One-Step, Room Temperature, Colorimetric Detection of Mercury (Hg2+) Using DNA/Nanoparticle Conjugates

Metal ion sensors based on DNAzymes and related DNA molecules

Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-error-dependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb(2+), Cu(2+), Hg(2+), and UO(2)(2+). In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes.

Colorimetric sensing of silver(I) and mercury(II) ions based on an assembly of Tween 20-stabilized gold nanoparticles

We have developed a rapid and homogeneous method for the highly selective detection of Hg(2+) and Ag(+) using Tween 20-modified gold nanoparticles (AuNPs). Citrate ions were found to still be adsorbed on the Au surface when citrate-capped AuNPs were modified with Tween 20, which stabilizes the citrate-capped AuNPs against conditions of high ionic strength. When citrate ions had reduced Hg(2+) and Ag(+) to form Hg-Au alloys and Ag on the surface of the AuNPs, Tween 20 was removed from the NP surface. As a result, the AuNPs were unstable under a high-ionic-strength solution, resulting in NP aggregation. The formation of Hg-Au alloys or Ag on the surface of the AuNPs was demonstrated by means of inductively coupled plasma mass spectroscopy and energy-dispersive X-ray spectroscopy. Tween 20-AuNPs could selectively detect Hg(2+) and Ag(+) at concentrations as low as 0.1 and 0.1 microM in the presence of NaCl and EDTA, respectively. Moreover, the probe enables the analysis of AgNPs with a minimum detectable concentration that corresponds to 1 pM. This probe was successfully applied to detect Hg(2+) in drinking water and seawater, Ag(+) in drinking water, and AgNPs in drinking water.

RNA aptazyme-tethered large gold nanoparticles for on-the-spot sensing of the aptazyme ligand

A single-step sensing system was developed to visually detect ligands of a cleavase-like RNA aptazyme at room temperature using aptazyme-tethered gold nanoparticles, the electrosteric stability of which was adjusted by increasing their diameter. In this system, the ligand induces self-cleavage of the aptazyme on gold nanoparticles to decrease the electrosteric stability of the gold nanoparticles, which causes them to visibly aggregate. In comparison to a previous multi-step system using aptazymes and gold nanoparticles separately, the present system requires only single handling and no special equipment, making it more suitable for on-the-spot sensing.

Highly sensitive, colorimetric detection of mercury(II) in aqueous media by quaternary ammonium group-capped gold nanoparticles at room temperature

We provide a highly sensitive and selective assay to detect Hg(2+) in aqueous solutions using gold nanoparticles modified with quaternary ammonium group-terminated thiols at room temperature. The mechanism is the abstraction of thiols by Hg(2+) that led to the aggregation of nanoparticles. With the assistance of solar light irradiation, the detection limit can be as low as 30 nM, which satisfies the guideline concentration of Hg(2+) in drinking water set by the WHO. In addition, the dynamic range of detection is wide (3 × 10(-8)-1 × 10(-2) M). This range, to our best knowledge, is the widest one that has been reported so far in gold nanoparticle (AuNP)-based assays for Hg(2+).

Highly Selective Anionic Counterion-based Fluorescent Sensor for Hg(2+) by Grafted Conjugated Polyelectrolytes

Grafted conjugated polyelectrolytes were synthesized for the first time and characterized. The polymers demonstrated properties of a convenient and efficient protocol for creating Hg(2+) sensors. The unique character of the new material comes from an anionic counterion nature with no external cofactors, and imparts high selectivity and fast detection for mercury ion in a fluorescence probe. The concept may be potentially applied to create new sensors for monitoring other ions.

Self-aligned nanolithography by selective polymer dissolution

We report a novel approach to the fabrication of self-aligned nanoscale trench structures in a thin polymer layer covering on conductive materials. By passing AC current through a polymer-coated nanowire in the presence of an appropriate solvent, a self-aligned nanotrench is formed in the polymer overlayer as a result of accelerated dissolution while the rest of the device remains covered. Similar results have been achieved for polymer-coated graphene ribbons. Such polymer-protected devices in which only the active component is exposed should find important applications as electrical sensors in aqueous solutions, particularly in cases where parasitic ionic currents often obscure sensing signals.

Chemical redox-regulated mesoporous silica-coated gold nanorods for colorimetric probing of Hg2+ and S2-

The past a few years have witnessed the wide use of metallic nanoparticles as ideal reporters for colorimetric detection, which generally involves an analyte-triggered alteration of aggregation degree of applied nanoparticles, and thus the change of colloidal color. However, these aggregation-based colorimetric probe are associated with a number of drawbacks, including poor stability of nanoaggregates, requirement of complicated functionalization and non-linearity of output signals. To address these problems, we herein employ mesoporous silica-coated gold nanorods (MS AuNRs) as novel nanocomposites for non-aggregation-based label-free colorimetric sensing relying on their chemical redox-modulated surface chemistry. In our sensing system, Hg(2+) ions are reduced to Hg(0) depositing on the surface of MS AuNPs and result in a great color change of MS AuNRs, while the subsequent introduction of S(2-) leads to a reverse process owing to the extraction of Hg(0) by S(2-). The experimental results for colorimetric sensing of Hg(2+) and S(2-) imply considerable sensitivity and specificity, suggesting the high potential of our approach for rapid environmental monitoring and bioanalysis in the future.

