Aptamer in bioanalytical applications

Fabrication of deferasirox-decorated aptamer-targeted superparamagnetic iron oxide nanoparticles (SPION) as a therapeutic and magnetic resonance imaging agent in cancer therapy

In the current study, the synthesis of a theranostic platform composed of superparamagnetic iron oxide nanoparticles (SPION)-deferasirox conjugates targeted with AS1411 DNA aptamer was reported. In this regard, SPION was amine-functionalized by (3-aminopropyl)trimethoxysilane (ATPMS), and then deferasirox was covalently conjugated onto its surface. Finally, to provide guided drug delivery to cancerous tissue, AS1411 aptamer was conjugated to the complex of SPION-deferasirox. The cellular toxicity assay on CHO, C-26 and AGS cell lines verified higher cellular toxicity of targeted complex in comparison with non-targeted one. The evaluation of in vivo tumor growth inhibitory effect in C26 tumor-bearing mice illustrated that the aptamer-targeted complex significantly enhanced the therapeutic outcome in comparison with both non-targeted complex and free drug. The diagnostic capability of the prepared platform was also evaluated implementing C26-tumor-bearing mice. Obtained data confirmed higher tumor accumulation and higher tumor residence time for targeted complex through MRI imaging due to the existence of SPION as a contrast agent in the core of the prepared complex. The prepared multimodal theranostic system provides a safe and effective platform for fighting against cancer.

Aptamer-mediated rolling circle amplification for label-free and sensitive detection of histone acetyltransferase activity

We develop for the first time an aptamer-mediated rolling circle amplification approach for label-free and sensitive detection of histone-modifying enzyme (HME) activity. This method can achieve femtomolar sensitivity for histone acetyltransferase Tip60 assay, which is the most sensitive HME assay reported so far. It can be further applied for inhibitor screening, enzyme kinetic analysis, and endogenous Tip60 measurement in cancer cells.

Self-replicating catalyzed hairpin assembly for rapid aflatoxin B1 detection

Herein, a rapid signal amplified aflatoxin B1 (AFB1) detection system based on self-replicating catalyzed hairpin assembly (SRCHA) has been constructed. In this SRCHA system, trigger DNA was initially blocked and two split trigger DNA sequences were integrated into two hairpin auxiliary probes, H1 and H2, respectively. In the presence of AFB1, the aptamer sequence was recognized by AFB1 and trigger DNA was released, which can initiate a CHA reaction and lead to the formation of a helix DNA H1-H2 complex. Then this complex can dissociate double-stranded probe DNA (F-Q) and the fluorescence signal was recovered. Meanwhile, the two split trigger DNA sequences came into close-enough proximity and a trigger DNA replica was formed. Then the obtained replicas can trigger an additional CHA reaction, leading to the rapid and significant enhancement of the fluorescence signal, and AFB1 can be detected within 15 min with a detection limit of 0.13 ng mL-1. This AFB1 detection system exhibits potential application in the on-site rapid detection of AFB1.

Effective Isolation for Lung Carcinoma Cells Based on Immunomagnetic Separation in a Microfluidic Channel

In this paper, we developed an isolation system for A549 human lung carcinoma cells as an effective factor for the early diagnosis of lung cancer. A microfluidic immunomagnetic method was used, in which the combination of immunomagnetic separation and a microfluidic system allowed for increased isolation efficiency with uncomplicated manipulation. In the microfluidic immunomagnetic strategy, A549 cells were combined with aptamer-conjugated carboxylated magnetic beads and then collected in a specified region by applying a magnetic field. The results were recorded using a fluorescence microscope, and the captured targets were then quantified. The isolation efficiency of A549 cells is up to 77.8%. This paper developed a simple working procedure, which is less time consuming, high-throughput, and trustworthy for the isolation of A549 cells. This procedure can be a useful reference method for the development of an effective diagnosis and treatment method for lung cancer in the future.

Electrochemical aptasensors for the detection of hepatocellular carcinoma-related biomarkers

Recent progress in electrochemical aptasensors for the detection of HCC-related biomarkers, including cancer cells, proteins, cell-derived exosomes, and nucleic acids, is reviewed.

Chemical conjugation of nucleic acid aptamers and synthetic polymers

This minireview describes the synthesis, characterization and properties of aptamer–polymer conjugates. This new class of polymer bioconjugates combines the advantages of synthetic polymers and folded nucleic acids.

Screening, Post-SELEX Optimization and Application of DNA Aptamers Specific for Tobramycin

Tobramycin (TOB) is an aminoglycoside antibiotic. The residue of TOB in animal-derived foods and environment will be harmful to human health, and therefore the specific detection of TOB residue in food and water is of great importance. Herein, through magnetic beads-based SELEX, overall 37 ssDNA aptamers specific for TOB were screened after ten rounds of selection. The affinity and specificity of these aptamers were evaluated, among which No. 32 aptamer (Ap 32) exhibits excellent performance. Then a post-SELEX optimization of Ap 32 was carried out based on rational design, through which a truncated aptamer with the length of 34 nucleotides (Ap 32-2) was identified as the best aptamer for TOB. Finally, the application of the screened aptamer was explored. A colorimetric assay of TOB was established based on the aptamer-modified gold nanoparticles (AuNPs). In the range from 100 to 1400 nM, the absorbance of AuNPs solution at 520 nm was linearly decreased with the increased concentration of TOB. The detection limit was estimated to be 37.9 nM. The assay was applied to detect TOB residue in honey samples.

