Heating promoted super sensitive electrochemical detection of p53 gene based on alkaline phosphatase and nicking endonuclease Nt.BstNBI-assisted target recycling amplification strategy at heated gold disk electrode

An ultrasensitive electrochemical biosensor for detecting p53 gene was fabricated based on heated gold disk electrode coupling with endonuclease Nt.BstNBI-assisted target recycle amplification and alkaline phosphatase (ALP)-based electrocatalytic signal amplification. For biosensor assembling, biotinylated ssDNA capture probes were first immobilized on heated Au disk electrode (HAuDE), then combined with streptavidin-alkaline phosphatase (SA-ALP) by biotin-SA interaction. ALP could catalyze the hydrolysis of ascorbic acid 2-phosphate (AAP) to produce ascorbic acid (AA). While AA could induce the redox cycling to generate electrocatalytic oxidation current in the presence of ferrocene methanol (FcM). When capture probes hybridized with p53, Nt.BstNBI would recognize and cleave the duplexes and p53 was released for recycling. Meanwhile, the biotin group dropt from the electrode surface and subsequently SA-ALP could not adhere to the electrode. The signal difference before and after cleavage was proportional to the p53 gene concentration. Furthermore, with electrode temperature elevated, the Nt.BstNBI and ALP activities could be increased, greatly improving the sensitivity and efficiency for p53 detection. A detection limit of 9.5 × 10^-17 M could be obtained (S/N = 3) with an electrode temperature of 40 °C, ca. four magnitudes lower than that at 25 °C.

Identification of single nucleotide polymorphisms by a peptide nucleic acid-based sandwich hybridization assay coupled with toehold-mediated strand displacement reactions

In this work, we developed a simple and accurate peptide nucleic acid (PNA)-based sandwich hybridization assay for single nucleotide polymorphisms (SNPs) in the p53 gene. Our approach combines the enzyme-free toehold-mediated strand displacement reaction (SDR) with real-time enzyme-linked immunosorbent assay (ELISA) to detect SNPs with high sensitivity and specificity. A PNA-DNA heteroduplex with an external toehold is designed and fixed on well surface of a 96-well plate. The strand displacement from PNA-DNA heteroduplexes is initiated by the hybridization of target sequence with the toehold domain and ends with the fully displacing of the incumbent DNA. Finally, the as formed PNA-target DNA duplex with overhang at its 5'-end hybridizes with a biotin-labeled reporter PNA to form a sandwich structure on surface for signal amplification. The proposed PNA-based sandwich biosensor displays high sensitivity and greatly enhanced discriminability to target p53 gene segments against single-base mutant sequences compared to its all-DNA counterpart. Furthermore, the probe design is elegantly simple and the sensing procedure is easy to operate. We believe that this strategy may provide a simple and universal strategy for SNPs detection through easily altering the sequences of probes according to the sequences around target SNPs.

A novel electrochemical biosensor based on MIL-101-NH2 (Cr) combining target-responsive releasing and self-catalysis strategy for p53 detection

A novel electrochemical biosensor was constructed to detect p53 gene based on MIL-101-NH₂ (Cr) by combining target-responsive releasing and self-catalysis strategy. MIL-101-NH₂ (Cr) with suitable pore structure was used to encapsulate methylene blue (MB) as signal probe. The hairpin DNA (HP) containing rich-G sequences was used as gatekeeper to seal up the pores and avoid MB leakage through covalent immobilization. The p53 gene could hybridize with the loop portion of HP for the formation of dsDNA, which had the specific nicking site of the nicking endonuclease (Nt.BstNBI). Then Nt.BstNBI recognized the specific recognition site and cleaved HP to open the pore for releasing of MB. Meanwhile, the cleavage of HP released the target DNA to trigger the target recycling for signal amplification. More importantly, the plentiful rich-G sequences were exposed to form Hemin/G-quadruplex DNAzymes, which could unite MIL-101-NH₂ (Cr) to catalyze redox reaction of MB released by itself for signal amplification. The biosensor for p53 had wide linear range from 1 × 10^-14 to 1 × 10^-7 M and a low detection limit of 1.4 × 10^-15 M. The combination of target-responsive releasing and self-catalysis strategy provided a promising way for constructing ultrasensitive and simple biosensor.

