A thymidine-terminated molecular beacon for selective Hg2+ or sequence-specific DNA assay

Highly sensitive and stable fluorescent aptasensor based on an exonuclease III-assisted amplification strategy for ATP detection

Fluctuations in intracellular adenosine triphosphate (ATP) concentration are closely associated with some cancer diseases. Thus, it is a worthwhile undertaking to predict sickness by monitoring changes in ATP levels. However, the detection limits of current fluorescent aptamer sensors for ATP detection are in the range of nmol L^-1 to μmol L^-1. It has become crucial to employ amplification strategies to increase the sensitivity of fluorescent aptamer sensors. In the current paper, a duplex hybrid aptamer probe was developed based on exonuclease III (Exo III)-catalyzed target recycling amplification for ATP detection. The target ATP forced the duplex probe configuration to change into a molecular beacon that can be hydrolyzed with Exo III to achieve the target ATP cycling to amplify the fluorescence signal. Significantly, many researchers ignore that FAM is a pH-sensitive fluorophore, leading to the fluorescence instability of FAM-modified probes in different pH buffers. The negatively charged ions on the surface of AuNPs were replaced by new ligands bis(p-sulfonatophenyl)phenylphosphine dihydrate dipotassium salt (BSPP) to improve the drawback of FAM instability in alkaline solutions in this work. The aptamer probe was designed to eliminate the interference of other similar small molecules, showing specific selectivity and providing ultra-sensitive detection of ATP with detection limits (3σ) as low as 3.35 nM. Such detection limit exhibited about 4-500-fold better than that of the other amplification strategies for ATP detection. Thus, a relatively general high sensitivity detection system can be established according to the wide target adaptability of aptamers, which can form specific binding with different types of targets.

A novel electrochemical biosensor for ultrasensitive Hg2+ detection via a triple signal amplification strategy

We developed a novel electrochemical biosensor for ultrasensitive Hg2+ detection via a triple signal amplification strategy of a DNA dual cycle, organic-inorganic hybrid nanoflowers (Cu3(PO4)2 HNFs) and gold nanoparticle (AuNP) probe. The DNA dual cycle was triggered by exonuclease III (Exo III) in the presence of Hg2+, and Cu3(PO4)2 HNFs were synthesized as an AuNP probe carrier. The electrochemical biosensor displayed high stability, high sensitivity and excellent specificity, which was improved by up to seven orders of magnitude compared to the World Health Organization (WHO) allowed Hg2+ levels in drinking water. This signal amplification strategy could be easily modified and extended to detect other hazardous heavy metals and nucleic acids.

Label-free fluorescent aptasensor berberine-based strategy for ultrasensitive detection of Hg2+ ion

A label-free fluorescent aptasensing platform was fabricated and a simple and rapid method to detect Hg²⁺ ion in aqueous solution was put forward by means of berberine and Hg²⁺ ion-aptamer are as the fluorescence probe and the recognition element, respectively. Various factors including the concentration of berberine, Hg²⁺ ion and Hg²⁺ ion-aptamer, pH effect and the reaction time were investigated in detail. Under the optimal experimental conditions, in the sensing system, the fluorescence intensity changes displayed a calibration response for Hg²⁺ ion in the range of 0.1 μM to 10.0 μM and the detection limit was of 7.7 nM (S/N = 3). The fabricated label-free fluorescence aptasensor is not only conveniently but also effectively applicable used for analysis of Hg²⁺ ion in blood serum and tap water samples and the recovery range is of 96.0%-105.7%. In brief, this study offers an easy, economical and stable assay system for detecting Hg²⁺ ion in rough condition.

Water-soluble mercury ion sensing based on the thymine-Hg2+-thymine base pair using retroreflective Janus particle as an optical signaling probe

Herein, we report an optical sensing platform for mercury ions (Hg²⁺) in water based on the integration of Hg²⁺-mediated thymine-thymine (T-T) stabilization, a biotinylated stem-loop DNA probe, and a streptavidin-modified retroreflective Janus particle (SA-RJP). Two oligonucleotide probes, including a stem-loop DNA probe and an assistant DNA probe, were utilized. In the absence of Hg²⁺, the assistant DNA probe does not hybridize with the stem-loop probe due to their T-T mismatch, so the surface-immobilized stem-loop DNA probe remains a closed hairpin structure. In the presence of Hg²⁺, the DNA forms a double-stranded structure with the loop region via Hg²⁺-mediated T-T stabilization. This DNA hybridization induces stretching of the stem-loop DNA probe, exposing biotin. To translate these Hg²⁺-mediated structural changes in DNA probe into measurable signal, SA-RJP, an optical signaling label, is applied to recognize the exposed biotin. The number of biospecifically bound SA-RJPs is proportional to the concentration of Hg²⁺, so that the concentration of Hg²⁺ can be quantitatively analyzed by counting the number of RJPs. Using the system, a highly selective and sensitive measurement of Hg²⁺ was accomplished with a limit of detection of 0.027nM. Considering the simplified optical instrumentation required for retroreflection-based RJP counting, RJP-assisted Hg²⁺ measurement can be accomplished in a much easier and inexpensive manner. Moreover, the detection of Hg²⁺ in real drinking water samples including tap and commercial bottled water was successfully carried out.