A protein triggering exponential amplification reaction enables label- and wash-free one-pot protein assay with high sensitivity

Methods capable of sensitive and facile quantification of low-abundant proteins play critical roles in disease diagnosis and treatment. Herein, on a rationally designed aptamer-based hairpin structure-switching template, we developed a protein triggering exponential amplification reaction (PTEXPAR) method. The platelet-derived growth factor BB (PDGF-BB) is used as model analyte in the current proof-of-concept experiments. This method can detect PDGF-BB specifically with a detection limit as low as 4.9 fM. Additionally, the proposed PTEXPAR strategy allows label- and wash-free one-pot quantification of protein within ~35 min. Moreover, it is potentially universal because hairpin template can be easily designed for other proteins by changing the corresponding aptamer sequence.

An enzyme-free fluorescent biosensor for highly sensitive detection of carcinoembryonic antigen based on aptamer-induced entropy-driven circuit

Carcinoembryonic antigen (CEA) is a disease biomarker, which can reflect the existence of tumors. The accurate detection of CEA in clinical samples is highly valuable for diagnosis of tumors. Herein, we developed an enzyme-free fluorescent biosensor for highly sensitive detection of CEA based on an aptamer-induced entropy-driven circuit. The aptamer hairpin specifically bound to CEA to expose the locked domain. Then, the exposed domain could trigger disassembly of multiple fluorophore strands from the three-strand complexes with the aid of fuel strands, leading to the production of remarkable amplified fluorescent signals. The one-step and homogeneous method exhibited high specificity and a wide linear range from 10 pg mL^-1 to 500 ng mL^-1 with a low limit of detection of 4.2 pg mL^-1. What's more, the whole detection process could be performed within 45 min and did not involve the use of any protein enzymes and antibodies. The developed strategy could also be applied to detect CEA in clinical samples with satisfactory results. Therefore, the strategy is an alternative sensing method for the detection of CEA.

Assembly and in vitro assessment of a powerful combination: aptamer-modified exosomes combined with gold nanorods for effective photothermal therapy

Due to good biocompatibility and plasma membrane similarity, the nanosized exosomes are ideal drug carriers. Near-infrared (NIR) photothermal therapy is an emerging method for cancer treatment in which photothermal agents absorb the energy of external NIR light to generate high temperatures in a targeted region to effectively kill cancer cells. Gold nanorods (AuNRs) have been found to provide a prominent photothermal performance, while aptamers can precisely target surface markers on cells with high affinity and specificity. In this study, exosomes were mildly functionalized by integrating them with aptamers and AuNRs to assemble a powerful combination Apt-Exos-AuNRs (AEARs) with good specificity and an effective photothermal killing action on cancer cells. The structure, hydrodynamic diameters, zeta potential, UV-vis absorption spectra and stability of the AEARs were further characterized. In addition, using a cell model, the cancer cell targeting ability of the AEARs and its cellular uptake were observed. Moreover, its photothermal killing effect on various human cancer cells in vitro was validated by a CCK-8 assay as well as apoptosis analysis, the results of which suggest this exosomes-based nanomaterial can serve as a novel and broad-spectrum platform for precision cancer therapy.

Visual Detection of Clostridium perfringens Alpha Toxin by Combining Nanometer Microspheres with Smart Phones

Clostridium perfringens α toxin (CPA) is an important virulence factor that causes livestock hemorrhagic enteritis and food poisoning by contaminated meat products. In this study, the nano-silica microspheres combined with smartphone image processing technology was developed to realize real-time CPA detection. First, the N-terminal and C-terminal domain of the CPA toxin (CPA_C3 and CPA_N) and their anti-sera were prepared. The silica microspheres coupled with the antibody of CPA_C3 was prepared to capture the toxin that existed in the detection sample and the fluorescent-labeled antibody of CPA_N was incubated. Moreover, the fluorescent pictures of gray value were performed in a cell phone app, corresponding to toxin concentration. The new assay takes 90 min to perform and can detect CPA as little as 32.8 ng/mL. Our results showed a sensitive, stable, and convenient CPA detection system, which provides a novel detection method of native CPA in foods.

Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer

Prostate-specific membrane antigen (PSMA) is a well-characterized tumor marker associated with prostate cancer and neovasculature of most solid tumors. PSMA-specific ligands are thus being developed to deliver imaging or therapeutic agents to cancer cells. Here, we report on a crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit. The analysis of the PSMA/aptamer interface allows for identification of key interactions critical for nanomolar binding affinity and high selectivity of A9g for human PSMA. Combined with in silico modeling, site-directed mutagenesis, inhibition experiments and cell-based assays, the structure also provides an insight into structural changes of the aptamer and PSMA upon complex formation, mechanistic explanation for inhibition of the PSMA enzymatic activity by A9g as well as its ligand-selective competition with small molecules targeting the internal pocket of the enzyme. Additionally, comparison with published protein-RNA aptamer structures pointed toward more general features governing protein-aptamer interactions. Finally, our findings can be exploited for the structure-assisted design of future A9g-based derivatives with improved binding and stability characteristics.