Highly sensitive and quantitative biodetection with lipid-polymer hybrid nanoparticles having organic room-temperature phosphorescence

A versatile organic room-temperature phosphorescence (RTP)-based "turn on" biosensor platform has been devised with high sensitivity by combining oxygen-sensitive lipid-polymer hybrid RTP nanoparticles with a signal-amplifying enzymatic oxygen scavenging reaction in aqueous solutions. When integrated with a sandwich-DNA hybridization assay on 96-well plates, our phosphorimetric sensor demonstrates sequence-specific detection of a cell-free cancer biomarker, a TP53 gene fragment, with a sub-picomolar (0.5 p.m.) detection limit. This assay is compatible with detecting cell-free nucleic acids in human urine samples. Simply by re-programming the detection probe, our unique methodology can be adapted to a broad range of biosensor applications for biomarkers of great clinical importance but difficult to detect due to their low abundance in vivo.

Sensitive biosensor for p53 DNA sequence based on the photothermal effect of gold nanoparticles and the signal amplification of locked nucleic acid functionalized DNA walkers using a thermometer as readout

A convenient photothermal biosensor was constructed for p53 DNA sequence detection based on the high discrimination capability of locked nucleic acid and high efficiency of signal amplification strategy of DNA walkers and difference photothermal effect between aggregated and dispersed gold nanoparticles (AuNPs). The presence of target activated the DNA walkers via the high affinity between target and complementary locked nucleic acid in the probe strand, resulting in the hybridization of the walker strand and substrate strand to form a specific enzyme recognition site. Under the cleavage of the endonuclease, single-stranded DNA (ssDNA) was released to the solution. Then the walker strand bound to a new substrate strand, and the next round of cleavage was triggered. The released ssDNA enhanced the stability of AuNPs against salt-induced aggregation. Given difference photothermal effects of the aggregated AuNPs and dispersed AuNPs under the near-infrared laser, the change of the temperature was detected by a common thermometer easily, which had a linear relationship with the target concentration in the range of 2.0-120.0 pM, the detection limit was 1.4 pM (S/N = 3). The proposed photothermal assay has been applied to detect p53 DNA sequence spiked complex samples with satisfying results.

Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis

Recently, there has been a rapid progress in the development of techniques for isothermal amplification of nucleic acids as an alternative to polymerase chain reaction (PCR). The advantage of these methods is that the nucleic acids amplification can be carried out at constant temperature, unlike PCR, which requires cyclic temperature changes. Moreover, isothermal amplification can be conducted directly in living cells. This review describes the principles of isothermal amplification techniques and demonstrates their high efficiency in designing new highly sensitive detection methods of nucleic acids and enzymes involved in their modifications. The data on successful application of isothermal amplification methods for the analysis of cells and biomolecules with the use of DNA/RNA aptamers are presented.

An Autonomous Nonenzymatic Concatenated DNA Circuit for Amplified Imaging of Intracellular ATP

A robust ATP aptasensor has been successfully constructed for intracellular imaging via the autonomous nonenzymatic cascaded hybridization chain reaction (Ca-HCR) circuit. This compact aptasensor is easily assembled by integrating the sensing module and amplification module, and is furtherly introduced for selective adenosine triphosphate (ATP) assay and for the sensitive tracking of varied ATP expressions in living cells. The ATP-targeting aptamer-encoded sensing module can specifically recognize ATP and release the initiator strand for successively motivating the two-layered HCR (hybridization chain reaction) circuit via the FRET transduction mechanism. The synergistic reaction acceleration of the two HCRs contributes to the high signal gain (amplification efficiency of N²). The whole reaction process was modeled and simulated by MATLAB to deeply explore the underlying molecular reaction mechanism, implying that the cascade HCR is sufficient enough to guarantee the ATP-recognition and amplification processes. The Ca-HCR-amplified aptasensor shows high sensitivity and selectivity for in vitro ATP assay, and can monitor these varied ATP expressions in living cells via intracellular imaging technique. Furthermore, the present aptasensor can be easily extended for monitoring other low-abundance biomarkers, which is especially important for precisely understanding these related biological processes.

