An Improved Turn-On Aptasensor for Thrombin Detection Using Split Aptamer Fragments and Graphene Oxide

A label-free logic gate hairpin aptasensor for sensitive detection of ATP based on graphene oxide and PicoGreen dye

Background

In this paper, a simple, enzyme-free, label-free fluorescence, high sensitivity logic gate hairpin aptasensor was developed for adenosine triphosphate (ATP) detection based on graphene oxide (GO) and PicoGreen dye.

Methods

Using single-strand deoxyribonucleic acid (DNA) and adenosine triphosphate (ATP) as input signal and fluorescence signal as output signal, if single-strand DNA (DNA-L), single-strand DNA (DNA-S), and ATP were present at the same time, one segment of DNA-L formed a hairpin ring with ATP, and the other segment of DNA-L formed a completely complementary hairpin stem with DNA-S. The hairpin DNA was detached from the GO surface, and PicoGreen dye was embedded into the hairpin stem, and the fluorescence signal was enhanced. The molecular logic gate was constructed through the establishment of logic histogram, logic circuit, truth table, and logic formula. The biosensor-related performances including sensitivity, selectivity, and linearity were investigated, respectively.

Results

We have successfully constructed a AND logic gate. The detection limit of ATP is 138.0 pmol/L (3σ/slope) with detection range of 50–500 nmol/L (R2 = 0.98951), and its sensitivity is 4.748 × 106–6.875 × 108 a.u. (mol/L)−1.

Conclusions

The logic gate hairpin aptamer sensor has the advantages of high sensitivity, low detection limit, and low cost, and can be successfully applied to the detection of adenosine triphosphate (ATP) in actual human urine samples.

Using Simple-Structured Split Aptamer for Gold Nanoparticle-based Colorimetric Detection of Estradiol

Demand for the detection of estradiol, which is a naturally occurring hormone, has been increasing. Gold nanoparticle-based colorimetric aptasensors have been developed for estradiol detection; however, the long sequence of aptamers due to the formation of the secondary structure likely affects the sensitivity of the aptasensors. Herein, a sensitive colorimetric biosensor is developed for label-free detection of estradiol by using an estradiol-specific split aptamer. The results demonstrate that a superior response is observed when a split aptamer with a high free energy of the secondary structure (ΔG > -3 kcal/mol) is used, in comparison to that observed using a split aptamer with a low free energy of the secondary structure (ΔG < -3 kcal/mol) at 27°C. After selecting the appropriate split aptamer, the standard calibration curve obtained for estradiol has a detection limit of 6.7 nM, with a linear range of 6.7 nM - 66.7 μM in the logarithmic scale. Furthermore, this assay is sensitive, easy-to-operate, inexpensive, and non-time-consuming (provides results within 50 min), thereby showing potential for clinical applications (detection of other small molecular targets).

Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors

In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.

A Label-Free Fluorescent DNA Machine for Sensitive Cyclic Amplification Detection of ATP

In this study, a target recycled amplification, background signal suppression, label-free fluorescent, enzyme-free deoxyribonucleic acid (DNA) machine was developed for the detection of adenosine triphosphate (ATP) in human urine. ATP and DNA fuel strands (FS) were found to trigger the operation of the DNA machine and lead to the cyclic multiplexing of ATP and the release of single stranded (SS) DNA. Double-stranded DNA (dsDNA) was formed on graphene oxide (GO) from the combination of SS DNA and complementary strands (CS′). These double strands then detached from the surface of the GO and in the process interacted with PicoGreen dye resulting in amplifying fluorescence intensity. The results revealed that the detection range of the DNA machine is from 100 to 600 nM (R² = 0.99108) with a limit of detection (LOD) of 127.9 pM. A DNA machine circuit and AND-NOT-AND-OR logic gates were successfully constructed, and the strategy was used to detect ATP in human urine. With the advantage of target recycling amplification and GO suppressing background signal without fluorescent label and enzyme, this developed strategy has great potential for sensitive detection of different proteins and small molecules.

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 Label-Free Fluorescent DNA Calculator Based on Gold Nanoparticles for Sensitive Detection of ATP

Herein we described a deoxyribonucleic acid (DNA) calculator for sensitive detection of the determination of adenosine triphosphate (ATP) using gold nanoparticles (GNP) and PicoGreen fluorescence dye as signal transducer, and ATP and single-stranded DNA (DNA-M′) as activators. The calculator-related performances including linearity, reaction time, logic gate, and selectivity were investigated, respectively. The results revealed that this oligonucleotide sensor was highly sensitive and selective. The detection range was 50–500 nmol/L (R² = 0.99391) and the detection limit was 46.5 nmol/L. The AND DNA calculator was successfully used for the ATP detection in human urine. Compared with other methods, this DNA calculator has the characteristics of being label-free, non-enzymic, simple, and highly sensitive.

A sandwich dipstick assay for ATP detection based on split aptamer fragments

Aptamer-based strip assay is an easy, highly efficient and low-cost detection method, which has been developed and easily applied to onsite detection. A new sensitive sandwich dipstick assay for adenosine triphosphate (ATP) detection was successfully developed based on specific recognition between split aptamer fragments and the target. In this method, the thiolated aptamer was first conjugated to the surface of gold nanoparticles (AuNPs), while the biotin-aptamer was immobilized on the surface of a nitrocellulose filter in the test line. In the presence of ATP, the thiol-aptamer/ATP/biotin-aptamer complexes were generated, which led to an obvious increase in optical signals at the test line. Under the optimal determination conditions, an excellent linear logarithmic response to the ATP concentration was obtained within the range of 0.5 μM to 5 mM. The limit of detection (LOD) of 0.5 μM was reached at a signal-to-noise ratio of 3. The dipstick assay showed a good average recovery of 96-108 % with the RSD of less than 20 % in urine samples. The proposed method exhibited high specificity against other nucleotides such as the uridine triphosphate (UTP), cytidine triphosphate (CTP), and guanosine triphosphate (GTP). The results indicated that the dipstick strip may be considered as an inexpensive screening tool for onsite ATP determination. Graphical Abstract A simple split aptamer fragments based sandwich-type dipstick assay was developed for ATP detection.

Dual-Target Electrochemical Biosensing Based on DNA Structural Switching on Gold Nanoparticle-Decorated MoS2 Nanosheets

A MoS2-based electrochemical aptasensor has been developed for the simultaneous detection of thrombin and adenosine triphosphate (ATP) based on gold nanoparticles-decorated MoS2 (AuNPs-MoS2) nanocomposites. Two different aptamer probes labeled with redox tags were simultaneously immobilized on an AuNPs-MoS2 film modified electrode via Au-S bonds. The aptamers presented structural switches with the addition of target molecules (thrombin and ATP), resulting in methylene blue (MB) far from or ferrocene (Fc) close to the electrode surface. Therefore, a dual signaling detection strategy was developed, which featured both "signal-on" and "signal-off" elements in the detection system because of the target-induced structure switching. This proposed aptasensor could simultaneously determine ATP and thrombin as low as 0.74 nM ATP and 0.0012 nM thrombin with high selectivity, respectively. In addition, thrombin and ATP could act as inputs to activate an AND logic gate.