Advances in intelligent DNA nanomachines for targeted cancer therapy

As an emerging field, DNA nanotechnology has been applied to the fabrication of drug delivery systems. Unprecedented spatial addressability and intrinsic sequence encoding enable DNA strands to self-assemble into well-defined 2D and 3D DNA nanostructures with specifically controlled sizes, shapes and surface charges. Multifunctional DNA nanostructures have been created and applied as promising platforms for drug delivery, imaging, and theranostics. Advantages of chemotherapy, gene therapy, and immunotherapy, among others, have been integrated into such functional nanodevices, showing potential in tumor-targeted therapy and diagnosis. In this review, we summarize general methods for the construction of DNA nanodevices and focus on targeting strategies favored by the compatibility of DNA nanotechnology. Additionally, we highlight the outlook and challenges facing the use of DNA nanotechnology in cancer therapy.

Aptamer-Based Colorimetric Probe for trans-Zeatin Detection Using Unmodified Gold Nanoparticle

Trans-Zeatin is the major active phytohormone in immature corn kernels. Herein, a highly sensitive, good selective and simple aptamer-based colorimetric method for the detection of trans-zeatin was constructed. The selected aptamer sequence binds with trans-zeatin and induces a duplex-to-aptamer structure switching. The gold nanoparticles (AuNPs) solution is stable with high-concentration salt, which is protected by red complementary DNA. In the absence of trans-zeatin, the color of AuNPs changed from red to blue because aptamer DNA and complementary DNA form double-stranded DNA. Thus, the ratio of absorbance intensities (A522/A650) of AuNPs is changed with the concentration of trans-zeatin. The color change could be observed by the naked eye. The linear range of this method covers a large variation of trans-zeatin concentration from 0.05 to 0.75 μM. The detection limit is 0.037 μM. Moreover, this method was applied successfully to detect trans-zeatin in real plant samples.

Graphene biosensors for bacterial and viral pathogens

The infection and spread of pathogens (e.g., COVID-19) pose an enormous threat to the safety of human beings and animals all over the world. The rapid and accurate monitoring and determination of pathogens are of great significance to clinical diagnosis, food safety and environmental evaluation. In recent years, with the evolution of nanotechnology, nano-sized graphene and graphene derivatives have been frequently introduced into the construction of biosensors due to their unique physicochemical properties and biocompatibility. The combination of biomolecules with specific recognition capabilities and graphene materials provides a promising strategy to construct more stable and sensitive biosensors for the detection of pathogens. This review tracks the development of graphene biosensors for the detection of bacterial and viral pathogens, mainly including the preparation of graphene biosensors and their working mechanism. The challenges involved in this field have been discussed, and the perspective for further development has been put forward, aiming to promote the development of pathogens sensing and the contribution to epidemic prevention.

Design of a ratiometric fluorescence sensor based on metal organic frameworks and Ru(bpy)32+-doped silica composites for 17β-Estradiol detection

17β-Estradiol (E2), an important endocrine disrupting compound, could be quantitatively detected by fluorescence resonance energy transfer (FRET) aptasensor, designed in this paper. Metal organic frameworks have large specific surface area and easily modifiable groups, which are helpful for the construction of aptasensor. Specifically, streptavidin was immobilized on the synthesized MIL-53-NH₂ by covalent bonding, and further linked with the biotin modified E2 aptamer (apt) through specific bonding between avidin and biotin to obtain the FRET donor probe (MIL-53-apt). Meanwhile, complementary DNA (cDNA) modified Ru(bpy)₃²⁺-doped silica nanoparticles (RuSiO₂-cDNA) were prepared through covalent bonding. They acted as the FRET acceptor probe, since its absorption spectrum showed large overlap with the emission spectrum of MIL-53-apt. In the presence of E2, aptamer modified donor probes tended to bind with E2, owing to their higher selectivity and affinity. Therefore, the optimal distance between FRET pairs was broken, resulting in the fluorescence emission recovery of donor and the fluorescence emission of acceptor decreased. Under optimal conditions, this proposed aptasensor displayed sensitive detection of E2 ranging from 0.5 to 1000 nM with a detection limit of 0.2 nM. Furthermore, the sensor provides a promising method for rapid and sensitive detection of other small biological molecules.

Aptamer-based surface-enhanced resonance Raman scattering assay on a paper fluidic platform for detection of cardiac troponin I

SIGNIFICANCE

Cardiac troponin I (cTnI) is a primary biomarker for diagnosis of myocardial infarction (MI). In contrast to central laboratory tests for cTnI, point-of-care (POC) testing has the advantage of providing results when the patient is first encountered, which helps high-risk patients to be treated more rapidly and low-risk patients to be released in a timely fashion. A paper fluidic platform is good for POC testing because the paper is abundant, low cost, and disposable. However, current cTnI assays on paper platforms use antibodies as the recognition element, which has limitations due to the high cost of production and antibody stability issues at the POC.

