Synthetic DNA aptamers to detect protein molecular variants in a high-throughput fluorescence quenching assay

Deep-Learning-Assisted Stratification of Amyloid Beta Mutants Using Drying Droplet Patterns

The development of simple and accurate methods to predict mutations in proteins remains an unsolved challenge in modern biochemistry. It is discovered that critical information about primary and secondary peptide structures can be inferred from the stains left behind by their drying droplets. To analyze the complex stain patterns, deep-learning neuronal networks are challenged with polarized light microscopy images derived from the drying droplet deposits of a range of amyloid beta (1-42) (Aβ₄₂ ) peptides. These peptides differ in a single amino acid residue and represent hereditary mutants of Alzheimer's disease. Stain patterns are not only reproducible but also result in comprehensive stratification of eight amyloid beta (Aβ) variants with predictive accuracies above 99%. Similarly, peptide stains of a range of distinct Aβ₄₂ peptide conformations are identified with accuracies above 99%. The results suggest that a method as simple as drying a droplet of a peptide solution onto a solid surface may serve as an indicator of minute, yet structurally meaningful differences in peptides' primary and secondary structures. Scalable and accurate detection schemes for stratification of conformational and structural protein alterations are critically needed to unravel pathological signatures in many human diseases such as Alzheimer's and Parkinson's disease.

Overview and emerging trends in optical fiber aptasensing

Optical fiber biosensors have attracted growing interest over the last decade and quickly became a key enabling technology, especially for the detection of biomarkers at extremely low concentrations and in small volumes. Among the many and recent fiber-optic sensing amenities, aptamers-based sensors have shown unequalled performances in terms of ease of production, specificity, and sensitivity. The immobilization of small and highly stable bioreceptors such as DNA has bolstered their use for the most varied applications e.g., medical diagnosis, food safety and environmental monitoring. This review highlights the recent advances in aptamer-based optical fiber biosensors. An in-depth analysis of the literature summarizes different fiber-optic structures and biochemical strategies for molecular detection and immobilization of receptors over diverse surfaces. In this review, we analyze the features offered by those sensors and discuss about the next challenges to be addressed. This overview investigates both biochemical and optical parameters, drawing the guiding lines for forthcoming innovations and prospects in this ever-growing field of research.

Aptamer-Based Detection of Circulating Targets for Precision Medicine

The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

Earlier diagnoses of acute leukemia by a sandwich type of electrochemical aptasensor based on copper sulfide-graphene composite

Due to high affinity and specificity of aptamers, they are widely considered for construction of aptasensor to specific recognizing of analytes in biological complex matrix. So, in this work we design a high selective and sensitive aptasensor for leukemia cancer cells (CCRF-CEM) via superior catalytic effect of copper sulfide-graphene (CuS-GR) nanocomposite as label and Au-GR nanocomposite as sensing platform. The CuS-GR nano-composite (label component) is CuS nanoparticles that wrapping on graphene sheets. Its catalytic activity (CuS-GR) increases the current of sensor in parallel with adding of CCRF-CEM and provide sensitive detection of analytes. The detailed of signal amplification and effect on the aptasensor performance completely discussed. This sensor has a linear range of 50-1 × 10⁶ cell mL^-1, with a limit of detection of 18 cell mL^-1. Also, the developed aptasensor has a significance specificity, high sensitivity and accuracy. It was used for the identification of CCRF-CEM cells in blood samples.

Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer

We report a method to detect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of a protein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of a fluorescent intercalating dye. Introduction of a target causes the primer region within the aptamer to become unavailable for binding to the circular template, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probes to bind to the RCA reaction product, it is possible to produce a generic protein-modulated RCA assay system that does not require fluorophore- or biotin-modified DNA species, substantially reducing complexity and cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.

