A universal and label-free aptasensor for fluorescent detection of ATP and thrombin based on SYBR Green I dye

Label-free ratiometric fluorescence detection of Pb2+via structure-specific fluorescent dyes and dual signal amplification

Lead ions (Pb2+) are a widely distributed and highly toxic heavy metal pollutant, which seriously threatens the environment, economy and human safety. Here, a label-free ratiometric fluorescent biosensor was constructed for Pb2+ detection using DNAzyme-driven target cycling and exonuclease III (Exo III)-mediated DNA cycling as a dual signal amplification strategy. The SYBR Green I (SGI) and N-methyl mesoporphyrin IX (NMM) used in this study are characterized by low cost, storage resistance, and short preparation time compared with conventional signaling probes labeled with fluorescent groups. Unlike the single-emission fluorescence strategy, monitoring the fluorescence intensity ratio of SGI and NMM can effectively reduce external interference to achieve accurate detection of Pb2+. DNAzyme structures on the surface of magnetic beads (MBs) can recognize Pb2+ and activate the target circulatory system to cleave single-stranded DNA (ssDNA). The ssDNA further initiated the Exo III-assisted DNA circulatory system to digest double-stranded DNA (dsDNA) and release guanine-rich G1. Finally, the fluorescence signals of SGI and NMM were weakened and enhanced, respectively. The sensing strategy achieved a wide linear range from 0.5 to 500 nM and a low limit of detection (LOD) of 26.4 pM. Furthermore, its anti-interference ability and potential applicability for Pb2+ detection in actual samples were verified. This work ingeniously combines the dual signal amplification strategy with the ratiometric sensing strategy constructed by structure-specific fluorescent dyes, which provides a promising method for constructing sensitive and accurate fluorescent biosensors.

An ATMND/SGI based three-way junction ratiometric fluorescent probe for rapid and sensitive detection of bleomycin

In this work, we developed a rapid and sensitive label-free ratiometric fluorescent (FL) probe for the detection of bleomycin (BLM). The probe consists of a DNA sequence (D6) and two fluorophore groups, 2-amino-5,6,7-trimethyl-1,8-naphthalene (ATMND) and SYBR Green I (SGI). The D6 sequence could be folded into a three-way junction structure containing a C-C mismatch position in the junction pocket. The unique "Y" structure not only could entrap ATMND in the mismatch pocket with high affinity, leading to FL quenching at 408 nm, but also embed SGI in the grooves of the double-stranded portion, resulting in FL enhancement at 530 nm. In the presence of BLM-Fe(II), the "Y" structure of D6 was destroyed due to the specific cleavage of the BLM recognition site, the 5'-GT-3' site in D6. This caused the release of ATMND and SGI and thus the ratiometric signal change of FL enhancement by ATMND and FL quenching by SGI. Under optimal conditions, the ratiometric probe exhibited a linear correlation between the intensity ratio of F408/F530 and the concentration of BLM in the range of 0.5-1000 nM, with a detection limit of 0.2 nM. In addition, the probe was applied to detect BLM in human serum samples with satisfactory results, indicating its good clinical application potential.

A tag-free fluorescent aptasensor for tobramycin detection using a hybridization of three aptamer strands and SYBR Green I dye

In this study, a sensitive fluorescent method is designed to detect tobramycin (TOB) drug applying a hybrid structure of three aptamer strands and SYBR Green I (SGI) fluorescent dye as the bioreceptor segment and signal indicator, respectively. The preferential binding of the aptamers to TOB resulted in the collapse of the hybridized aptamer skeleton to the single strands. So, the intercalation of SGI molecules reduced that quenched the fluorescence response. The aptasensing assay provided the superior target specificity with a detection limit (LOD) of 0.153 pM and a wide linear dynamic range over 0.5 pM-300 μM. The aptasensor could successfully quantify TOB in human serum samples. The tag-free sensor with the remarkable advantages of simplicity, easy-to-use, cost-effectiveness, and high sensitivity is superior to be applicable for clinical samples.

Surfactant-Assisted Label-Free Fluorescent Aptamer Biosensors and Binding Assays

Using DNA staining dyes such as SYBR Green I (SGI) and thioflavin T (ThT) to perform label-free detection of aptamer binding has been performed for a long time for both binding assays and biosensor development. Since these dyes are cationic, they can also adsorb to the wall of reaction vessels leading to unstable signals and even false interpretations of the results. In this work, the stability of the signal was first evaluated using ThT and the classic adenosine aptamer. In a polystyrene microplate, a drop in fluorescence was observed even when non-binding targets or water were added, whereas a more stable signal was achieved in a quartz cuvette. Equilibrating the system can also improve signal stability. In addition, a few polymers and surfactants were also screened, and 0.01% Triton X-100 was found to have the best protection effect against fluorescence signal decrease due to dye adsorption. Three aptamers for Hg²⁺, adenosine, and cortisol were tested for their sensitivity and signal stability in the absence and presence of Triton X-100. In each case, the sensitivity was similar, whereas the signal stability was better for the surfactant. This study indicates that careful control experiments need to be designed to ensure reliable results and that the reliability can be improved by using Triton X-100 and a long equilibration time.

Exploring the Trans-Cleavage Activity with Rolling Circle Amplification for Fast Detection of miRNA

MicroRNAs (miRNAs) are a class of endogenous short noncoding RNA. They regulate gene expression and function, essential to biological processes. It is necessary to develop an efficient detection method to determine these valuable biomarkers for the diagnosis of cancers. In this paper, we proposed a general and rapid method for sensitive and quantitative detection of miRNA by combining CRISPR-Cas12a and rolling circle amplification (RCA) with the precircularized probe. Eventually, the detection of miRNA-21 could be completed in 70 min with a limit of detection of 8.1 pM with high specificity. The reaction time was reduced by almost 4 h from more than 5 h to 70 min, which makes detection more efficient. This design improves the efficiency of CRISPR-Cas and RCA-based sensing strategy and shows great potential in lab-based detection and point-of-care test.