AIM

To develop an aptamer-based assay on a paper strip using surface-enhanced resonance Raman spectroscopy (SERRS) for detection of cTnI in the clinically relevant range at the POC.

APPROACH

Gold nanoparticles (AuNPs) were functionalized with a Raman reporter molecule, malachite green isothiocyanate. The functionalized AuNPs were encapsulated in a silica shell and provided a SERRS signal using a handheld Raman system with a 638-nm excitation wavelength. A primary aptamer and a secondary aptamer of cTnI were used in a sandwich assay format to bind the cTnI on a test line of a paper fluidic platform. By measuring the SERRS signal from the test line, the concentration of cTnI was quantitatively determined.

RESULTS

The aptamer-based SERRS assay on a paper strip had a detection range of 0.016 to 0.1  ng  /  ml for cTnI, had good selectivity for cTnI compared to three other markers, had good stability over 10 days, and had good performance in the more complex serum sample matrix.

CONCLUSIONS

The aptamer-based SERRS assay on a paper strip has the potential to provide a sensitive, selective, stable, repeatable, and cost-effective platform for the detection of cTnI toward eventual use in diagnosis of MI at the POC.

Nanomaterial-based aptamer sensors for analysis of illicit drugs and evaluation of drugs consumption for wastewater-based epidemiology

The abuse of illicit drugs usually associated with dramatic crimes may cause significant problems for the whole society. Wastewater-based epidemiology (WBE) has been demonstrated to be a novel and cost-effective way to evaluate the abuse of illicit drugs at the community level, and has been used as a routine method for monitoring and played a significant role for combating the crimes in some countries, e.g. China. The method can also provide temporal and spatial variation of drugs of abuse. The detection methods mainly remain on the conventional liquid chromatography coupled with mass spectrometry, which is extremely sensitive and selective, however needs advanced facility and well-trained personals, thus limit it in the lab. As an alternative, sensors have emerged to be a powerful analytical tool for a wide spectrum of analytes, in particular aptamer sensors (aptasensors) have attracted increasing attention and could act as an efficient tool in this field due to the excellent characteristics of selectivity, sensitivity, low cost, miniaturization, easy-to-use, and automation. In this review, we will briefly introduce the context, specific assessment process and applications of WBE and the recent progress of illicit drug aptasensors, in particular focusing on optical and electrochemical sensors. We then highlight several recent aptasensors for illicit drugs in new technology integration and discuss the feasibility of these aptasensor for WBE. We will summarize the challenges and propose our insights and opportunity on aptasensor for WBE to evaluate community-wide drug use trends and public health.

Detection Strategies of Zearalenone for Food Safety: A Review

Zearalenone (ZEN) is a toxic compound produced by the metabolism of fungi (genus Fusarium) that threaten the food and agricultural industry belonging to the in foods and feeds. ZEN has toxic effects on human and animal health due to its mutagenicity, teratogenicity, carcinogenicity, nephrotoxicity, immunotoxicity, and genotoxicity. To ensure food safety, rapid, precise, and reliable analytical methods can be developed for the detection of toxins such as ZEN. Different selective molecular diagnostic elements are used in conjunction with different detection strategies to achieve this goal. In this review, the use of electrochemical, colorimetric, fluorometric, refractometric as well as other strategies were discussed for ZEN detection. The success of the sensors in analytical performance depends on the development of receptors with increased affinity to the target. This requirement has been met with different immunoassays, aptamer-assays, and molecular imprinting techniques. The immobilization techniques and analysis strategies developed with the combination of nanomaterials provided high precision, reliability, and convenience in ZEN detection, in which electrochemical strategies perform the best.

Dual-Probe Approach for Mass Spectrometric Quantification of MUC1-Specific Terminal Gal/GalNAc In Situ

Protein glycosylation is a prevalent post-translational modification that mediates a variety of cellular processes. For membrane proteins, glycosylation at their terminal motif is usually more functional. Among the various glycosylation types found in membrane proteins, O-glycosylation is the most common and is closely correlated with a variety of cancer types, including breast cancer. Slightly aberrant expression of certain O-glycans can significantly affect cancer progression, especially at the cancer-related membrane protein level. To collect biological information on protein-specific glycosylation and further explore clinical applications, quantitative detection of glycosylation is essential. However, few assays have been reported for the in situ detection of protein-specific glycosylation to date. Herein, we developed a dual-probe approach for mass spectrometric quantification of protein-specific glycosylation using the terminal galactose/N-acetylgalactosamine (Gal/GalNAc) of MUC1 as a model. The dual-probe (i.e., protein probe and glycan probe) system was first designed and built. The protein probe contained an aptamer for MUC1 protein recognition and a capture DNA sequence. Correspondingly, the glycan probe had a DNA sequence complementary to that of the capture DNA, a substrate peptide containing a reporter peptide, and a tryptic cleavage site, and could be covalently linked with the terminal Gal/GalNAc. Exonuclease III enabled recycling of the hybridization-dehybridization process in a restricted space. Finally, the reporter peptide was tryptically released and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The mass response of the reporter peptide represented the amount of MUC1-specific terminal Gal/GalNAc. This dual-probe approach was applied for in situ detection of MUC1-specific terminal Gal/GalNAc in three human breast cancer cell lines and 32 pairs of matched breast cancer tissue samples. The relationship between MUC1-specific terminal Gal/GalNAc expression and breast cancer diagnosis/prognosis was also assessed.