Sensing of transcription factor through controlled-assembly of metal nanoparticles modified with segmented DNA elements

We have developed a unique metal nanoparticle (mNPs)-based assay to detect sequence-specific interactions between transcription factor and its corresponding DNA-binding elements. This assay exploits the interparticle-distance dependent optical properties of noble mNPs as sensing element and utilizes specific protein-DNA interactions to control the dispersion status of the mNPs. The assay involves two sets of double-stranded (ds)DNA modified-mNPs, each carrying a half site segment of a functional DNA sequence for the protein of interest. Each of these half sites is designed to contain a short complementary sticky end that introduces base-pairing forces to facilitate particle aggregation and to form a transient full dsDNA sequence. The detection of specific protein-DNA binding is founded on the premise that the mixture of these two sets of dsDNA-mNPs experiences a remarkable particle aggregation under certain salt conditions; whereas the aggregation can be retarded in the presence of a specific protein that binds and stabilizes the transient full dsDNA structure and therefore introduces steric protection forces between particles. We have demonstrated the concept using estrogen receptor α and its response elements, with gold and silver NPs as the sensing platform. UV-vis spectroscopy, transmission electron spectroscopy, and dynamic light scattering measurements were conducted to provide full characterization of the particle aggregation/dispersion mechanism. Differing from most of the mNP-based colorimetric sensors that are designed based on the analyte-induced aggregation mechanism, current protein binding-stabilization sensing strategy reduces the false signals caused by unrelated particle destabilizing effects. It is expected that this assay principle can be directed toward other transcription factors by simply changing the recognition sequence to form different segmented dsDNA-mNP constructs.

Selective fluorescence sensing of deoxycytidine 5'-monophosphate (dCMP) employing a bis(diphenylphosphate)diimine ligand

A new bis(diphenylphosphate)diimine ligand (BP1) was prepared and evaluated for its ability for selective detection of deoxycytidine 5'-monophosphate (dCMP). BP1 exhibited off-type fluorescence in the presence of dCMP. The fluorescence of BP1 was significantly quenched upon the addition of 2.5 × 10(-4) M dCMP and the detection limit was 1.25 × 10(-5) M in MeCN-H(2)O (1:1, v/v). The binding ratio between BP1 and dCMP was determined to be 1:1 with the binding constant of 3.98 ± 0.60 × 10(-3) M(-1).

Selective detection of Hg2+ in the microenvironment of double-stranded DNA with an intercalator crown-ether conjugate

9-[2-(1,4-Dioxa-7,13-dithia-10-azacyclopentadecyl)phenyl]amino-benzo[b]quinolizinium enables the unambiguous fluorimetric and polarimetric detection of Hg(2+) in the close proximity of double-stranded nucleic acids without interfering background signals from the complexes of this compound with Hg(2+) or DNA alone.

Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity

The catalytic beacon has emerged as a general platform for sensing metal ions and organic molecules. However, few reports have taken advantage of the true potential of catalytic beacons in signal amplification through multiple enzymatic turnovers, as existing designs require either equal concentrations of substrate and DNAzyme or an excess of DNAzyme in order to maintain efficient quenching, eliminating the excess of substrate necessary for multiple turnovers. On the basis of the large difference in the melting temperatures between the intramolecular molecular beacon stem and intermolecular products of identical sequences, we here report a general strategy of catalytic and molecular beacon (CAMB) that combines the advantages of the molecular beacon for highly efficient quenching with the catalytic beacon for amplified sensing through enzymatic turnovers. Such a CAMB design allows detection of metal ions such as Pb(2+) with a high sensitivity (LOD = 600 pM). Furthermore, the aptamer sequence has been introduced into DNAzyme to use the modified CAMB for amplified sensing of adenosine with similar high sensitivity. These results together demonstrate that CAMB provides a general platform for amplified detection of a wide range of targets.

Label-free fluorescent functional DNA sensors using unmodified DNA: a vacant site approach

A general methodology to design label-free fluorescent functional DNA sensors using unmodified DNA via a vacant site approach is described. By extending one end of DNA with a loop, a vacant site that binds an extrinsic fluorophore, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), could be created at a selected position in the DNA duplex region of DNAzymes or aptamers. When the vacant site binds ATMND, ATMND's fluorescence is quenched. This fluorescence can be recovered when one strand of the duplex DNA is released through either metal ion-dependent cleavage by DNAzymes or analyte-dependent structural-switching by aptamers. Through this design, label-free fluorescent sensors for Pb(2+), UO(2)(2+), Hg(2+), and adenosine have been successfully developed. These sensors have high selectivity and sensitivity; detection limits as low as 3 nM, 8 nM, 30 nM, and 6 microM have been achieved for UO(2)(2+), Pb(2+), Hg(2+) and adenosine, respectively. Control experiments using vacant-site-free DNA duplexes and inactive variants of the functional DNAs indicate that the presence of the vacant site and the activity of the functional DNAs are essential for the performance of the proposed sensors. The vacant site approach demonstrated here can be used to design many other label-free fluorescent sensors to detect a wide range of analytes.