Sensitive and selective detection of the p53 gene based on a triple-helix magnetic probe coupled to a fluorescent liposome hybridization assembly via rolling circle amplification

Developing a sensitive and selective sensing platform for the p53 gene and its mutation analysis is essential and may aid in early cancer screening and assessment of prognosis.

Switchable supramolecular catalysis using DNA-templated scaffolds

Switchable β-cyclodextrin (β-CD)-induced hydrolysis of m-tert-butylphenyl acetate is demonstrated in the presence of supramolecular β-CD/adamantane oligonucleotide scaffolds. In one system, a duplex between a β-CD-functionalized nucleic acid and an adamantane-nucleic acid leads to a switchable catalytic system. In a second system, a β-CD/adamantane duplex is cooperatively generated by K(+)-stabilized G-quadruplex units. The binding of hemin to the second system yields a bifunctional DNA scaffold with alternate catalytic functions.

Recent advances in salivary cancer diagnostics enabled by biosensors and bioelectronics

There is a high demand for a non-invasive, rapid, and highly accurate tool for disease diagnostics. Recently, saliva based diagnostics for the detection of specific biomarkers has drawn significant attention since the sample extraction is simple, cost-effective, and precise. Compared to blood, saliva contains a similar variety of DNA, RNA, proteins, metabolites, and microbiota that can be compiled into a multiplex of cancer detection markers. The salivary diagnostic method holds great potential for early-stage cancer diagnostics without any complicated and expensive procedures. Here, we review various cancer biomarkers in saliva and compare the biomarkers efficacy with traditional diagnostics and state-of-the-art bioelectronics. We summarize biomarkers in four major groups: genomics, transcriptomics, proteomics, and metabolomics/microbiota. Representative bioelectronic systems for each group are summarized based on various stages of a cancer. Systematic study of oxidative stress establishes the relationship between macromolecules and cancer biomarkers in saliva. We also introduce the most recent examples of salivary diagnostic electronics based on nanotechnologies that can offer rapid, yet highly accurate detection of biomarkers. A concluding section highlights areas of opportunity in the further development and applications of these technologies.

Amplified binding-induced homogeneous assay through catalytic cycling of analyte for ultrasensitive protein detection

Amplified binding-induced homogeneous assay through catalytic cycling of analytes for ultrasensitive protein detection.

Enzyme-assisted target recycling (EATR) for nucleic acid detection

Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed.

Diagnosing the miR-141 prostate cancer biomarker using nucleic acid-functionalized CdSe/ZnS QDs and telomerase

The microRNA, miR-141, is a promising biomarker for prostate cancer. We implement here a two-step sensing platform for the sensitive detection of miR-141. The first step involves the use of semiconductor CdSe/ZnS quantum dots (QDs) modified by FRET quencher-functionalized nucleic acids, that include the recognition sequence for miR-141 and a telomerase primer sequence for the second step of the analytical platform. Subjecting the probe-modified QDs to miR-141, in the presence of duplex specific nuclease, DSN, leads to the formation of a miR-141/probe duplex and to its DSN-mediated cleavage, while regenerating the miR-141. The DSN-induced cleavage of the quencher units leads to the activation of the fluorescence of the QDs, thus allowing the optical detection of miR-141 with a sensitivity corresponding to 1.0 × 10-12 M. The nucleic acid residues associated with the QDs after cleavage of the probe nucleic acids by DSN act as primers for telomerase. The subsequent telomerase/dNTPs-stimulated elongation of the primer units forms G-quadruplex telomer chains. Incorporation of hemin in the resulting G-quadruplex telomer chains yields horseradish peroxidase-mimicking DNAzyme units, that catalyze the generation of chemiluminescence in the presence of luminol/H2O2. The resulting chemiluminescence intensities provide a readout signal for miR-141, DL = 2.8 × 10-13 M. The first step of the sensing platform is non-selective toward miR-141 and the resulting fluorescence may be considered only as an indicator for the existence of miR-141. The second step in the sensing protocol, involving telomerase, provides a selective chemiluminescence signal for the existence of miR-141. The two-step sensing platform is implemented for the analysis of miR-141 in serum samples from healthy individuals and prostate cancer carriers. Impressive discrimination between healthy individuals and prostate cancer carriers is demonstrated.

