Mg(2+)-dependent deoxyribozymes. Each new Zn(2+)-dependent deoxyribozyme mediates the reaction of a specific nucleophile on one RNA substrate with a 2',3'-cyclic phosphate on a second RNA substrate. Some of the Zn(2+)-dependent deoxyribozymes create native 3'-5' RNA linkages (with k(obs) up to 0.02 min(-)(1)), whereas all of our previous Mg(2+)-dependent deoxyribozymes that use a 2',3'-cyclic phosphate create non-native 2'-5' RNA linkages. On this basis, Zn(2+)-dependent deoxyribozymes have promise for synthesis of native 3'-5'-linked RNA using 2',3'-cyclic phosphate RNA substrates, although these particular Zn(2+)-dependent deoxyribozymes are likely not useful for this practical application. Some of the new Zn(2+)-dependent deoxyribozymes instead create non-native 2'-5' linkages, just like their Mg(2+) counterparts. Unexpectedly, other Zn(2+)-dependent deoxyribozymes synthesize one of three unnatural linkages that are formed upon the reaction of an RNA nucleophile other than a 5'-hydroxyl group. Two of these unnatural linkages are the 3'-2' and 2'-2' linear junctions created when the 2'-hydroxyl of the 5'-terminal guanosine of one RNA substrate attacks the 2',3'-cyclic phosphate of the second RNA substrate. The third unnatural linkage is a branched RNA that results from attack of a specific internal 2'-hydroxyl of one RNA substrate at the 2',3'-cyclic phosphate. When compared with the consistent creation of 2'-5' linkages by Mg(2+)-dependent ligation, formation of this variety of RNA ligation products by Zn(2+)-dependent deoxyribozymes highlights the versatility of transition metals such as Zn(2+) for mediating nucleic acid catalysis.     

Ultrasensitive and dual functional colorimetric sensors for mercury (II) ions and hydrogen peroxide based on catalytic reduction property of silver nanoparticles

The method provides an innovative dual functional sensors for mercury (II) ions and hydrogen peroxide. The addition of H(2)O(2) to the mixture of silver nanoparticles (AgNPs) and Hg(2+) induced color changes of the solution within several seconds even at 2.0 nM Hg(2+). Other metallic ions could not induce color change even at 10 μM. Of importance, this probe was not only successfully applied to detect Hg(2+), but also it could be used to sense H(2)O(2) at a concentration as low as 50 nM (by naked-eye). The outstanding sensitivity and selectivity property for Hg(2+) and H(2)O(2) resulted from the AgNPs mediated reduction of Hg(2+) to elementary Hg in the presence of H(2)O(2), causing the aggregation and colorimetric response of AgNPs. This sensitive and selective colorimetric assay opens up a fresh insight of development facile and fast detection methods for metal ions and biomolecules using the special catalytic reactivity of AgNPs.     

Novel missense mutations in red/green opsin genes in congenital color-vision deficiencies

Lipocortin I-S100 (calcyclin) heterotetramer exhibited ATPase activity in the presence of dsDNA but not ssDNA. To demonstrate its helicase activity, an 80-mer polynucleotide complementary to the replication origin of M13mp18 was synthesized, and the oligonucleotide, (dC)(20), was ligated to either its 5'- or 3'- end for binding to lipocortin. Lipocortin I heterotetramer displaced chains of the partially Y-shaped duplexes with a dC-tail at either the 5'- or 3'- end. The chain displacement required ATP and Mg(2+). Nonhydrolyzable ATP analogues were not effective. Lipocortin I heterotetramer also catalyzed annealing of the polynucleotides to M13mp18. Ca(2+) and phospholipids but not ATP and Mg(2+) were essential for this reaction. Since the chain displacing and annealing reactions were inhibited by monospecific anti-lipocortin I or anti-S100 antibodies, the present observations suggest that the lipocortin I heterotetramer regulates unwinding and annealing of DNA by Mg(2+) (plus ATP) and Ca(2+) (and phospholipids), respectively.     

“Off-On”switching electrochemiluminescence biosensor for mercury(II) detection based on molecular recognition technology

A novel “off-On” electrogenerated chemiluminescence (ECL) biosensor has been developed for the detection of mercury(II) based on molecular recognition technology. The ECL mercury(II) biosensor comprises two main parts: an ECL substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Ruthenium(II) tris-(bipyridine)(Ru(bpy)₃²⁺)/Cyclodextrins-Au nanoparticles(CD-AuNps)/Nafion on the surface of glass carbon electrode (GCE), and the ECL intensity switch is the single hairpin DNA probe designed according to the “molecular recognition” strategy which was functionalized with ferrocene tag at one end and attached to Cyclodextrins (CD) on modified GCE through supramolecular noncovalent interaction. We demonstrated that, in the absence of Hg(II) ion, the probe keeps single hairpin structure and resulted in a quenching of ECL of Ru(bpy)₃²⁺. Whereas, in the presence of Hg(II) ion, the probe prefers to form the T-Hg(II)-T complex and lead to an obvious recovery of ECL of Ru(bpy)₃²⁺, which provided a sensing platform for the detection of Hg(II) ion. Using this sensing platform, a simple, rapid and selective “off-On” ECL biosensor for the detection of mercury(II) with a detection limit of 0.1 nM has been developed.     

DNA strand scission by neocarzinostatin: molecular recognition process responsible for site-specificity

A series of hexanucleotides possessing A-T, G-C, inosine (I)-C and 2-aminoadenine (ANH2)-T base pairs at 5'-side of the target thymine were prepared and their selectivity for C-5' and C4' oxidation in the NCS-mediated degradation was investigated. Quantitative product analysis indicated that preferential C5' oxidation of deoxyribose moiety of the target T occurs at -5'-AT- and 5'-IT- sites, whereas C5' and C4' oxidation occurs competitively at T of -5'-GT- and -5'-ANH2T- sites. Based on the experimental results, an intercalation model that permits competitive hydrogen abstraction from C5' and C4' of deoxyribose moiety has been proposed.     

NMR spectroscopic study of a DNA duplex with mercury-mediated T-T base pairs

Recently, we reported that T-T mismatches can specifically recognize Hg(II) (T-Hg(II)-T pair formation). In order to understand the properties of the T-Hg(II)-T pair, we recorded NMR spectra for a DNA duplex, d(CGCGTTGTCC).d(GGACTTCGCG), with two successive T-T mismatches (Hg (II)-binding sites). We assigned 1H resonances for mercury-free and di-mercurated duplexes, and performed titration experiments with Hg(II) by using 1D 1H NMR spectra. Because of the above mentioned assignments, we could confirm the existence of mono-mercurated species, because individual components gave independent NMR signals in the titration spectra.