Nile blue as reporter dye in salt aggregation based-colorimetric aptasensors for peptide, small molecule and metal ion detection

Herein, we report a novel approach for the design of a colorimetric aptasensor, relying on a Dye Salt Aggregation-based Colorimetric Oligonucleotide assay (DYSACO assay). This method is based on the use of an intercalating agent, Nile Blue (NB), whose aggregation capacities (and thus modification of its absorption spectrum) are drastically amplified by adding salts to the working solution. The presence of an aptamer could protect NB from such aggregation process due to its intercalation into double-stranded DNA and/or interaction with nucleobases. In response to the addition of the specific ligand, the competition between NB and the target for binding to the aptamer occurs, resulting in an increase in the dye salt aggregation and then in the blue-to-blank color change of the solution. The proof-of-principle was demonstrated by employing the anti-l-tyrosinamide aptamer and the assay was successfully applied to the trace enantiomer detection, allowing the detection of an enantiomeric impurity down to approximately 2% in a non-racemic sample. Through a reversed mechanism based on the increased capture of NB by DNA upon analyte binding, the sensing platform was further demonstrated for the Hg(II) detection. Water samples of different origin were spiked with Hg(II) analyte at final range concentrations comprised between (0.5-15 μM). An excellent overall recovery of 122 ± 14%; 105 ± 14%; 99 ± 9%; was respectively obtained from river, tap and mineral water, suggesting that the sensor can be used under real sample conditions. The assay was also shown to work for sensing the ochratoxin A and d-arginine vasopressin compounds, revealing its simplicity and generalizability potentialities.

An off-on fluorescence aptasensor for trace thrombin detection based on FRET between CdS QDs and AuNPs

An off-on fluorescence aptasensor was developed for trace thrombin detection based on fluorescence resonance energy transfer (FRET) between CdS QDs and gold nanoparticles (AuNPs). Using DNA pairwise hybridization of the aptamer to the complementary DNA (cDNA), the CdS QDs (energy donor) were tightly coupled to the AuNPs (energy acceptor), resulting in the occurrence of FRET and there was a dramatic fluorescence quenching of CdS QDs (turn off). When the thrombin was added to the fluorescence aptasensor, the specific binding of the aptamer to the target formed a G-quadruplex that caused the AuNPs receptor to detach and the DNA duplex to be disassembled. The process would inhibit the FRET which contribute to the recovery of fluorescence (turn on) and an "off-on" fluorescence aptasensor for thrombin detection was constructed accordingly. Under optimal conditions, the fluorescence recovery showed good linearity with the concentration of thrombin in the range of 1.35-54.0 nmol L-1, and the detection limit was 0.38 nmol L-1 (S/N = 3, n = 9). Importantly, the fluorescence aptasensor presented excellent specificity for thrombin, and was successfully applied to the quantitative determination of thrombin in real serum with satisfactory recoveries of 98.60-102.2%.

Potential Universal Engineering Component: Tetracycline Response Nanoswitch Based on Triple Helix-Graphene Oxide

The overuse of antibiotics can lead to the emergence of drug resistance, preventing many common diseases from being effectively treated. Therefore, based on the special composite platform of P1/graphene oxide (GO) and DNA triple helix, a programmable DNA nanoswitch for the quantitative detection of tetracycline (TC) was designed. The introduction of GO as a quenching agent can effectively reduce the background fluorescence; stabilizing the trigger strand with a triplex structure minimizes errors. It is worth mentioning that the designed model has been verified and analyzed by both computer simulation and biological experiments. NUPACK predicts the combined mode and yield of each strand, while visual DSD flexibly predicts the changes in components over time during the reaction. The feasibility analysis preliminarily confirmed the realizability of the designed model, and the optimal reaction conditions were obtained through optimization, which laid the foundation for the subsequent quantitative detection of TC, while the selective experiments in different systems fully demonstrated that the model had excellent specificity.

CRISPR-Cas12a-mediated luminescence resonance energy transfer aptasensing platform for deoxynivalenol using gold nanoparticle-decorated Ti3C2Tx MXene as the enhanced quencher

Deoxynivalenol (DON) is a typical mycotoxin in cereals and poses tremendous threats to the ecological environment and public health. Therefore, exploiting sensitive and robust analytical methods for DON is particularly important. Here, we fabricated a CRISPR-Cas12a-mediated luminescence resonance energy transfer (LRET) aptasensor to detect DON by using single-stranded DNA modified upconversion nanoparticles (ssDNA-UCNPs) as anti-interference luminescence labels and gold nanoparticle-decorated Ti₃C₂T_x MXene nanosheets (MXene-Au) as enhanced quenchers. The DON aptamer can activate the trans-cleavage activity of Cas12a to indiscriminately cut nearby ssDNA-UCNPs into small fragments, which prevents ssDNA-UCNPs from adsorbing onto MXene-Au, and the upconversion luminescence (UCL) remains. Upon the binding of the aptamer with DON, the trans-cleavage activity of Cas12a was suppressed, and the ssDNA-UCNPs were not cleaved and easily adsorbed onto MXene-Au, which caused UCL quenching. Under optimized conditions, the limit of detection was determined to be 0.64 ng/mL with a linear range of 1 - 500 ng/mL. In addition, the sensor was successfully applied to detect DON in corn flour and Tai Lake water with recoveries of 96.2 - 105% and 95.2 - 104%, respectively. This platform achieves a sensitive and specific analysis of DON and greatly broadens the detection range of CRISPR-Cas sensors for non-nucleic acids hazards in the environment and food.

Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation

Nucleic acid aptamers are bio-molecular recognition agents that bind to their targets with high specificity and affinity, and hold promise in a range of biosensor and therapeutic applications. In the case of small molecule targets, their small size and limited number of functional groups constitute challenges for their detection by aptamer-based biosensors because bio-recognition events may both be weak and produce poorly transduced signals. The binding affinity is principally used to characterize aptamer-ligand interactions; however a structural understanding of bio-recognition is arguably more valuable in order to design a strong response in biosensor applications. Using a combination of nuclear magnetic resonance, circular dichroism, and isothermal titration calorimetry, we propose a binding model for a new methamphetamine aptamer and determine the main interactions driving complex formation. These measurements reveal only modest structural changes to the aptamer upon binding and are consistent with a conformational selection binding model. The aptamer-methamphetamine complex formation was observed to be entropically driven, apparently involving hydrophobic and electrostatic interactions. Taken together, our results exemplify a means of elucidating small molecule-aptamer binding interactions, which may be decisive in the development of aptasensors and therapeutics, and may contribute to a deeper understanding of interactions driving aptamer selection.

A turn-on fluorescence sensor for rapid sensing of ATP based on luminescence resonance energy transfer between upconversion nanoparticles and Cy3 in vivo or vitro

Adenosine triphosphate (ATP) is an energy molecule of significant importance, and, the monitoring of ATP in living cells is considerable for the clinical diagnosis of many related diseases, including cancer. Upconversion nanoparticles (UCNPs) have recently been attracting widespread interest in biomedical applications due to their chemical and thermal stability, high sensitivity, good biocompatibility, and excellent tissue penetration. Herein, a Cy3-aptamer-cDNA- UCNPs nanosensor was synthesized, based on the luminescence resonance energy transfer (LRET) between UCNPs and Cy3 for monitoring ATP in living cells. It showed a selective sensing ability for ATP levels by changes of fluorescence intensity of UNCPs at 536 nm. The investigated biosensor showed a precise, efficient detection with sufficient selectivity which was achieved through the optimization of conditions. In the range of 1-1000 μM, the ATP-induced changes of the fluorescence intensity were linearly proportional to the ATP concentrations. Furthermore, the cytotoxicity assay revealed that the UCNPs sensor exhibited favorable biocompatibility, implicating the use of UCNPs in vivo imaging. This study highlights the potential of using a combination of UCNPs and ATP-binding aptamer to design an ATP-activatable probe for fluorescence-mediated imaging in living cells. These results implied that the nanosensor can be applicable for the monitoring of intracellular ATP by fluorescence imaging and the quantitative analysis of biological liquids.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.

Development of non-equilibrium rapid replacement aptamer assay for ultra-fast detection of phthalic acid esters

In this paper, we developed a non-equilibrium rapid replacement aptamer (NERRA) assay that performed ultra-fast (in 30 s) quantitative detection of phthalic acid esters (PAEs) without waiting for the reaction to reach equilibrium. NERRA assay employed fluorescence PoPo3 dye intercalated in an ssDNA aptamer to selectively detect and quantify the PAEs in water. As the intercalated dye was replaced by the PAEs and quenched in the water, the rate of fluorescence change became proportional to PAEs concentration. The sensitivity of NERRA assay was first evaluated with a commercial spectrofluorometer. The selectivity for PAE mixture, individual PAEs, and non-phthalate compounds were also investigated. NERRA assay was also able to quantitatively detect the PAEs in a common plastic product (picnic mat), and the results were compared with those of gas chromatography mass spectrometry. Finally, a custom analyzer (8.5 cm × 8.5 cm × 16.5 cm) was built to demonstrate the portability of the NERRA assay. Using a commercial spectrofluorometer, NERRA assay was able to quantitatively detect a PAE mixture in 30 min with an LOQ of 0.1 μg/L. Using the portable custom analyzer, the detection time was shortened to 30 s with a tradeoff in the LOQ (1 μg/L). In both cases, the LOQs remain within the environmentally relevant PAE concentrations of 0.1-1472 μg/L.

Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers

Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na⁺ -binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na⁺ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.

Engineering base-excised aptamers for highly specific recognition of adenosine

The DNA aptamer for adenosine and ATP has been used as a model system for developing analytical biosensors. For practical reasons, it is important to distinguish adenosine from ATP, although this has yet to be achieved despite extensive efforts made on selection of new aptamers. We herein report a strategy of excising an adenine nucleotide from the backbone of a one-site adenosine aptamer, and the adenine-excised aptamer allowed highly specific binding of adenosine. Cognate analytes including AMP, ATP, guanosine, cytidine, uridine, and theophylline all failed to bind to the engineered aptamer according to the SYBR Green I (SGI) fluorescence spectroscopy and isothermal titration calorimetry (ITC) results. Our A-excised aptamer has two binding sites: the original aptamer binding site in the loop and the newly created one due to base excision from the DNA backbone. ITC demonstrated that the A-excised aptamer strand can bind to two adenosine molecules, with a K_d of 14.8 ± 2.1 μM at 10 °C and entropy-driven binding. Since the wild-type aptamer cannot discriminate adenosine from AMP and ATP, we attributed this improved specificity to the excised site. Further study showed that these two sites worked cooperatively. Finally, the A-excised aptamer was tested in diluted fetal bovine serum and showed a limit of detection of 46.7 μM adenosine. This work provides a facile, cost-effective, and non-SELEX method to engineer existing aptamers for new features and better applications.

The DNA aptamer for adenosine and ATP has been used as a model system for developing analytical biosensors.

SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding

BACKGROUND

Aptamers, single-stranded DNAs or RNAs, can be selected from a library containing random sequences using a method called Systematic Evolution of Ligands by EXponential Enrichment (SELEX). In SELEX, monitoring the enriching statuses of aptamer candidates during the process is a key step until today. Conformational change of an aptamer caused by target-binding in gel can be used to indicate its statuses of binding.

