Sensitive, selective and label-free protein detection using a smart polymeric transducer and aptamer/ligand system

Cationic conjugated polymer-based FRET aptasensor for label-free and ultrasensitive ractopamine detection

A label-free fluorescence resonance energy transfer (FRET) platform based on cationic conjugated polymers and aptamers for ultrasensitive and specific ractopamine detection was constructed. This method exhibited a wide linear range from 0.05 to 500 μM and a low limit of detection of 47 nM, which make it an attractive assay platform for foodborne doping.

A label-free fluorescence resonance energy transfer (FRET) platform based on cationic conjugated polymers and aptamer has established for ultrasensitive and specific ractopamine (RAC) detection.

A lysosome-targeted near-infrared fluorescent probe for imaging of acid phosphatase in living cells

Fluorescent probes for the detection of acid phosphatases (ACP) are important in the investigation of the pathology and diagnosis of diseases. We reported a lysosome-targeted near-infrared (NIR) fluorescent probe SHCy-P based on a novel NIR-emitting thioxanthene-indolium dye for the detection of ACP. The probe showed a long wavelength fluorescence emission at λ_em = 765 nm. Due to the ACP-catalyzed cleavage of the phosphate group in SHCy-P, the probe exhibited high selectivity and sensitivity for the 'turn-on' detection of ACP with a limit of detection as low as 0.48 U L^-1. The probe SHCy-P could also be used to detect and image endogenous ACP in lysosomes. In light of these prominent properties, we envision that SHCy-P will be an efficient optical imaging approach for investigating the ACP activity in disease diagnosis.

A cascade toehold-mediated strand displacement strategy for label-free and sensitive non-enzymatic recycling amplification detection of the HIV-1 gene

In this work, a label-free fluorescence biosensor for simple detection of the HIV-1 gene was proposed by using toehold-mediated strand displacement reactions (TMSDRs) combined with a non-enzymatic target recycling amplification strategy. In this system, two TMSDRs were used. In the presence of the HIV-1 gene, an autocatalytic DNA machine can be activated. This leads to the generation of numerous free G-rich sequences, which can associate with a fluorescent dye N-methylmesoporphyrin IX (NMM) to yield an amplified fluorescence signal for the target detection. This sensing platform showed a high sensitivity towards the HIV-1 gene with a detection limit as low as 1.9 pM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits an excellent selectivity for the HIV-1 gene compared with other interference DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the HIV-1 gene in a real biological sample with satisfactory results, suggesting that this method is promising for simple and early clinical diagnosis of HIV infection. Thanks to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a universal platform for the detection of other genes by substituting the target-recognition element.

Aptamer-Based Sandwich Assay for Measurement of Thymidine Kinase 1 in Serum of Cancerous Patients

Thymidine kinase 1 (TK1) is traditionally a serum biomarker that is elevated in the early stages of malignancies. The diagnostic and prognostic role of TK1 for screening and monitoring human malignancies has recently been investigated. Anti-human TK1 aptamers were selected through 12 iterative rounds of systematic evolution of ligands by exponential enrichment from a DNA library. The aptamer pool of round 12 was amplified, and the polymerase chain reaction product was cloned on the TA vector. Of the 85 colonies obtained, 52 were identified as positive clones. These aptamers were screened for TK1 with surface plasmon resonance, where apta37 and apta69 showed the highest affinity for TK1. The TK1_apta37 and TK1_apta69 aptamers were used in a sandwich assay platform and successfully detected TK1 in the concentration range of 54-3500 pg mL^-1. Clinical samples from 60 cancerous patients were also tested with this assay system and compared using the conventional antibody-based enzyme-linked immunosorbent assay kit. The aptamer sandwich assay demonstrated a dynamic range for TK1 at clinically relevant serum levels, covering subpicogram per milliliter concentrations. The new approach offers a simple and robust method for detecting serum biomarkers that have low and moderate abundance. The results of this study demonstrate the screening capability of the aptamer sandwich assay platform and its potential applicability to the point-of-care testing system.