Manganese(ii) enhanced fluorescent nitrogen-doped graphene quantum dots: a facile and efficient synthesis and their applications for bioimaging and detection of Hg2+ ions

Manganese ion (Mn²⁺) bonded nitrogen-doped graphene quantum dots (Mn(ii)-NGQDs) with water solubility have been successfully synthesized by a simple, one-pot hydrothermal carbonization, using sodium citrate, glycine and manganese chloride as raw materials.

A dual-channel detection of mercuric ions using a label free G-quadruplex-based DNAzyme molecule

We have constructed a ‘turn-off’ and label free bio-sensor using a DNAzyme molecule.

A reversible metal ion fueled DNA three-way junction molecular device for "turn-on and -off" fluorescence detection of mercury ions (II) and biothiols respectively with high selectivity and sensitivity

We constructed a reversible molecular device in the nanoscale based on a DNA three-way junction (3WJ) fueled by Hg(2+) binding and sequestration. It is highly responsive to external stimuli, which brings about optically detectable global structural changes. Such a DNA device can serve as a novel "turn-on and -off" fluorescent sensor for Hg(2+) and biothiol detection with high selectivity and sensitivity.

Dual-channel detection of metallothioneins and mercury based on a mercury-mediated aptamer beacon using thymidine-mercury-thymidine complex as a quencher

A novel dual-channel strategy for the detection of metallothioneins (MTs) and Hg(2+) has been developed based on a mercury-mediated aptamer beacon (MAB) using thymidine-mercury-thymidine complex as a quencher for the first time. In the presence of Hg(2+), the T-rich oligonucleotide with a 6-carboxyfluorescein (TRO-FAM) can form an aptamer beacon via the formation of T-Hg(2+)-T base pairs, which results in a fluorescence quenching of the sensing system owing to the fluorescence resonance energy transfer (FRET) from the fluorophore of FAM to the terminated T-Hg(2+)-T base pair. The addition of MTs into this solution leads to the disruption of the T-Hg(2+)-T complex, resulting in an increase of the fluorescent signal of the system. In the optimizing condition, ΔF was directly proportional to the concentrations ranging from 5.63 nM to 0.275 μM for MTs, and 14.2 nM to 0.30 μM for Hg(2+) with the detection limits of 1.69 nM and 4.28 nM, respectively. The proposed dual-channel method avoids the label steps of a quencher in common molecular beacon strategies, without tedious procedure or the requirement of sophisticated equipment, and is rapid, inexpensive and sensitive.

Isothermal amplified detection of DNA and RNA

This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.

Ethynyl and π-stacked thymine-Hg2+-thymine base pairs enhanced fluorescence quenching via photoinduced electron transfer and simple and sensitive mercury ion sensing

Ethynyl triggered enhanced fluorescence quenching effect was first reported based on photoinduced electron transfer (PET) between fluorophore and ethynyl. Ethynyl and 6-carboxyl-fluorescein (FAM) were labeled at the 5'- and 3'-termini of a poly d(T) sequence containing three thymine units, respectively. In the presence of Hg(2+), Hg(2+) binds to two thymine residues through T-Hg(2+)-T interactions and the formed T-Hg(2+)-T base pairs bring FAM and ethynyl from two matched sequences into close proximity. On the one hand, π-stacked T-Hg(2+)-T mediates and accepts electron transfer of the excited state of FAM and quenches the fluorescence through PET. On the other hand, π-stacked interactions between ethynyl and FAM also provide a de-excitation process for the excited state of FAM via PET and trigger an enhanced fluorescence quenching. On the basis of fluorescence quenching, a simple, rapid, and sensitive Hg(2+) sensor was constructed; under optimum conditions, a good linear relationship was obtained over the concentration range of 5-150 nM for Hg(2+) and a very low detection limit (0.42 nM) was reached. The developed system was further designed as a cysteine (Cys) sensor based on fluorescence recovery resulted from the strong interaction between Cys and Hg(2+); the proposed Cys sensor has a linear range of 10-550 nM and a detection limit of 2.5 nM. The two sensors were used for analysis of real samples and the satisfactory results were achieved.

An elegant biosensor molecular beacon probe: challenges and recent solutions

Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.