Detection of target collagen peptides with single amino acid mutation using two fluorescent peptide probes

Collagen with a single amino acid substitution is the main cause of a plethora of heritable disorders such as Osteogenesis Imperfecta and Ehlers-Danlos syndrome. Though significant advances have been achieved in the development of protein assays, it remains very challenging to distinguish a protein with a single amino acid mutation from the wild-type protein. A novel fluorescent self-quenching assay has been constructed to detect target collagen peptides with a single amino acid mutation using two probe peptides. The hybridization of the probe peptide and the natural target collagen peptide results in a complete heterotrimer and strong fluorescence, whereas the mixture of the probe peptide and the mutation collagen sequences leads to a partial homotrimer and pronounced fluorescence self-quenching. The extent of fluorescence quenching is dependent on the identity of the residue replacing Gly following the order of Ala < Ser < Arg, while the Gly-Ala mutation causes the mildest fluorescence loss. The probe peptide-based fluorescence self-quenching assay facilitates specific detection of the target collagen sequence with a single Gly mutation at the nM level. The simultaneous utilization of both probe peptides enables efficient discrimination between different mutation peptides. To our knowledge, our work may be the first report of a robust analytical assay that can identify collagen fragments with single amino acid mutation, which will greatly contribute to deciphering the molecular mechanism of Osteogenesis Imperfecta as well as developing novel diagnostic strategies.

Sensitive and specific detection of proteins based on target-responsive DNA polymerase activity

We herein describe a novel method for the detection of target protein based on the target-responsive DNA polymerase activity. In the sensor, two different types of DNA aptamers with the respective functions: one binds to the target protein and the other binds to DNA polymerase, are rationally engineered and combined to form the detection probe that regulates DNA polymerase activity in response to the target protein. In the presence of target protein, the detection probe becomes destabilized and stops the inhibition of DNA polymerase activity. Consequently, the active DNA polymerase initiates the primer extension reaction on the target-specific DNA aptamer, which recycles the target protein to promote another activation cycle of DNA polymerase. In addition, DNA polymerase also catalyzes the primer extension reaction on the primer/template complex in conjugation with TaqMan probe, leading to the significantly enhanced fluorescence intensities. With this novel strategy, we detected a model target protein, lysozyme with a limit of detection as low as 0.80 nM. In addition, the practical applicability of this system was successfully demonstrated by determining lysozyme in human serum.

Selection, Identification, and Binding Mechanism Studies of an ssDNA Aptamer Targeted to Different Stages of E. coli O157:H7

Enterohemorrhagic Escherichia coli O157:H7 ( E. coli O157:H7) is known as an important food-borne pathogen related to public health. In this study, aptamers which could bind to different stages of E. coli O157:H7 (adjustment phase, log phase, and stationary phase) with high affinity and specificity were obtained by the whole cell-SELEX method through 14 selection rounds including three counter-selection rounds. Altogether, 32 sequences were obtained, and nine families were classified to select the optimal aptamer. To analyze affinity and specificity by flow cytometer, an ssDNA aptamer named Apt-5 was picked out as the optimal aptamer that recognizes different stages of E. coli O157:H7 specifically with the K_d value of 9.04 ± 2.80 nM. In addition, in order to study the binding mechanism, target bacteria were treated by proteinase K and trypsin, indicating that the specific binding site is not protein on the cell membrane. Furthermore, when we treated E. coli O157:H7 with EDTA, the result showed that the binding site might be lipopolysaccharide (LPS) on the outer membrane of E. coli O157:H7.

Recent advances on aptamer-based biosensors to detection of platelet-derived growth factor

Platelet-derived growth factor (PDGF-BB), a significant serum cytokine, is an important protein biomarker in diagnosis and recognition of cancer, which straightly rolled in proceeding of various cell transformations, including tumor growth and its development. Fibrosis, atherosclerosis are certain appalling diseases, which PDGF-BB is near to them. Generally, the expression amount of PDGF-BB increases in human life-threatening tumors serving as an indicator for tumor angiogenesis. Thus, identification and quantification of PDGF-BB in biomedical fields are particularly important. Affinity chromatography, immunohistochemical methods and enzyme-linked immunosorbent assay (ELISA), conventional methods for PDGF-BB detection, requiring high-cost and complicated instrumentation, take too much time and offer deficient sensitivity and selectivity, which restrict their usage in real applications. Hence, it is essential to design and build enhanced systems and platforms for the recognition and quantification of protein biomarkers. In the past few years, biosensors especially aptasensors have been received noticeable attention for the detection of PDGF-BB owing to their high sensitivity, selectivity, accuracy, fast response, and low cost. Since the role and importance of developing aptasensors in cancer diagnosis is undeniable. In this review, optical and electrochemical aptasensors, which have been applied by many researchers for PDGF-BB cancer biomarker detection, have been mentioned and merits and demerits of them have been explained and compared. Efforts related to design and development of aptamer-based biosensors using nanoparticles for sensitive and selective detection of PDGF-BB have been reviewed considering: Aptamer importance as recognition elements, principal, application and the recent improvements and developments of aptamer based optical and electrochemical methods. In addition, commercial biosensors and future perspectives for rapid and on-site detection of PDGF-BB have been summarized.