Ultrasensitive and simple fluorescence biosensor for detection of the mecA gene of Staphylococcus aureus by using an exonuclease III-assisted cascade signal amplification strategy

In this work, a label-free fluorescence biosensor for ultrasensitive and simple detection of the mecA gene of Staphylococcus aureus was proposed by using an exonuclease III (Exo III)-assisted cascade signal amplification strategy. The 3' end-extruding hairpin probe (HP) acted as the target recognition element and the caged G-quadruplex was used as the signal reporter. Without the mecA gene, the HP probe cannot be digested by Exo III, as the G-rich sequences are blocked in the stem of the HP probe. In the presence of the mecA gene, the hybridization of the mecA gene with the 3' end-extruding HP probe triggers the digestion reaction of Exo III, liberating the mecA gene and the mecA gene analogue. Both the released mecA gene and the mecA gene analogue can hybridize with other HP probes and activate another round of the cleavage reaction. Consequently, the released free G-quadruplex is "lit up" by N-methylmesoporphyrin IX (NMM), displaying a dramatically enhanced fluorescence intensity. This sensing platform showed a high sensitivity towards the mecA gene with a detection limit as low as 2.4 fM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits excellent selectivity for the mecA gene in the presence of other interfering DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the mecA gene in a real food sample with satisfactory results. Owing to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a promising platform for the detection of other genes by substituting the target-recognition element.

A reusable aptasensor of thrombin based on DNA machine employing resonance light scattering technique

The design of molecular nanodevices attracted great interest in these years. Herein, a reusable, sensitive and specific aptasensor was constructed based on an extension-contraction movement of DNA interconversion for the application of human thrombin detection. The present biosensor was based on resonance light scattering (RLS) using magnetic nanoparticles (MNPs) as the RLS probe. MNPs coated with streptavidin can combine with biotin labeled thrombin aptamers. The combined nanoparticles composite is monodispersed in aqueous medium. When thrombin was added a sandwich structure can form on the surface of MNPs, which induced MNPs aggregation. RLS signal was therefore enhanced, and there is a linear relationship between RLS increment and thrombin concentration in the range of 60pM-6.0nM with a limit of detection at 3.5pM (3.29S_B/m, according to the recent recommendation of IUPAC). The present aptasensor can be repeatedly used for at least 6 cycling times by heat to transfer G-quadruplex conformation to single strand of DNA sequence and release thrombin. MNPs can be captured by applying the external magnetic field. Furthermore, the proposed biosensor was successfully applied to detect thrombin in human plasma.

Recent advances in thiol and sulfide reactive probes

Because of the biological relevance of thiols and sulfides such as cysteine, homocysteine, glutathione and hydrogen sulfide, their detection has attracted a great deal of research interest. Fluorescent probes are emerging as a new strategy for thiol and hydrogen sulfide analysis due to their high sensitivity, low cost, and ability to detect and image thiols in biological samples. In this short review, we have summarized recent advances in the development of thiol and hydrogen sulfide reactive fluorescent probes. These probes are compared and contrasted with regard to their designing strategies, mechanisms, photophysical properties, and/or reaction kinetics. Biological applications of these probes are also discussed.

Cellulosome-based, Clostridium-derived multi-functional enzyme complexes for advanced biotechnology tool development: advances and applications