RESULTS

In this study, an easy-to-implement gel-based diffusion method (GBDM) was developed to monitor the interaction between enriched aptamer candidates and their targets. In order to prove the concept, characterization of aptamers targeting their targets including protein (thrombin) and non-protein molecules (acetamiprid, ATP, atrazine, profenofos and roxithromycin), respectively, were performed using mini gels. Our method has advantages over the common methods including easy performed with labor- and time- saving in experimental operation. The concept has been proven by monitoring enrichment of dynamic aptamer candidate libraries targeting a small molecule 2,2-bis(4-chlorophenyl) acetic acid (DDA) during SELEX process. A mini gel cassette was designed and fabricated by our laboratory to make mini agarose gels for diffusion with different directions.

CONCLUSIONS

These results indicate that GBDM, in particular, chasing diffusion is suitable for monitoring the interaction between enriched aptamer candidates and their targets. These pioneering efforts are helpful for novel aptamer selection by breaking through the technical bottleneck of aptamer development and helpful for development of novel aptasensors.

Label-free probes using DNA-templated silver nanoclusters as versatile reporters

DNA-templated silver nanoclusters (DNA-AgNCs) have demonstrated pervasive applications in analytical chemistry recently. As a way of signal output in DNA-based detection methods, DNA-AgNCs have prominent advantages: first, the recognition and synthesizing sequences are naturally integrated in one DNA probe without any chemical modification or connection; second, the emissive wavelength of DNA-AgNCs can be adjusted in a wide range by employing different sequences; third, DNA-AgNCs can be utilized for producing not only fluorescence, also electrochemiluminescence and electrochemical signals. Besides, they also show potential applications for cell imaging, and are considered to be one of the most ideal nanomaterials for in-vivo imaging due to their ultra-small particle size. In this review, a brief and comprehensive introduction of DNA-AgNCs is firstly given, then label-free probes using DNA-AgNCs are classified and summarized, lastly concluding perspectives are provided on the defects and application potentials.

Green fluorescent carbon quantum dots functionalized with polyethyleneimine, and their application to aptamer-based determination of thrombin and ATP

Brightly fluorescent carbon quantum dots coated with polyethylenimine (PEI-CDs) were prepared using malic acid and PEI as the precursors. The PEI-CDs have a high quantum yield (41%) and green emission (peaking at 502 nm under 430 nm excitation), both of which are not affected by high ionic strength. The PEI-CDs have a positive charge at physiological pH values and can electrostatically bind aptamers with their negative charge. This is shown for aptamers binding thrombin or ATP. Binding of aptamers results in quenching of fluorescence. If thrombin or ATP are introduced, the respective aptamer will bind them, and the complex is then released from the PEI-CDs. Fluorescence increases in proportion to the analyte concentration. Under optimized conditions, thrombin and ATP can be sensitively and selectively detected by fluorometry with lower detection limits of 1.2 and 13 nM, respectively. The assay was successfully applied to the determination of thrombin and of ATP in spiked serum samples. Graphical abstract Green fluorescent carbon quantum dots were functionalized with polyethyleneimine. They were applied to aptamer-based determination of thrombin and ATP. The PEI-functionalized carbon quantum dots (PEI-CDs) have bright green fluorescence are were synthesized by one-step hydrothermal treatment of malic acid and PEI. Employing the PEI-CDs, a fluorometric aptamer-based assay was developed for the determination of thrombin and ATP.

An Enzyme- and Label-Free Fluorescence Aptasensor for Detection of Thrombin Based on Graphene Oxide and G-Quadruplex

An enzyme- and label-free aptamer-based assay is described for the determination of thrombin. A DNA strand (S) consisting of two parts was designed, where the first (Sa) is the thrombin-binding aptamer and the second (Se) is a G-quadruplex. In the absence of thrombin, Sa is readily adsorbed by graphene oxide (GO), which has a preference for ss-DNA rather than for ds-DNA. Upon the addition of the N-methyl-mesoporphyrin IX (NMM), its fluorescence (with excitation/emission at 399/610 nm) is quenched by GO. In contrast, in the presence of thrombin, the aptamer will bind thrombin, and thus, be separated from GO. As a result, fluorescence will be enhanced. The increase is linear in the 0.37 µM to 50 µM thrombin concentration range, and the detection limit is 0.37 nM. The method is highly selective over other proteins, cost-effective, and simple. In our perception, it represents a universal detection scheme that may be applied to other targets according to the proper choice of the aptamer sequence and formation of a suitable aptamer-target pair.

Label-Free Fluorescent Aptasensor for Small Targets via Displacement of Groove Bound Curcumin Molecules

Signal transduction based on fluorescence is one of the most common optical aptasensors for small molecules. Sensors with a number of unique features including high sensitivity, low cost, and simple operation can be constructed easily. However, the label-free fluorescent approach is limited to synthetic dyes that bind strongly to the aptamer sequence and result in a diminished sensor operation with high detection limits. In this study, we report the use of curcumin as a fluorescent probe to signal aptamer/small target binding events. A substantial enhancement in curcumin's fluorescent emission was observed when bound into the grooves of vitamin D₃ (VTD3) binding aptamer, as an example. However, the introduction of the target molecule causes the aptamer to undergo a conformational change that favors complexing the target molecule over binding the curcumin dye. The sensor was able to detect VTD3 down to 1 fM concentration in buffer solutions and extracted blood samples, operate at a wide dynamic range, and discriminate against potential biological interfering molecules including VTD2. The operation of the curcumin based fluorescent sensor is at least six orders of magnitude more sensitive than a VTD3 sensor constructed with the synthetic dye SYBR Green I. The generality of the reported label-free approach was applied with a previously isolated 75-mer bisphenol-A (BPA) aptamer, confirming that the reported sensing strategy is not confined on a particular aptamer sequence. Our work not only reports a novel sensor format for the detection of small molecules, but also serves fluorescent sensor's most pressing need being novel fluorophores for multiplex targets detection.