Programmable Mg2+-dependent DNAzyme switch by the catalytic hairpin DNA assembly for dual-signal amplification toward homogeneous analysis of protein and DNA

The catalytic hairpin DNA assembly-programmed Mg²⁺-dependent DNAzyme switch was proposed for dual-signal amplified detection of protein and DNA.

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.

Nicking enzyme and graphene oxide-based dual signal amplification for ultrasensitive aptamer-based fluorescence polarization assays

In this work, two different configurations for novel amplified fluorescence polarization (FP) aptasensors based on nicking enzyme signal amplification (NESA) and graphene oxide (GO) enhancement have been developed for ultrasensitive and selective detection of biomolecules in homogeneous solution. One approach involves the aptamer-target binding induced the stable hybridization between an aptamer probe and a fluorophore-labeled DNA probe linked to GO, and forms a nicking site-containing duplex DNA region due to the enhancement of base stacking. The second analytical method involves the target induced the assembly of two aptamer subunits into an aptamer-target complex, and then hybridizes with a fluorophore-labeled DNA probe linked to GO, forming a nicking site-containing duplex DNA region. The formation of the duplex DNA region in both methods triggers the NESA process, resulting in the release of many short DNA fragments carrying the fluorophore from GO, generating a significant decrease of the FP value that provides the readout signal for the amplified sensing process. By using the NESA coupled GO enhancement path, the sensitivity of the developed aptasensors can be significantly improved by four orders of magnitude over traditional aptamer-based homogeneous assays. Moreover, these aptasensors also exhibit high specificity for target molecules, which are capable of detecting target molecule in biological samples. Considering these qualities, the proposed FP aptasensors based NESA and GO enhancement can be expected to provide an ultrasensitive platform for amplified analysis of target molecules.

Amplified and multiplexed detection of DNA using the dendritic rolling circle amplified synthesis of DNAzyme reporter units

The amplified, highly sensitive detection of DNA using the dendritic rolling circle amplification (RCA) is introduced. The analytical platform includes a circular DNA and a structurally tailored hairpin structure. The circular nucleic acid template includes a recognition sequence for the analyte DNA (the Tay-Sachs mutant gene), a complementary sequence to the Mg(2+)-dependent DNAzyme, and a sequence identical to the loop region of the coadded hairpin structure. The functional hairpin in the system consists of the analyte-sequence that is caged in the stem region and a single-stranded loop domain that communicates with the RCA product. The analyte activates the RCA process, leading to DNA chains consisting of the Mg(2+)-dependent DNAzyme and sequences that are complementary to the loop of the functional hairpin structure. Opening of the coadded hairpin releases the caged analyte sequence, resulting in the dendritic RCA-induced synthesis of the Mg(2+)-dependent DNAzyme units. The DNAzyme-catalyzed cleavage of a fluorophore/quencher-modified substrate leads to a fluorescence readout signal. The method enabled the analysis of the target DNA with a detection limit corresponding to 1 aM. By the design of two different circular DNAs that include recognition sites for two different target genes, complementary sequences for two different Mg(2+)-dependent DNAzyme sequences and two different functional hairpin structures, the dendritic RCA-stimulated multiplexed analysis of two different genes is demonstrated. The amplified dendritic RCA detection of DNA is further implemented to yield the hemin/G-quadruplex horseradish peroxidase (HRP)-mimicking DNAzyme as catalytic labels that provide colorimetric or chemiluminescent readout signals.

An ultrasensitive colorimetric aptasensor for ATP based on peptide/Au nanocomposites and hemin–G-quadruplex DNAzyme

A self-assembled peptide nanosphere was firstly applied to construct biosensors. A new signal amplification strategy was proposed for colorimetric aptasensor based on PNS/AuNPs composite. The colorimetric aptasensor displayed an ultra-high sensitivity for ATP detection with a LOD of 1.35 pM.

A cascade signal amplification strategy for sensitive and label-free DNA detection based on Exo III-catalyzed recycling coupled with rolling circle amplification

A sensitive and label-free DNA detection method was developed based on cascade amplification combining exonuclease-III recycling with rolling circle amplification.