The cellulosome is one of nature's most elegant and elaborate nanomachines and a key biological and biotechnological macromolecule that can be used as a multi-functional protein complex tool. Each protein module in the cellulosome system is potentially useful in an advanced biotechnology application. The high-affinity interactions between the cohesin and dockerin domains can be used in protein-based biosensors to improve both sensitivity and selectivity. The scaffolding protein includes a carbohydrate-binding module (CBM) that attaches strongly to cellulose substrates and facilitates the purification of proteins fused with the dockerin module through a one-step CBM purification method. Although the surface layer homology (SLH) domain of CbpA is not present in other strains, replacement of the cell surface anchoring domain allows a foreign protein to be displayed on the surface of other strains. The development of a hydrolysis enzyme complex is a useful strategy for consolidated bioprocessing (CBP), enabling microorganisms with biomass hydrolysis activity. Thus, the development of various configurations of multi-functional protein complexes for use as tools in whole-cell biocatalyst systems has drawn considerable attention as an attractive strategy for bioprocess applications. This review provides a detailed summary of the current achievements in Clostridium-derived multi-functional complex development and the impact of these complexes in various areas of biotechnology.

Label-free and fluorescence turn-on aptasensor for protein detection via target-induced silver nanoclusters formation

A simple turn-on and homogeneous aptasensor, which relies on target induced formation of silver nanoclusters (Ag NCs), was developed for the determination of platelet-derived growth factor B-chain homodimer (PDGF-BB). The aptasensor contains two hairpin DNA probes termed as P1 and P2. P1 consists of the aptamer sequence of PDGF-BB. Meanwhile, P2 contains the Ag NCs nucleation sequence, which is blocked by the hairpin stem region. P1 and P2 can co-exist metastably in the absence of PDGF-BB and maintain hairpin structure. However, in the presence of PDGF-BB, the binding of PDGF-BB with aptamer will result in the hybridization between P1 and P2, and release the Ag NCs nucleation sequence. In this case, Ag NCs can be formed via the reduction of Ag(+) by NaBH(4). By monitoring the increase in fluorescence intensity, we could detect the target protein with high sensitivity. The detection limit of this aptasensor is 0.37 nM, which is comparable with that of other reported aptasensors. Furthermore, this proposed aptasensor shows high selectivity toward its target protein. Thus, the proposed aptasensor based on target induced formation of Ag NCs could be used as a sensitive and selective platform for the detection of target protein.

Continuous and sensitive acid phosphatase assay based on a conjugated polyelectrolyte

We report a novel continuous and sensitive fluorescence turn-on assay for ACPs, which consists of a cationic conjugated polyelectrolyte (PPE4+) and a commonly used phosphatase substrate p-nitrophenyl phosphate (pNPP). The kinetics of the ACP catalyzed hydrolysis of the substrate pNPP was monitored by the fluorescence change of PPE4+ and corresponding kinetic parameters were derived to be consistent with the literature reports. The applications of PPE4+/pNPP-based ACP assay in high-throughput screening of ACP inhibitors and detection of prostatic acid phosphotase (PAP) in vitro were demonstrated.

Applications of aptasensors in clinical diagnostics

Aptamers are artificial oligonucleotides (DNA or RNA) selected in vitro that bind a broad range of targets with high affinity and specificity; a sensitive yet simple method to utilize aptamers as recognition elements for the development of biosensors (aptasensors) is to transduce the signal electrochemically. So far, aptasensors have been applied to clinical diagnostics and several technologies are in development. Aptasensors will extend the limits of current clinical diagnostics. Although the potential diagnostic applications are unlimited, the most current applications are foreseen in the areas of biomarker detection, cancer clinical testing, detection of infectious microorganisms and viruses. This review attempts to list examples of the research progresses of aptamers in biosensor platforms that have been published in recent years; in particular, we display cases of aptasensors that are already incorporated in clinical diagnostics or have potential applications in clinical diagnostics.

