Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation

A label-free electrochemical aptasensor for the analysis of the potassium ion

Herein, a simple and novel electrochemical method for the detection of potassium ions (K(+)) was developed. In the presence of potassium ions, the potassium ions aptamer will form a G-quadruplex complex. Thus, further addition of hemin in the presence of potassium ions will lead to the formation of a recombined G-quadruplex. Then the electroactive label, hemin, will give an electrochemical response. The linear range of the method covered a large variation of K(+) concentration from 0.1 nM to 0.1 μ M and the detection limit of 0.1 nM was obtained. Moreover, this assay was able to detect K(+) with high selectivity and had great potential applications.

Functional nucleic acid-based sensors for heavy metal ion assays

Heavy metal contaminants such as lead ions (Pb(2+)), mercury ions (Hg(2+)) and silver ions (Ag(+)) can cause significant harm to humans and generate enduring bioaccumulation in ecological systems. Even though a variety of methods have been developed for Pb(2+), Hg(2+) and Ag(+) assays, most of them are usually laborious and time-consuming with poor sensitivity. Due to their unique advantages of excellent catalytic properties and high affinity for heavy metal ions, functional nucleic acids such as DNAzymes and aptamers show great promise in the development of novel sensors for heavy metal ion assays. In this review, we summarize the development of functional nucleic acid-based sensors for the detection of Pb(2+), Hg(2+) and Ag(+), and especially focus on two categories including the direct assay and the amplification-based assay. We highlight the emerging trends in the development of sensitive and selective sensors for heavy metal ion assays as well.

A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins

DNA aptazymes are allosteric DNAzymes activated by the targets of DNA aptamers. They take the advantages of both aptamers and DNAzymes, which can recognize specific targets with high selectivity and catalyze multiple-turnover reactions for signal amplification, respectively, and have shown their great promise in many analytical applications. So far, however, the available examples of DNA aptazyme sensors are still limited in utilizing only several DNAzymes and DNA aptamers, most likely due to the lack of a general and simple approach for rational design. Herein, we have developed such a general approach for designing fluorescent DNA aptazyme sensors. In this approach, aptamers and DNAzymes are connected at the ends to avoid any change in their original sequences, therefore enabling the general use of different aptamers and DNAzymes in the design. Upon activation of the aptazymes by the targets of interest, the rate of fluorescence enhancement via the cleavage of a dually labeled substrate by the active aptazymes is then monitored for target quantification. Two DNAzymes and two aptamers are used as examples for the design of three fluorescent aptazyme sensors, and they all show high selectivity and sensitivity for the detection of their targets. More DNA aptazyme sensors for a broader range of targets could be developed by this general approach as long as suitable DNAzymes and aptamers are used.

Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing

In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd²⁺ due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA, a single phosphorothioate modification might boost its affinity for thiophilic metals without complicating the selection process or using bases that are not commercially available. In this work, the first such in vitro selection for Cd²⁺ is reported. After using a blocking DNA and negative selections to rationally direct the library outcome, a highly specific DNAzyme with only 12 nucleotides in the catalytic loop is isolated. This DNAzyme has a cleavage rate of 0.12 min⁻¹ with 10 μM Cd²⁺ at pH 6.0. The R_p form of the substrate is cleaved ∼100-fold faster than the S_p form. The DNAzyme is most active with Cd²⁺ and its selectivity against Zn²⁺ is over 100 000-fold. Its application in detecting Cd²⁺ is also demonstrated. The idea of introducing single modifications in the fixed region expands the scope of DNA/metal interactions with minimal perturbation of DNA structure and property.

Switchable catalytic DNA catenanes

Two-ring interlocked DNA catenanes are synthesized and characterized. The supramolecular catenanes show switchable cyclic catalytic properties. In one system, the catenane structure is switched between a hemin/G-quadruplex catalytic structure and a catalytically inactive state. In the second catenane structure the catenane is switched between a catalytically active Mg(2+)-dependent DNAzyme-containing catenane and an inactive catenane state. In the third system, the interlocked catenane structure is switched between two distinct catalytic structures that include the Mg(2+)- and the Zn(2+)-dependent DNAzymes.