Monitoring of dynamic ATP level changes by oligomycin-modulated ATP synthase inhibition in SW480 cancer cells using fluorescent "On-Off" switching DNA aptamer

Adenosine triphosphate (ATP) is the main energy source in cells and an important biomolecule participating in cellular reactions in living organisms. Since the ATP level changes dynamically reflecting the development of a debilitating disease or carcinogenesis, we have focused in this work on monitoring of the oligomycin (OMC)-modulated ATP synthase inhibition using a fluorescent-switching DNA aptamer designed for the detection of ATP (Apt(ATP)), as the model for studies of dynamic ATP level variation. The behavior of the ATP aptamer has been characterized using fluorescence spectroscopy. The Intramolecular fluorescence resonance energy transfer (iFRET) operates in the proposed aptamer from the FAM dye moiety to guanines of the aptamer G-quadruplex when the target ATP is present and binds to the aptamer changing its conformation. The iFRET process enables the detection of ATP down to the limit of detection, LOD = 17 μM, without resorting to any extra chemi-amplification schemes. The selectivity coefficients for relevant interferent triphosphates (UTP, GTP, and CTP) are low for the same concentration as that of ATP. We have demonstrated an efficient transfection of intact cells and OMC-treated SW480 colon cancer cells with Apt(ATP), using microscopic imaging, iFRET measurements, and cell viability testing with MTT method. The applicability of the switching DNA aptamer for the analysis of real samples, obtained by lysis of SW480 cells, was also tested. The proposed Apt(ATP) may be considered as a viable candidate for utilization in measurements of dynamic ATP level modulation in cells in different stages of cancer development and testing of new drugs in pharmacological studies.

A label-free hairpin aptamer probe for colorimetric detection of adenosine triphosphate based on the anti-aggregation of gold nanoparticles

A facile and rapid colorimetric approach was described for selective and sensitive determination of adenosine triphosphate (ATP) based on a hairpin aptamer probe and the anti-aggregation of AuNPs. Poly(diallyldimethylammonium chloride) (PDDA) can induce the aggregation of AuNPs due to the electrostatic interaction causing a red to blue color change. Upon the addition of ATP, aptamer-based hairpin probe is opened and releases flexible ssDNA ends. The released flexible ssDNA ends can interact with PDDA and prevent PDDA-induced AuNPs aggregation. Thus, a visible color change from blue to red and a decrease in the absorption ratio (A₆₁₀/A₅₂₀) are observed. Under the optimal conditions, the hairpin aptamer-based colorimetric assay exhibits high sensibility and selectivity for the detection of ATP with a detection limit of 1.7nM. Moreover, this assay is successfully used in the rapid determination of ATP in spiked human serum samples with good recoveries in the range of 102.88 to 104.07%.

Transcription immunoassay: light-up RNA aptamer-based immunoassay using in vitro transcription

Here, we present an ultra-enhanced immunoassay for sensitive and reliable biomarker detection using layer-by-layer assembly and transcription-assisted light-up aptamer generation to induce signal amplification. This dendrimer structure-based transcription immunoassay is ∼1500 times more sensitive than commercial fluorescence ELISA, achieving a detection limit of 108 aM.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

Zero background and triple-signal amplified fluorescence aptasensor for antibiotics detection in foods

It's important to eliminate matrix interference for accurate detecting antibiotic residues in complex food samples. In this study, we designed a zero-backgrounded fluorescence aptasensor to achieve on-site detection of antibiotic residues, with chloramphenicol (CAP) as representative analyte. Moreover, a three stir-bars assisted target recycling system (TSBTR) was designed to achieve triple signal amplification and increase the sensitivity. The bars included one magnetic stir-bar modified with two kinds of long DNA chains, and two gold stir-bars modified with Y shape-duplex DNA probes respectively. In the presence of CAP, the target could recurrently react with the probes on the bars and replace a large amount of long DNA chains into supernatant. After then, the bars were taken out and SYBR green dye was added to the solution. The dye can specifically intercalate into the duplex structures of DNA chains to emit fluorescence while not emitting a signal in its free state. Under the optimized experimental conditions, a wide linear response range of 5 orders of magnitude from 0.001 ng mL^-1 to 10 ng mL^-1 was achieved with a detection limit of 0.033 pg mL^-1 CAP. The assay was successfully employed to detect CAP in food samples (milk & fish) with consistent results with ELISA's. High selectivity and sensitivity were attributed to the zero background signal and triple signal-amplification strategy. Moreover, the detection time can be shortened to 40 min due to that three signal amplified process can occur simultaneously. The fluorescent aptasensor was also label- and enzyme-free. All these ensure the platform to be rapid, cost-effective, easily-used, and is especially appropriate for detection antibiotics in food safety.

Multiplex detection of quality indicator molecule targets in urine using programmable hairpin probes based on a simple double-T type microchip electrophoresis platform and isothermal polymerase-catalyzed target recycling

Recently, it has been crucial to be able to detect and quantify small molecular targets simultaneously in biological samples. Herein, a simple and conventional double-T type microchip electrophoresis (MCE) based platform for the multiplex detection of quality indicator molecule targets in urine, using ampicillin (AMPI), adenosine triphosphate (ATP) and estradiol (E2) as models, was developed. Several programmable hairpin probes (PHPs) were designed for detecting different targets and triggering isothermal polymerase-catalyzed target recycling (IPCTR) for signal amplification. Based on the target-responsive aptamer structure of PHP (Domain I), target recognition can induce PHP conformational transition and produce extension duplex DNA (dsDNA), assisted by primers & Bst polymerase. Afterwards, the target can be displaced to react with another PHP and initiate the next cycle. After several rounds of reaction, the dsDNA can be produced in large amounts by IPCTR. Three targets can be simultaneously converted to dsDNA fragments with different lengths, which can be separated and detected using MCE. Thus, a simple double-T type MCE based platform was successfully built for the homogeneous detection of multiplex targets in one channel. Under optimal conditions, the assay exhibited high throughput (48 samples per hour at most, not including reaction time) and sensitivity to three targets in urine with a detection limit of 1 nM (ATP), 0.05 nM (AMPI) and 0.1 nM (E2) respectively. The multiplex assay was successfully employed for the above three targets in several urine samples and combined the advantages of the high specificity of programmable hairpin probes, the excellent signal amplification of IPCTR, and the high through-put of MCE which can be employed for screening in biochemical analysis.