DNA nanostructure-decorated surfaces for enhanced aptamer-target binding and electrochemical cocaine sensors

The sensitivity of aptamer-based electrochemical sensors is often limited by restricted target accessibility and surface-induced perturbation of the aptamer structure, which arise from imperfect packing of probes on the heterogeneous and locally crowded surface. In this study, we have developed an ultrasensitive and highly selective electrochemical aptamer-based cocaine sensor (EACS), based on a DNA nanotechnology-based sensing platform. We have found that the electrode surface decorated with an aptamer probe-pendant tetrahedral DNA nanostructure greatly facilitates cocaine-induced fusion of the split anticocaine aptamer. This novel design leads to a sensitive cocaine sensor with a remarkably low detection limit of 33 nM. It is also important that the tetrahedra-decorated surface is protein-resistant, which not only suits the enzyme-based signal amplification scheme employed in this work, but ensures high selectivity of this sensor when deployed in sera or other adulterated samples.

Highly sensitive and selective detection of thiol-containing biomolecules using DNA-templated silver deposition

In this work, we report a new fluorescent method for the label-free assay of thiol-containing amino acids and peptide by use of silver deposited DNA duplex and the intercalating dye. The sensing approach is based on the specific interactions between thiols and DNA-templated silver deposition via robust Ag-S bonds. In the presence of thiols, the intercalating dye gives a dramatic increase in fluorescence as a result of the strong interaction between the intercalator and the released DNA from silver surfaces. The detection limit of this method is lower than or at least comparable to previous fluorescence-based methods, and the turn-on sensing mode offers additional advantage to efficiently reduce background noise. Moreover, the detection and discrimination process can be observed by the naked eye with the aid of an UV transilluminator. This method also exhibits excellent selectivity for these thiol-containing biomolecules over various other amino acids. As far as we know, our method is the first example using the specific interaction between thiols and silver-coated DNA to fabricate a turn-on fluorescent sensor for biological thiols with high sensitivity and selectivity.

A label-free, quadruplex-based functional molecular beacon (LFG4-MB) for fluorescence turn-on detection of DNA and nuclease

We demonstrate a novel concept for the construction of a label-free, quadruplex-based functional molecular beacon (LFG4-MB) by using G-quadruplex motif as a substitute for Watson-Crick base pairing in the MB stem and a specific G-quadruplex binder, N-methyl mesoporphyrin IX (NMM) as a reporter. It shows high sensitivity in assays for UDG activity/inhibition and detection of DNA sequence based on the unique fluorescence increase that occurs as a result of the strong interaction between NMM and the folded quadruplex upon removal of uracil by UDG or displacement of block sequence by target DNA. The LFG4-MB is simple in design, fast in operation and could be easily transposed to other biological relevant target analysis by simply changing the recognition portion. The LFG4-MB does not require any chemical modification for DNA, which offers the advantages of simplicity and cost efficiency and obviates the possible interference with the affinity and specificity of the MB as well as the kinetic behavior of the catalysts caused by the bulky fluorescent groups. More importantly, the LFG4-MB offers great extent of freedom to tune the experimental conditions for the general applicability in bioanalysis.

A facile scanometric strategy for ultrasensitive detection of protein using aptamer-initiated rolling circle amplification

A pragmatic and simple strategy was developed for ultrasensitive detection of protein with good specificity and low matrix effect, which combined aptamer-initiated rolling circle amplification with a Au nanoparticle probe and convenient scanometric readout.

Logic gates and pH sensing devices based on a supramolecular telomere DNA/conjugated polymer system

A conceptually new class of telomere DNA/conjugated polymer system has been constructed to enable sensing of pH changes and create robust logic gates capable of multiplex logic operations. It combines the advantages of quadruplex-duplex conversion and efficient energy transfer from the polymer to the DNA binding molecule. The system is simple in design, fast in operation, and allows the detection of pH changes with high accuracy and sensitivity. In addition, the approach could be adopted for the investigation of other biomolecular conformational changes upon binding to their targets. More importantly, the present logic operations showed advantages over other nucleic acid-based logic gates: (1) The system does not require any CP modification or oligonucleotide labeling, which offers the advantages of simplicity and cost efficiency. (2) The reversibility of the switch makes the logic gates feasible to realize system reset. (3) The system could be implemented to perform multiple logic functions by using distinct input signals.