Autonomous replication of nucleic acids by polymerization/nicking enzyme/DNAzyme cascades for the amplified detection of DNA and the aptamer-cocaine complex

The progressive development of amplified DNA sensors and aptasensors using replication/nicking enzymes/DNAzyme machineries is described. The sensing platforms are based on the tailoring of a DNA template on which the recognition of the target DNA or the formation of the aptamer-substrate complex trigger on the autonomous isothermal replication/nicking processes and the displacement of a Mg(2+)-dependent DNAzyme that catalyzes the generation of a fluorophore-labeled nucleic acid acting as readout signal for the analyses. Three different DNA sensing configurations are described, where in the ultimate configuration the target sequence is incorporated into a nucleic acid blocker structure associated with the sensing template. The target-triggered isothermal autonomous replication/nicking process on the modified template results in the formation of the Mg(2+)-dependent DNAzyme tethered to a free strand consisting of the target sequence. This activates additional template units for the nucleic acid self-replication process, resulting in the ultrasensitive detection of the target DNA (detection limit 1 aM). Similarly, amplified aptamer-based sensing platforms for cocaine are developed along these concepts. The modification of the cocaine-detection template by the addition of a nucleic acid sequence that enables the autonomous secondary coupled activation of a polymerization/nicking machinery and DNAzyme generation path leads to an improved analysis of cocaine (detection limit 10 nM).

An aptasensing platform for simultaneous detection of multiple analytes based on the amplification of exonuclease-catalyzed target recycling and DNA concatemers

In the present study, an ultrasensitive electrochemical aptasensor for the simultaneous detection of thrombin (TB) and ochratoxin A (OTA) was fabricated by using exonuclease-catalyzed target recycling and DNA concatemers for signal amplification. The previously hybridized double-stranded DNAs (SH-cTBA/TBA and SH-cOBA/OBA) were self-assembled on a gold electrode. In the presence of targets, the formation of aptamer-target complexes would lead to not only the dissociation of aptamers (TBA and OBA) from the double-stranded DNAs but also the transformation of the complementary DNAs (SH-cTBA and SH-cOBA) into hairpin structures. Subsequently, owing to employment of RecJf exonuclease, which is a single-stranded DNA-specific exonuclease to selectively digest the appointed DNAs (TBA and OBA), the targets could be liberated from the aptamer-target complexes for recycling of the analytes. Thereafter, probe DNAs (T1 and T2) were employed to hybridize with SH-cTBA and SH-cOBA respectively to provide primers for the concatemer reaction. After that, when four auxiliary DNA strands S1, anthraquinone-2-carboxylic acid (AQ)-labeled S2, S3, S4, as well as hemin were introduced, extended dsDNA polymers with lots of AQ moieties and hemin-G-quadruplex complexes could form on the electrode surface. Then, based on the signal of the AQ and hemin-G-quadruplex complex, an electrochemical aptasensor for the simultaneous detection of TB and OTA was successfully fabricated.

Dendrimer functionalized reduced graphene oxide as nanocarrier for sensitive pseudobienzyme electrochemical aptasensor

A novel sensitive sandwich-type pseudobienzyme aptasensor was developed by dendrimer functionalized reduced graphene oxide (PAMMA-rGO) as nanocarrier and hemin/G-quadruplex as NADH oxidase and HRP-mimicking DNAzyme. Greatly enhanced sensitivity for the target thrombin was achieved by using a dual signal amplification strategy: first, the PAMMA-rGO not only constructed an effective platform for anchoring larger amounts of electron mediator thionine (TH) and hemin/G-quadruplex bioelectrocatalytic complex with high stability and bioactivity but also accelerated the electron transfer process assisted by the conductive rGO with amplified electrochemical signal output. Second, the hemin/G-quadruplex simultaneously acting as an NADH oxidase and HRP-mimicking DNAzyme for constructing pseudobienzyme amplifying system could in situ biocatalyze formation of H₂O₂ with high local concentrations and low transfer loss that lead to obvious signal enhancements. On the basis of the dual signal amplification strategy of PAMMA-rGO and the pseudobienzyme amplifying, the developed aptasensor could respond to 0.1 pM thrombin with a linear calibration range from 0.0002 to 30.0 nM. Compared with protein enzymes assisted bienzyme aptasensor, this new aptasensor avoided the fussy labeling process and the spatial distribution of each sequentially acting enzyme, which provided ideal candidate for the development of sensitive and simple bioanalytical platform.