Label-free optical biosensor for target detection based on simulation-assisted catalyzed hairpin assembly

The development of efficient and convenient strategy without involving enzyme or complex nanomaterial for the micro molecules detection has profound meaning in the diagnosis of diseases. Herein, taking the advantages of the strong affinity of aptamer and catalyzed hairpin assembly, we develop a new non-label optical amplified strategy for thrombin detection in this work. To support both biological inquiry and technological innovation, thermodynamic models are introduced to predict the minimum energy secondary structure of interacting nucleic acid strands and calculate the partition function and equilibrium concentration for complexes in our system. Then, the thermodynamics properties of interacting DNA strands and the reactions of toehold strand displacement-driven assembly have been simulated, validating the feasibility of the theory and optimizing the follow-up lab tests. Following that, our strategy for thrombin detection is proved to be feasible and effective in biological experiment. Taken together, such a biosensor has a good potential in bioactive molecules detection and disease diagnosis for future biological research.

An engineered one-site aptamer with higher sensitivity for label-free detection of adenosine on graphene oxide

The 27-nucleotide DNA aptamer for adenosine and ATP, originally selected by the Szostak lab in 1995, has been a very popular model system for biosensor development. This unique aptamer has two target binding sites, and we recently showed that it is possible to remove either site while the other one still retains binding. From an analytical perspective, tuning the number of binding sites has important implications in modulating sensitivity of the resulting biosensors. In this work, we report that the engineered one-site aptamer showed excellent signaling properties with a 2.6-fold stronger signal intensity and also a 4.2-fold increased detection limit compared with the wild-type two-site aptamer. The aptamer has a hairpin structure, and the length of the hairpin stem was systematically varied for the one-site aptamers. Isothermal titration calorimetry and a label-free fluorescence signaling method with graphene oxide and SYBR Green I were respectively used to evaluate binding and sensor performance. Although longer stemmed aptamers produced better adenosine binding affinity, the signaling was quite independent of the stem length as long as more than three base pairs were left. This was explained by the higher affinity of binding to GO by the longer aptamers, cancelling out the higher affinity for adenosine binding. This work further confirms the analytical applications of such one-site adenosine aptamers, which are potentially useful for improved ATP imaging and for developing new biosensors.

A Label-Free Fluorescent AND Logic Gate Aptasensor for Sensitive ATP Detection

In this study, a label-free fluorescent, enzyme-free, simple, highly sensitive AND logic gate aptasensor was developed for the detection of adenosine triphosphate (ATP). Double-stranded deoxyribonucleic acid (DNA) with cohesive ends was attached to graphene oxide (GO) to form an aptasensor probe. ATP and single-stranded DNA were used as input signals. Fluorescence intensity of PicoGreen dye was used as an output signal. The biosensor-related performances, including the logic gate construction, reaction time, linearity, sensitivity, and specificity, were investigated and the results showed that an AND logic gate was successfully constructed. The ATP detection range was found to be 20 to 400 nM (R² = 0.9943) with limit of detection (LOD) of 142.6 pM, and the sensitivity range was 1.846 × 10⁶ to 2.988 × 10⁶ M^-1. This method for the detection of ATP has the characteristics of being simple, low cost, and highly sensitive.

A Personal Glucose Meter for Label-Free and Washing-Free Biomolecular Detection

We developed a label-free and washing-free method for biomolecular detection using a personal glucose meter (PGM). ATP was selected as a model target, and cascade enzymatic reactions promoted by hexokinase and pyruvate kinase were adopted to link the amount of ATP to glucose that is detectable by a hand-held PGM. In principle, the presence of target ATP enables hexokinase to catalyze the conversion of glucose to glucose 6-phosphate by providing a phosphate group to glucose, and thus the amount of glucose is decreased in proportion to the amount of ATP. In addition, adenosine 5'-diphosphate (ADP), which is generated after hexokinase-catalyzed enzymatic reaction, is recovered to ATP by a pyruvate kinase enzyme. The regenerated ATP is again supplemented to catalyze multiple rounds of cascade enzymatic reactions, leading to signal amplification. As a result, the change of glucose amount that is inversely proportional to ATP amount is simply measured by a hand-held PGM. By employing this strategy, we successfully determined ATP down to 49 nM with high selectivity even in real samples such as tap water, human serum, and bovine urine. Importantly, the developed system does not require expensive modification and washing steps but is conveniently operated with a commercially available PGM, which would pave the way for the development of a simple and cost-effective sensing platform.

A Non-Label and Enzyme-Free Sensitive Detection Method for Thrombin Based on Simulation-Assisted DNA Assembly

Taking advantage of the high selectivity of aptamers and enzyme-free catalyzed hairpin assembly (CHA) amplification strategy, we herein describe a label-free and enzyme-free sensitive fluorescent and colorimetric strategy for thrombin detection in this paper. In the presence of target, the corresponding aptamer of the partial dsDNA probes will bind to the target and liberate the initiation strand, which is artfully designed as the “on” switch for hairpin assembly. Moreover, the displaced initiation strand partakes in a multi-cycle process and produces numerous G-quadruplexes, which have a remarkable enhancement in fluorescent/colorimetric signal from NMM (N-methyl-mesoporphyrin IX) and TMB (3,3′,5,5′-tetramethylbenzidine), respectively. The proposed amplification strategy for thrombin detection is of high sensitivity, down to 2.4 pM, and also achieves colorimetric signals that are able to be distinguished by naked eye. More importantly, the thermodynamics of interacting DNA strands used in our work, and the process of toehold strand displacement-driven assembly are simulated before biological testing, verifying the feasibility theoretically, and simplifying the subsequent actual experiments. Therefore, our approach and simulation have a certain potential application in biomarker detection and quantitatively monitor for disease diagnosis.