Bioluminescent Protein-Inhibitor Pair in the Design of a Molecular Aptamer Beacon Biosensing System

Although bioluminescent molecular beacons designed around resonance quenchers have shown higher signal-to-noise ratios and increased sensitivity compared with fluorescent beacon systems, bioluminescence quenching is still comparatively inefficient. A more elegant solution to inefficient quenching can be realized by designing a competitive inhibitor that is structurally very similar to the native substrate, resulting in essentially complete substrate exclusion. In this work, we designed a conjugated anti-interferon-γ (IFN-γ) molecular aptamer beacon (MAB) attached to a bioluminescent protein, Gaussia luciferase (GLuc), and an inhibitor molecule with a similar structure to the native substrate coelenterazine. To prove that a MAB can be more sensitive and have a better signal-to-noise ratio, a bioluminescence-based assay was developed against IFN-γ and provided an optimized, physiologically relevant detection limit of 1.0 nM. We believe that this inhibitor approach may provide a simple alternative strategy to standard resonance quenching in the development of high-performance molecular beacon-based biosensing systems.

The Ca2+ -Regulated Photoprotein Obelin as a Tool for SELEX Monitoring and DNA Aptamer Affinity Evaluation

Bioluminescent solid-phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer-target complexes during design and development of the specific aptamers. The assay involves Ca²⁺ -regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.

Multi-praseodymium-and-tungsten bridging octameric tellurotungstate and its 2D honeycomb composite film for detecting estrogen

Under coordination driving force of tungsten and rare-earth (RE) bridges, we synthesized a novel giant multi-tungsten-and-RE-bridging octameric tellurotungstate (TT) [H₂N(CH₃)₂]₁₆K₈Na₆H₁₀[Pr₈(H₂O)₂₀W₁₆O₄₈][B-α-TeW₉O₃₃]₈·70H₂O (1) in CH₃CN-H₂O mixed solvent. The cluster anion {[Pr₈(H₂O)₂₀W₁₆O₄₈][B-α-TeW₉O₃₃]₈}^40- features sixteen W^VI bridges, eight Pr^III bridges and eight trivacant Keggin [B-α-TeW₉O₃₃]^8- fragments, which the square {W₄O₁₂} cluster can be imagined as a seed to induce the aggregation of eight [B-α-TeW₉O₃₃]^8- fragments by coordination driving force of additional twelve W^VI bridges and eight Pr^III ions. Furthermore, the 2D 1@DODA (dimethyldioctadecyl ammonium bromide = DODA·Br) honeycomb composite material was prepared. The honeycomb morphology of the 1@DODA composite material provides rich binding sites for electrodepositing Au nanoparticles to make Au/1@DODA electrodes. The aptamer of 17β-estradiol (E2) hormone can be grafted to the Au/1@DODA electrodes via Au-S bonding interaction to construct the Au/1@DODA aptamer biosensors. By virtue of the specific recognition interaction of aptamer and the electrochemical signal amplification function of methylene blue and cDNA, the Au/1@DODA aptamer biosensors can realize the electrochemical detection of E2. This finding not only offers an electrochemical biosensing platform for detecting E2, but also expands POM-based composite materials in the applications of clinical detection and biological analysis.

Structure and Function Analysis of DNA Monolayers Created from Self-Assembling DNA-Dendron Conjugates

Short sequences of DNA immobilized on gold surfaces can be used to capture an array of target molecules because of their high level of specificity. Depending on the nature of the target molecules, the proper density and distribution of the immobilized DNA molecules are fundamental to the quality of the sensor. With the aim to control the packing density and minimize the heterogeneity of the surfaces, DNA-dendron conjugate molecules were synthesized in solution and used to make self-assembled monolayers of single-stranded DNA surfaces on gold. The headgroups used were polyamido amine dendrons (cleaved cystamine core dendrimers) of generations two through five. The structural composition of these self-assembled monolayers was characterized using grazing angle Fourier-transform infrared and X-ray photoelectron spectroscopies. Surface plasmon resonance was used to measure surface densities of the probe monolayers and each monolayer's ability to capture fully complementary DNA strands from solution. The surface density of the probe monolayers was found to decrease with increasing dendron generation number, while the hybridization efficiency increased with increasing dendron generation number.