A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect

In vitro selection of RNA-cleaving DNAzymes was performed using three heavy lanthanide ions (Ln³⁺): Ho³⁺, Er³⁺ and Tm³⁺. The resulting sequences were aligned together and about half of the library contained a new family of DNAzyme. These DNAzymes have a simple loop structure, and they are active only with the seven heavy Ln³⁺. Among the tested non-lanthanide ions, only Y³⁺ induced cleavage and even Pb²⁺ failed to cleave, suggesting a very high specificity. A representative DNAzyme, Tm7, has a sigmoidal metal binding curve with a Hill coefficient of 3, indicating that three metal ions are involved in the catalytic step. Its pH-rate profile has a slope of 1, suggesting a single deprotonation step is involved in the rate-limiting step. Tm7 has a cleavage rate of 1.6 min⁻¹ at pH 7.8 with 10 μM Er³⁺. Phosphorothioate substitution at the cleavage junction completely inhibits the activity, which cannot be rescued by Cd²⁺ alone, or by a mixture of Er³⁺ and Cd²⁺, suggesting that two interacting metal ions are involved in direct bonding to both non-bridging oxygen atoms. A new model involving three lanthanide ions is proposed based on this study. A biosensor is engineered using Tm7 to detect Dy³⁺ down to 14 nM.

In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides

Developing biosensors for lanthanides is an important but challenging analytical task. To address this problem, in vitro selection of RNA-cleaving DNAzymes was carried out using a library containing a region of 35 random nucleotides in the presence of Lu(3+), since Lu(3+) was reported to be the most efficient lanthanide for RNA cleavage. The resulting DNA sequences can be aligned to a single family with two conserved stretches of nucleotides. One of the representative DNAzymes (named Lu12) was further studied. Lu12 is more active with smaller lanthanides and has the lowest activity in the presence of the largest lanthanide (lutetium). Its cleavage rate is 0.12 min(-1) in the presence of 10 μM Nd(3+) at pH 6.0. This is a new DNAzyme, and a catalytic beacon sensor is designed by attaching a fluorophore/quencher pair, detecting Nd(3+) down to 0.4 nM (72 parts-per-trillion). This DNAzyme is highly selective for lanthanides as well, showing cleavage only with two nonlanthanide ions: Y(3+) and Pb(2+). We previously reported a DNAzyme named Ce13d, which has similar responses to all the trivalent lanthanides. Combining these two allows for a ratiometric assay that identifies a few large lanthanides.

Isothermal nucleic acid amplification strategy by cyclic enzymatic repairing for highly sensitive microRNA detection

Technologies enabling highly sensitive and selective detection of microRNAs (miRNAs) are critical for miRNA discovery and clinical theranostics. Here we develop a novel isothermal nucleic acid amplification technology based on cyclic enzymatic repairing and strand-displacement polymerase extension for highly sensitive miRNA detection. The enzymatic repairing amplification (ERA) reaction is performed via replicating DNA template using lesion bases by DNA polymerase and cleaving the DNA replicate at the lesions by repairing enzymes, uracil-DNA glycosylase, and endonuclease IV, to prime a next-round replication. By utilizing the miRNA target as the primer, the ERA reaction is capable of producing a large number of reporter sequences from the DNA template, which can then be coupled to a cyclic signal output reaction mediated by endonuclease IV. The ERA reaction can be configured as a single-step, close-tube, and real-time format, which enables highly sensitive and selective detection of miRNA with excellent resistance to contaminants. The developed technology is demonstrated to give a detection limit of 0.1 fM and show superb specificity in discriminating single-base mismatch. The results reveal that the ERA reaction may provide a new paradigm for efficient nucleic acid amplification and may hold the potential for miRNA expression profiling and related theranostic applications.

Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide

Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg(2+)-T15 and Ag(+)-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials.

Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes

Cadmium, mercury, and lead are collectively banned by many countries and regions in electronic devices due to their extremely high toxicity. To date, no sensing method can detect them as a group and also individually with sufficient sensitivity and selectivity. An RNA-cleaving DNAzyme (Ce13d) was recently reported to be active with trivalent lanthanides, which are hard Lewis acids. In this work, phosphorothioate (PS) modifications were systematically made on Ce13d. A single PS modification at the substrate cleavage site shifts the activity from being dependent on lanthanides to soft thiophilic metals. By incorporating the PS modification to another DNAzyme, a sensor array was prepared to detect each metal. Individual sensors have excellent sensitivity (limit of detection = 4.8 nM Cd(2+), 2.0 nM Hg(2+), and 0.1 nM Pb(2+)). This study provides a new route to obtain metal-specific DNAzymes by atomic replacement and also offers important mechanistic insights into metal binding and DNAzyme catalysis.

Two Pb2+-specific DNAzymes with opposite trends in split-site-dependent activity

By splitting the catalytic core of DNAzymes into two halves, two Pb(2+)-specific DNAzymes retain partial activity, while they show opposite trends of activity as a function of the split site, revealing important nucleotides for catalysis and metal binding.

Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing

A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.