Highly sensitive detection of microRNAs based on isothermal exponential amplification-assisted generation of catalytic G-quadruplex DNAzyme

It is well-known that microRNAs (miRNAs) have become an ideal class of biomarker candidates for clinical diagnosis of cancers, thus sensitive and selective detection of microRNAs is of great significance in understanding biological functions of miRNAs, early-phase diagnosis of cancers, as well as discovery of new targets for drugs. In this work, we have developed a sensitive method for microRNAs detection based on isothermal exponential amplification-assisted generation of catalytic G-quadruplex DNAzyme, and demonstrated its practical application in biological sample of cell lysate. The assay involves a combination of polymerase strand extension, single-strand nicking and catalytic reaction of G-quadruplex/hemin complex. It is designed such that, the target miRNA initiates the efficient synthesis of two kinds of short oligonucleotide fragments in the continuous cycle of the polymerization, nicking and displacement reactions, by means of thermostable polymerase and nicking endonuclease. One fragment has the same sequence as the target miRNA, except that the deoxyribonucleotides and thymine replace the ribonucleotides and uridine in the miRNA, to activate new cyclic chain reactions of polymerization, nicking and displacement reactions as the target miRNA. The other is the signal molecule of horseradish peroxidase (HRP)-mimicking G-quadruplex DNAzyme. With such designed signal amplification processes, the proposed assay showed a quantitative analysis of sequence-specific miRNAs in a wide range from 1 fM to 100 nM with a low detection limit of 1 fM. Moreover, this assay demonstrated excellent differentiation ability for the mismatch miRNAs targets and good performance in biological samples.

Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction

Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.

A universal amplified strategy for aptasensors: enhancing sensitivity through allostery-triggered enzymatic recycling amplification

A universal amplified sensing strategy based on endonuclease was developed for designing fluorescence aptasensors. By employing hairpin-structured design for both recognition and reporter probes to decrease background signal, and a nicking endonuclease to perform target-triggered enzymatic recycling amplification, the proposed biosensor showed high sensitivity to target protein. To demonstrate the feasibility of the design, immunoglobulin E (IgE) was studied as a model target. Upon the addition of target protein, the specific formation of IgE/aptamer complex induced the releasing of the 37-mer fragment which partially hybridized with the molecular beacon (MB) probe. In the presence of endonuclease Nt.BbvCI, the MB was cleaved into two parts. Then, the released 37-mer fragment hybridized with another MB, and triggered the second cycle of cleavage, leading to an accumulation of fluorescence signals. Under the optimal conditions, a detection limit of 5 pM was obtained. The proposed sensing system was used for detection of IgE in complex biological samples with satisfactory results.

Sensitive and homogeneous protein detection based on target-triggered aptamer hairpin switch and nicking enzyme assisted fluorescence signal amplification

Specific and sensitive detection of proteins in biotechnological applications and medical diagnostics is one of the most important goals for the scientific community. In this study, a new protein assay is developed on the basis of hairpin probe and nicking enzyme assisted signal amplification strategy. The metastable state hairpin probe with short loop and long stem is designed to contain a protein aptamer for target recognition. A short Black Hole Quencher (BHQ)-quenching fluorescence DNA probe (BQF probe) carrying the recognition sequence and cleavage site for the nicking enzyme is employed for fluorescence detection. Introduction of target protein into the assay leads to the formation change of hairpin probe from hairpin shape to open form, thus faciliating the hybridization between the hairpin probe and BQF probe. The fluorescence signal is amplified through continuous enzyme cleavage. Thrombin is used as model analyte in the current proof-of-concept experiments. This method can detect thrombin specifically with a detection limit as low as 100 pM. Additionally, the proposed protein detection strategy can achieve separation-free measurement, thus eliminating the washing steps. Moreover, it is potentially universal because hairpin probe can be easily designed for other proteins by changing the corresponding aptamer sequence.

Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin

For the first time, hemin/G-quadruplex was employed to simultaneously serve as NADH oxidase and an HRP-mimicking DNAzyme for constructing a simple and sensitive pseudobienzyme-amplifying electrochemical aptasensor for thrombin detection.