Computational predictive approaches for interaction and structure of aptamers

Aptamers are short single-strand sequences that can bind to their specific targets with high affinity and specificity. Usually, aptamers are selected experimentally via systematic evolution of ligands by exponential enrichment (SELEX), an evolutionary process that consists of multiple cycles of selection and amplification. The SELEX process is expensive, time-consuming, and its success rates are relatively low. To overcome these difficulties, in recent years, several computational techniques have been developed in aptamer sciences that bring together different disciplines and branches of technologies. In this paper, a complementary review on computational predictive approaches of the aptamer has been organized. Generally, the computational prediction approaches of aptamer have been proposed to carry out in two main categories: interaction-based prediction and structure-based predictions. Furthermore, the available software packages and toolkits in this scope were reviewed. The aim of describing computational methods and tools in aptamer science is that aptamer scientists might take advantage of these computational techniques to develop more accurate and more sensitive aptamers.

Chiral Interaction Is a Decisive Factor To Replace d-DNA with l-DNA Aptamers

Nucleic acid aptamers have been widely used in various fields such as biosensing, DNA chip, and medical diagnosis. However, the high susceptibility of nucleic acids to ubiquitous nucleases reduces the biostability of aptamers and limits their applications in biological contexts. Therefore, improving the biostability of aptamers becomes an urgent need. Herein, we present a simple strategy to resolve this problem by directly replacing the d-DNA-based aptamers with left-handed l-DNA. By testing several reported aptamers against respective targets, we found that our proposed strategy stood up well for nonchiral small molecule targets (e.g., Hemin and cationic porphyrin) and chiral targets whose interactions with aptamers are chirality-independent (e.g., ATP). We also found that the l-DNA aptamers were indeed endowed with greatly improved biostability due to the extraordinary resistance of l-DNA to nuclease digestion. With respect to other small-molecule targets whose interactions with aptamers are chirality-dependent (e.g., kanamycin) and biomacromolecules (e.g., tyrosine kinase-7), however, the proposed strategy was not entirely effective likely due to the participation of the DNA backbone chirality into the target recognition. In spite of this limitation, this strategy indeed paves an easy way to screen highly biostable aptamers important for the applications in many fields.

Rolling Circle Amplification-Based Polyvalent Molecular Beacon Probe-Assisted Signal Amplification Strategies for Sensitive Detection of B16 Cells

We developed a simple and sensitive signal amplification method for the detection of B16 cells based on the combination of rolling circle amplification (RCA) and molecular beacons (MBs). A long-chain structure of DNA synthesized by RCA was used to turn on aptamer-based MBs. Because of the multiple complementary repeat units, the RCA scaffold hybridized tens or hundreds of MBs to form polyvalent aptamer probes. The unfold ability and the fluorescence intensity of MBs were both improved by RCA, as compared to short single chains. The cell experiment results demonstrated that RCA-based polyvalent MBs were significantly more effective than monovalent MBs in targeting B16 cells and signal sensitivity because of their multivalent effects. The establishment of this strategy would provide a powerful platform for early clinical diagnostics of cancer cells.

An antibody-aptamer sandwich cathodic photoelectrochemical biosensor for the detection of progesterone

The progesterone (P4) level in body fluids can act as an indicator for early pregnancy diagnosis and offers insight into mammalian somatic function. In this work, we designed an antibody-aptamer based sandwich assay as a cathodic photoelectrochemical (PEC) biosensor for P4 detection. The composites of carbon dots and graphene oxide (CDs-GO) with favorable cathodic photocurrent response were used as photoactive materials on which the antibody (Ab) of P4 was immobilized. Meanwhile, high affinity truncated P4 aptamer was immobilized on Au-CuO-Cu₂O to act as a bioconjugate. When P4 was present, the aptamer-Au-CuO-Cu₂O bioconjugate could amplify the cathodic photocurrent of CDs-GO modified electrode through Ab-P4-aptamer interactions. Under optimum conditions, the cathodic photocurrent of the constructed PEC biosensor was found to increase linearly with P4 in a wide concentration range from 0.5 nM to 180 nM, with a low detection limit (3S/N) of 0.17 nΜ. The proposed cathodic PEC sensing platform demonstrated high selectivity, satisfying reproducibility, good stability. The sensor was successfully applied in the determination of P4 in human serum samples.

Architecting of a biodevice based on a screen-printed carbon electrode modified with the NiONP nanolayer and aptamer in BCM-7 detection

In this study, an ultrasensitive and robust biodevice implemented on a screen-printed carbon electrode (SPCE) surface is introduced. The β-casomorphin-7 (BCM-7) peptide as an early warning sign of autism disorder is distinguished in this system. The SPCE surface was directly electrodeposited with a nanolayer of the nickel oxide nanoparticles (NiONP). In next step, an Apt sequence as a capture of the BCM-7 was strongly attached on this surface. The embedded sensing interface offered some admirable characterizes to detect the BCM-7. The obtained DPV signals were reversely proportional to the concentrations of the BCM-7 through a stable binding reaction in two working linear ranges from 0.5 × 10^-9-1.5 μmol l-. Also, an unrivaled limit of detection (LOD) value of 166.6 aM was achieved that is so superior by other reported methods in the BCM-7 sensing. This hand-held biodevice was satisfactorily tested for the BCM-7 detection in human urine and blood sample with an average recovery rate of ∼101.87 %. More importantly, this strategy is free from labeling steps, complex sample processing and interference from common biomolecules in blood or urine. Due to the inherent advantages of the SPCE and the NiONP, utilizing this facile sensing interface may be an ideal choice in constructing of the ultrasensitive biodevice with low cost for distinguishing of the autism disorder.