A new approach to design ratiometric fluorescent probe for mercury(II) based on the Hg(2+)-promoted deprotection of thioacetals

On the basis of the protection reaction between ethanethiol and aldehyde, we designed and synthesized two new ratiometric fluorescent chemosensors, 3 and 4, by using intramolecular charge transfer (ICT) as a signaling mechanism. Upon the addition of Hg(2+) ion, both probes displayed apparent luminescence color changes, which could be observed by naked eyes under a UV lamp. Unexpectedly, both chemosensors also gave response to the addition of trace silver ions, making this kind of chemosensors as the first example of ratiometric fluorescent probe that showed dual channel fluorescence for both Hg(2+) and Ag(+). The test strips experiments suggested that 3 and 4 could serve as practical fluorescent probes for rapid detection of Hg(2+) ion.

L-cysteine functionalized gold nanoparticles for the colorimetric detection of Hg2+ induced by ultraviolet light

A simple, cost-effective yet rapid and sensitive colorimetric sensor for the detection of Hg(2+) using L-cysteine functionalized gold nanoparticles induced by ultraviolet radiation was developed. The sensitivity and selectivity of detection was also investigated. The L-cysteine modified gold nanoparticles can be induced to aggregate quickly in the presence of Hg(2+), especially with the assistance of ultraviolet radiation. The presence of Hg(2+) can be monitored by the colorimetric response of gold nanoparticles. The detection of Hg(2+) could be realized, after measuring the UV-vis spectra, with a detection limit of 100 nM. The selectivity of this method has been investigated by other divalent metal ions. The effective colorimetric sensor can be used for on-site and real-time Hg(2+) detection.

Multiplex single-nucleotide polymorphism typing by nanoparticle-coupled DNA-templated reactions

A novel chip-based detection approach for single-nucleotide polymorphism (SNP) typing based on nanoparticle-coupled DNA-templated ligation reactions is reported. In contrast to conventional methods or recently developed techniques, this approach does not need costly instrumentation and complex stringency washing processes and offers both rapid multiplex SNP detection capability and ultrahigh sensitivity. The ability of the approach to quickly identify the precise location of the single-base mismatch may provide a time-efficient method for high-throughput multiplex SNP genotyping.

Aptamer-functionalized nano-biosensors

Nanomaterials have become one of the most interesting sensing materials because of their unique size- and shape-dependent optical properties, high surface energy and surface-to-volume ratio, and tunable surface properties. Aptamers are oligonucleotides that can bind their target ligands with high affinity. The use of nanomaterials that are bioconjugated with aptamers for selective and sensitive detection of analytes such as small molecules, metal ions, proteins, and cells has been demonstrated. This review focuses on recent progress in the development of biosensors by integrating functional aptamers with different types of nanomaterials, including quantum dots, magnetic nanoparticles (NPs), metallic NPs, and carbon nanotubes. Colorimetry, fluorescence, electrochemistry, surface plasmon resonance, surface-enhanced Raman scattering, and magnetic resonance imaging are common detection modes for a broad range of analytes with high sensitivity and selectivity when using aptamer bioconjugated nanomaterials (Apt-NMs). We highlight the important roles that the size and concentration of nanomaterials, the secondary structure and density of aptamers, and the multivalent interactions play in determining the specificity and sensitivity of the nanosensors towards analytes. Advantages and disadvantages of the Apt-NMs for bioapplications are focused.

Gold nanoparticle-based colorimetric assay for selective detection of aluminium cation on living cellular surfaces

A colorimetric assay based on pentapeptide (CALNN) functionalized gold nanoparticles exhibits high sensitivity and selectivity for detection of aluminium cation (Al(3+)) both in aqueous solution and on living cellular surfaces under physiological condition.

Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb(2+) and adenosine with high sensitivity, selectivity, and tunable dynamic range

An abasic site called dSpacer has been introduced into duplex regions of the 8-17 DNAzyme and adenosine aptamer for label-free fluorescent detection of Pb(2+) and adenosine, respectively. The dSpacer can bind an extrinsic fluorescent compound, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), and quench its fluorescence. Addition of Pb(2+) enables the DNAzyme to cleave its substrate and release ATMND from DNA duplex, recovering the fluorescence of ATMND. Similarly, the presence of adenosine induces structural switching of the aptamer, resulting in the release of ATMND from the DNA duplex and a subsequent fluorescence enhancement. Under optimized conditions, this label-free method exhibits detection limits of 4 nM for Pb(2+) and 3.4 muM for adenosine, which are even lower than those of the corresponding labeled-DNAzyme and aptamer sensors. These low detection limits have been obtained without compromising any of the selectivity of the sensors. Finally, the dynamic range of the adenosine sensor has been tuned by varying the number of hybridized base-pairs in the aptamer duplex. The method demonstrated here can be applied for label-free detection and quantification of a broad range of analytes using other DNAzymes and aptamers.