A nonenzymatic DNA nanomachine for biomolecular detection by target recycling of hairpin DNA cascade amplification

Synthetic enzyme-free DNA nanomachine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA nanomachine biosensor for biomolecule (such as nucleic acid, thrombin and adenosine) detection is developed by target-assisted enzyme-free hairpin DNA cascade amplifier. The whole DNA nanomachine system is constructed on gold nanoparticle which decorated with hundreds of locked hairpin substrate strands serving as DNA tracks, and the DNA nanomachine could be activated by target molecule toehold-mediated exchange on gold nanoparticle surface, resulted in the fluorescence recovery of fluorophore. The process is repeated so that each copy of the target can open multiplex fluorophore-labeled hairpin substrate strands, resulted in amplification of the fluorescence signal. Compared with the conventional biosensors of catalytic hairpin assembly (CHA) without substrate in solution, the DNA nanomachine could generate 2-3 orders of magnitude higher fluorescence signal. Furthermore, the DNA nanomachine could be used for nucleic acid, thrombin and adenosine highly sensitive specific detection based on isothermal, and homogeneous hairpin DNA cascade signal amplification in both buffer and a complicated biomatrix, and this kind of DNA nanomachine could be efficiently applied in the field of biomedical analysis.

An ion quencher operated lamp for multiplexed fluorescent bioassays

A novel and adjustable lamp based on competitive interaction among dsDNA-SYBR Green I (SGI), ion quencher, and analyte was designed for bioanalysis. The "filament" and switch of the lamp could be customized by employing different dsDNA and ion quencher. The poly(AT/TA) dsDNA was successfully screened as the most effective filament of the lamp. Two common ions, Hg²⁺ and Fe³⁺, were selected as the model switch, and the corresponding ligand molecules cysteine (Cys) and pyrophosphate ions (PPi) were selected as the targets. When the fluorescence-quenched dsDNA/SGI-ion complex was introduced into a target-containing system, ions could be bound by competitive molecules and separate from the complex, thereby lighting the lamp. However, no light was observed if the biomolecule could not snatch the metal ions from the complex. Under the optimal conditions, sensitive and selective detection of Cys and PPi was achieved by the lamp, with practical applications in fetal bovine serum and human urine. This ion quencher regulated lamp for fluorescent bioassays is simple in design, fast in operation, and is more convenient than other methods. Significantly, as many molecules could form stable complexes with metal ions selectively, this ion quencher operated lamp has potential for the detection of a wide spectrum of analytes. Graphical abstract A novel and adjustable lamp on the basis of competitive interaction among dsDNA-SYBR Green I, ions quencher and analyte was designed for bioanalysis. The filament and switch of lamp could be customized by employing different dsDNA and ions quencher.

Fluorescent and colorimetric dual-mode aptasensor for thrombin detection based on target-induced conjunction of split aptamer fragments

Since the lack of detection diversity of the single-signal readout strategy, it is urgent to develop fast and multisignal assay strategies. A highly selective and sensitive assay method with colorimetric and fluorometric dual signals readouts is presented in this paper. It is based on the principle that the target induced conjunction of split aptamer fragments assembled on the surface of Au nanoparticles (AuNPs). In the presence of targets, the color of solution changed from wine red to blue and can be measured both visual inspection and spectrophotometry because of the aggregation of AuNPs. At the same time, the report probes which are original hybrid with the anchoring aptamer fragments on the AuNPs surface can be released and recovers the fluorescence. By use of this detection strategy, the limit of detection for thrombin (TMB), as a model of analyte, were 0.45 and 0.16nM, respectively. Furthermore, this protocol can discriminate TMB from other analogue with high selectivity and can be used to detect TMB in human serum samples. The results came from the two signals were well consistent with each other, which demonstrated that it has application potential for detection of TMB in complex matrix.

ATP-Activatable Photosensitizer Enables Dual Fluorescence Imaging and Targeted Photodynamic Therapy of Tumor

Targeted delivery of intracellular stimuli-activatable photosensitizers (PSs) into tumor cells to achieve selective imaging and on-demand photodynamic therapy (PDT) of tumors has provided a vital opportunity for precise cancer diagnosis and therapy. In this paper, we report a tumor targeting and adenosine triphosphate (ATP)-activatable nanophotosensitizer Apt-HyNP/BHQ₂ by modifying hybrid micellar nanoparticles with both nucleolin-targeting aptamer AS1411 and quencher BHQ₂-labeled ATP-binding aptamer BHQ₂-ATP-apt. We demonstrated that both of the fluorescence emissions at 555 and 627 nm were quenched by BHQ₂ in Apt-HyNP/BHQ₂, resulting in low PDT capacity. After selective entry into tumor cells through nucleolin-mediated endocytosis, the high concentration of intracellular ATP could bind to BHQ₂-ATP-apt and trigger Apt-HyNP/BHQ₂ dissociation, leading to turning "on" both fluorescence and PDT. The "off-on" fluorescence emissions at both 555 and 627 nm were successfully applied for dual color fluorescence imaging of endogenous ATP levels and real-time monitoring of intracellular activation of Apt-HyNP/BHQ₂ in tumor cells. Moreover, imaging-guided precise PDT of tumors in living mice was also demonstrated, allowing for selective ablation of tumors without obvious side effects. This study highlights the potential of using a combination of tumor-targeting and ATP-binding aptamers to design ATP-activatable PSs for both fluorescence imaging and imaging-guided PDT of tumors in vivo.