Dual-Aptamer Modified Graphene Field-Effect Transistor Nanosensor for Label-Free and Specific Detection of Hepatocellular Carcinoma-Derived Microvesicles

Cancerous microvesicles (MVs), which are heterogeneous membrane-bound nanovesicles shed from the surfaces of cancer cells into the extracellular environment, have been widely recognized as promising "biofingerprints" for various cancers. High-performance identification of cancerous MVs plays a vital role in the early diagnosis of cancer, yet it is still technically challenging. Herein, we report a gold nanoparticle (AuNP)-decorated, dual-aptamer modified reduced graphene oxide (RGO) field-effect transistor (AAP-GFET) nanosensor for the label-free, specific, and sensitive quantification of HepG2 cell-derived MVs (HepG2-MVs). After GFET chips were fabricated, AuNPs were then decorated on the RGO surface. For specific capture and detection of HepG2-MVs, both sulfhydrylated HepG2 cell specific TLS11a aptamer (Apt_TLS11a) and epithelial cell adhesion molecule aptamer (Apt_EpCAM) were immobilized on the AuNP surface through an Au-S bond. This developed nanosensor delivered a broad linear dynamic range from 6 × 10⁵ to 6 × 10⁹ particles/mL and achieved a high sensitivity of 84 particles/μL for HepG2-MVs detection. Moreover, this AAP-GFET platform was able to distinguish HepG2-MVs from other liver cancer-related serum proteins (such as AFP and CEA) and MVs derived from human normal cells and other cancer cells of lung, pancreas, and prostate, suggesting its excellent method specificity. Compared with those modified with a single type of aptamer alone (Apt_TLS11a or Apt_EpCAM), such an AAP-GFET nanosensor showed greatly enhanced signals, suggesting that the dual-aptamer-based bio-nano interface was uniquely designed and could realize more sensitive quantification of HepG2-MVs. Using this platform to detect HepG2-MVs in clinical blood samples, we found that there were significant differences between healthy controls and hepatocellular carcinoma (HCC) patients, indicating its great potential in early HCC diagnosis.

Label-free electrochemical aptasensor for progesterone detection in biological fluids

A label-free electrochemical progesterone (P4) aptasensor was successfully developed by covalently immobilizing NH₂-functionalized P4-specific aptamer on the electrode surface. The NiO-Au hybrid nanofibers were synthesized by the electrospinning technique. GQDs-NiO-AuNFs nanocomposite was prepared by dispersing of electrospun NiO-AuNFs in the as-synthesized graphene quantum dots (GQDs) solution and stirring for 24 h. Novel GQDs-NiO-AuNFs nano-architecture in combination with functionalized multiwalled carbon nanotubes (f-MWCNTs) were further utilized to modify screen printed carbon electrode (SPCE) in order to construct an effective immobilization matrix with plenty of carboxylic functional groups. The stepwise assembly process of the designed aptasensor was characterized by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The aptamer-progesterone complex formation led to a hindered electron transfer reaction on the sensing interface, which decreased the redox probe peak current. Based on of this, progesterone could be quantitatively detected by monitoring the decrease of differential pulse voltammetric (DPV) responses of [Fe(CN)₆]^3-/4- peak current with increasing the progesterone concentration. Under optimized experimental parameters, the aptasensor exhibited a dynamic concentration range from 0.01 to 1000 nM and a detection limit of 1.86 pM. The proposed aptasensor was successfully employed for the determination of progesterone in human serum samples and pharmaceutical formulations.

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.

Engineering repeat proteins of the immune system

Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.

Enabling Molecular Gapping and Bridging on a Biosensing Surface via Electrochemical Cross-Linking and Cleavage

Protein detection in complicated biological samples requires robust design and a rigorous rinsing process. Many recently developed artificial targeting probes, however, often do not possess antibody-like binding strength that enables them to endure harsh biosensing conditions, and the classic 2-to-1 sandwich binding pattern is unavailable for many targets, often necessitating a complicated indirect signal conversion mechanism. Here, an attempt is made to provide innovative "covalent" solutions to such problems by employing peptide reactivity to form a covalent and robust biosensing structure upon target binding. Both the cross-coupling and cleavage of peptide chains are employed to achieve the classic 2-to-1 binding when only one targeting probe is available. Specifically, a targeting probe against the protein and a signaling probe are coimmobilized onto the sensing interface. The ratio between the two probes and their surface density is modulated so that direct cross-linking between the two immobilized probes is suppressed by the average distance between two such probes. Upon protein binding, the protein molecule may bridge that gap by itself. The signaling probe can carry any motif of signal amplification. And here a Cu-ion-complexed motif, which can exhibit peroxidase-like activity upon electrochemical agitation, is employed multipurposely as the catalyst for cross-linking, cleavage, and signal amplification. Three nonhomologous target proteins can be sensitively quantified in serum-spiked samples and clinical sample detection of one of them is also successful; these results suggest the potential of the proposed method in future clinical applications.

Capture and selective release of multiple types of circulating tumor cells using smart DNAzyme probes

The effective capture, release and reanalysis of circulating tumor cells (CTCs) are of great significance to acquire tumor information and promote the progress of tumor therapy. Particularly, the selective release of multiple types of CTCs is critical to further study; however, it is still a great challenge. To meet this challenge, we designed a smart DNAzyme probe-based platform. By combining multiple targeting aptamers and multiple metal ion responsive DNAzymes, efficient capture and selective release of multiple types CTCs were realized. Sgc8c aptamer integrated Cu2+-dependent DNAzyme and TD05 aptamer integrated Mg2+-dependent DNAzyme can capture CCRF-CEM cells and Ramos cells respectively on the substrate. With the addition of Cu2+ or Mg2+, CCRF-CEM cells or Ramos cells will be released from the substrate with specific selectivity. Furthermore, our platform has been successfully demonstrated in the whole blood sample. Therefore, our capture/release platform will benefit research on the molecular analysis of CTCs after release and has great potential for cancer diagnosis and individualized treatment.

Electrochemical biosensors based on nucleic acid aptamers

During recent decades, nucleic acid aptamers have emerged as powerful biological recognition elements for electrochemical affinity biosensors. These bioreceptors emulate or improve on antibody-based biosensors because of their excellent characteristics as bioreceptors, including limitless selection capacity for a large variety of analytes, easy and cost-effective production, high stability and reproducibility, simple chemical modification, stable and oriented immobilization on electrode surfaces, enhanced target affinity and selectivity, and possibility to design them in target-sensitive 3D folded structures. This review provides an overview of the state of the art of electrochemical aptasensor technology, focusing on novel aptamer-based electroanalytical assay configurations and providing examples to illustrate the different possibilities. Future prospects for this technology are also discussed. Graphical abstract.

An aptasensor for the label-free detection of thrombin based on turn-on fluorescent DNA-templated Cu/Ag nanoclusters

A highly sensitive thrombin aptasensor was constructed based on the alteration of the aptamer conformation induced by the target recognition and the turn-on fluorescence due to the proximity of two darkish DNA-templated copper/silver nanoclusters (DNA-Cu/Ag NCs). Two DNA templates were designed as the functional structures consisting of the Cu/Ag NC-nucleation segment located at two termini or one terminus and the aptamer segment in the middle of a DNA template. Two darkish DNA-Cu/Ag NCs came close to each other when the aptamer combined with the target due to the conformational alteration of the aptamer structure, resulting in an increased fluorescence signal readout. Thrombin was sensitively determined as low as 1.6 nM in the range of 1.6–8.0 nM with a high selectivity. Finally, this sensor succeeded in detecting thrombin in a real fetal bovine serum.

A highly sensitive thrombin aptasensor was constructed based on the alteration of the aptamer conformation induced by the target recognition and the turn-on fluorescence due to the proximity of two darkish DNA-templated copper/silver nanoclusters (DNA-Cu/Ag NCs).

Highly sensitive detection for cocaine using an aptamer–cocaine–aptamer method

In this study, a thiol-modified aptamer was immobilized on a gold nanoparticle-modified molybdenum disulfide composite material (MoS₂@AuNPs), which could remove the interference of physical adsorption and reduce false positive signals.

One-Pot SELEX: Identification of Specific Aptamers against Diverse Steroid Targets in One Selection

Aptamers are well-established biorecognition molecules used in a wide variety of applications for the detection of their respective targets. However, individual SELEX processes typically performed for the identification of aptamers for each target can be quite time-consuming, labor-intensive, and costly. An alternative strategy is proposed herein for the simultaneous identification of different aptamers binding distinct but structurally similar targets in one single selection. This one-pot SELEX approach, using the steroids estradiol, progesterone, and testosterone as model targets, was achieved by combining the benefits of counter-SELEX with the power of next-generation sequencing and bioinformatics analysis. The pools from the last stage of the selection were compared in order to discover sequences with preferential abundance in only one of the pools. This led to the identification of aptamer candidates with potential specificity to a single steroid target. Binding studies demonstrated the high affinity of each selected aptamer for its respective target, and low nanomolar range dissociation constants calculated were similar to those previously reported for steroid-binding aptamers selected using traditional SELEX approaches. Finally, the selected aptamers were exploited in microtiter plate assays, achieving nanomolar limits of detection, while the specificity of these aptamers was also demonstrated. Overall, the one-pot SELEX strategy led to the discovery of aptamers for three different steroid targets in one single selection without compromising their affinity or specificity, demonstrating the power of this approach of aptamer discovery for the simultaneous selection of aptamers against multiple targets.