A fluorescence aptasensor based on two-dimensional sheet metal-organic frameworks for monitoring adenosine triphosphate

In the present study, a facile fluorescence aptasensor based on two-dimensional sheet metal-organic frameworks of N,N-bis(2-hydroxyethyl)dithiooxamidato copper(II) (H₂dtoaCu) was developed for the sensitive detection of adenosine triphosphate (ATP). The sensing mechanism was based on the noncovalent interaction between FAM-labeled (fluorescein amidite) ATP aptamers and H₂dtoaCu. In the absence of ATP, the FAM-labeled aptamer readily adsorbs onto H₂dtoaCu, mainly via π-π stacking and hydrogen bond interactions between the nucleotide bases and the H₂dtoaCu surface, leading to the reduction of fluorescence intensity of the FAM by photoinduced electron transfer (PET). In the presence of ATP, the FAM-labeled aptamer specifically forms ATP-binding aptamer complexes which exhibit only weak adsorption on the H₂dtoaCu surface. Thus, the fluorescence of the FAM-labeled ATP aptamer remained largely unchanged. The fluorescence aptasensor exhibited a good linear relationship between the fluorescence intensity and the logarithm concentration of ATP over a range of 25-400 nM, with a detection limit of 8.19 nM (3S/N). ATP analogs such as guanosine triphosphate, uridine triphosphate, and cytidine triphosphate have negligible effect on the aptasensor performance due to the high selectivity of the ATP aptamer to its target, showing promising potential in real sample analysis.

Water-Soluble Conjugated Polymer as a Fluorescent Probe for Monitoring Adenosine Triphosphate Level Fluctuation in Cell Membranes during Cell Apoptosis and in Vivo

Adenosine triphosphate (ATP) is used as the energy source in cells and plays crucial roles in various cellular events. The cellular membrane is the protective barrier for the cytoplasm of living cells and involved in many essential biological processes. Many fluorescent probes for ATP have been successfully developed, but few of these probes were appropriate for visualizing ATP level fluctuation in cell membranes during the apoptotic cell death process. Herein, we report the synthesis of a new water-soluble cationic polythiophene derivative that can be utilized as a fluorescent sensor for detecting ATP in cell membranes. Poly((3-((4-methylthiophen-3-yl)oxy)propyl)triphenylphosphonium chloride) (PMTPP) exhibits high sensitivity and good selectivity to ATP, and the detection limit is 27 nM. The polymer shows low toxicity to live cells and excellent photostability in cell membranes. PMTPP was practically utilized for real-time monitoring of ATP levels in the cell membrane through fluorescence microscopy. We have demonstrated that the ATP levels in cell membranes increased during the apoptotic cell death process. The probe was also capable of imaging ATP levels in living mice.

A simple and sensitive aptasensor for colorimetric detection of adenosine triphosphate based on unmodified gold nanoparticles

A simple and sensitive colorimetric aptasensor for rapid and facile detection of adenosine triphosphate (ATP) has been demonstrated here based on aptamer-based hairpin probes and unmodified gold nanoparticles (AuNPs). The hairpin probe is constructed by adding another five nucleotides to the 5'-end of an anti-ATP aptamer which can hybridize to nucleotides at the 3'-end of the aptamer, forming a hairpin-shaped structure. In the absence of ATP, the hairpin probes are rigid, and the AuNPs are susceptible to salt-induced aggregation. Conversely, upon binding with target ATP, the hairpin probes undergo conformational changes, forming aptamer-ATP complexes and exposing flexible ends which coat the surface of AuNPs to inhibit their aggregation in the high salt solution. Subsequently, a blue-to-red color change can be recognized by the naked eye. The aptasensor achieved selective responses toward ATP with a detection limit of 0.1μM, and exhibited high-quality detection performance in biological samples. In addition, this detection method is simple, rapid and cost-effective, holding great potential for further applications in point-of-care research.

Silver Nanoclusters Beacon as Stimuli-Responsive Versatile Platform for Multiplex DNAs Detection and Aptamer-Substrate Complexes Sensing

An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved. Additionally, with the introduction of aptamer for the design of the molecular beacon, the detections of small molecule adenosine triphosphate (ATP) and biomacromolecule thrombin have also been realized. This is the first time that an activatable fluorescent silver nanoclusters (Ag NCs)-based probe and the target recognition have been integrated into a single process, which provides a versatile platform for different analytes in a facile way. The successful application of our proposed ASNCB in real sample analysis and ATP imaging in living cells further displayed its promising potential for fluorescence sensing.

A DNA nanoswitch-controlled reversible nanosensor

We present a conceptually new reversible nanosensor regulated by a DNA nanoswitch. This system is not only responsive to external stimuli (e.g. ATP) but also can be reversibly switched between ‘OFF’ and ‘ON’ states via toehold mediated strand displacement reactions. It functions like a molecular net woven by DNA to capture or release the target molecules. As a proof-of-principle experiment, ATP is here chosen as the model to demonstrate our new strategy, which holds great promise for applications such as switchable DNA nanomachines and nanocarriers for drug delivery.

Target-triggered catalytic hairpin assembly and TdT-catalyzed DNA polymerization for amplified electronic detection of thrombin in human serums

Specific and sensitive detection of protein biomarkers is of great importance in biomedical and bioanalytical applications. In this work, a dual amplified signal enhancement approach based on the integration of catalytic hairpin assembly (CHA) and terminal deoxynucleotidyl transferase (TdT)-mediated in situ DNA polymerization has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. The presence of the target thrombin leads to the unfolding and capture of a significant number of hairpin signal probes with free 3'-OH termini on the sensor electrode. Subsequently, TdT can catalyze the elongation of the signal probes and formation of many G-quadruplex sequence replicates with the presence of dGTP and dATP at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a completely label-free fashion. The sensor shows a linear range of 0.5pM-10.0nM and a detection limit of 0.12pM for thrombin. Moreover, the developed sensor can selectively discriminate the target thrombin against other non-target proteins and can be employed to monitor thrombin in human serum samples.