Quantifying the Degree of Aggregation from Fluorescent Dye-Conjugated DNA Probe by Single Molecule Photobleaching Technology for the Ultrasensitive Detection of Adenosine

In this work, we demonstrated a single molecule photobleaching-based strategy for the ultrasensitive detection of adenosine. A modified split aptamer was designed to specifically recognize individual adenosine molecules in solution. The specific binding of dye-labeled short strand DNA probes onto the elongated aptamer strand in the presence of adenosine resulted in a concentration-dependent self-aggregation process. The degree-of-aggregation (DOA) of the short DNA probes on the elongated aptamer strand could then be accurately determined based on the single molecule photobleaching measurement. Through statistically analyzing the DOA under different target concentrations, a well-defined curvilinear relationship between the DOA and target molecule concentration (e.g., adenosine) was established. The limit-of-detection (LOD) is down to 44.5 pM, which is lower than those recently reported results with fluorescence-based analysis. Owing to the high sensitivity and excellent selectivity, the sensing strategy described herein would find broad applications in biomolecule analysis under complicated surroundings.

Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics

Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.

Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins

Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high-salt solution. In the presence of exosomes, the non-specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.

Recent progresses in biomedical applications of aptamer-functionalized systems

Aptamers, known as "chemical antibodies" are screened via a combinational technology of systematic evolution of ligands by exponential enrichment (SELEX). Due to their specific targeting ability, high binding affinity, low immunogenicity and easy modification, aptamer-functionalized systems have been extensively applied in various fields and exhibit favorable results. However, there is still a long way for them to be commercialized, and few aptamer-functionalized systems have yet successfully entered clinical and industrial use. Thus, it is necessary to overview the recent research progresses of aptamer-functionalized systems for the researchers to improve or design novel and better aptamer-functionalized systems. In this review, we first introduce the recent progresses of aptamer-functionalized systems' applications in biosensing, targeted drug delivery, gene therapy and cancer cell imaging, followed by a discussion of the challenges faced with extensive applications of aptamer-functionalized systems and speculation of the future prospects of them.

Selection, characterization, and application of DNA aptamers for detection of Mycobacterium tuberculosis secreted protein MPT64

Rapid detection of Mycobacterium tuberculosis (Mtb), an etiological agent of tuberculosis (TB), is important for global control of this disease. Aptamers have emerged as a potential rival for antibodies in therapeutics, diagnostics and biosensing due to their inherent characteristics. The aim of the current study was to select and characterize single-stranded DNA aptamers against MPT64 protein, one of the predominant secreted proteins of Mtb pathogen. Aptamers specific to MPT64 protein were selected in vitro using systematic evolution of ligands through exponential enrichment (SELEX) method. The selection was started with a pool of ssDNA library with randomized 40-nucleotide region. A total of 10 cycles were performed and seventeen aptamers with unique sequences were identified by sequencing. Dot Blot analysis was performed to monitor the SELEX process and to conduct the preliminary tests on the affinity and specificity of aptamers. Enzyme linked oligonucleotide assay (ELONA) showed that most of the aptamers were specific to the MPT64 protein with a linear correlation of R² = 0.94 for the most selective. Using Surface Plasmon Resonance (SPR), dissociation equilibrium constant K_D of 8.92 nM was obtained. Bioinformatics analysis of the most specific aptamers revealed the existence of a conserved as well as distinct sequences and possible binding site on MPT64. The specificity was determined by testing non-target ESAT-6 and CFP-10. Negligible cross-reactivity confirmed the high specificity of the selected aptamer. The selected aptamer was further tested on clinical sputum samples using ELONA and had sensitivity and specificity of 91.3% and 90%, respectively. Microscopy, culture positivity and nucleotide amplification methods were used as reference standards. The aptamers studied could be further used for the development of medical diagnostic tools and detection assays for Mtb.

Multidimensional hybrid conductive nanoplate-based aptasensor for platelet-derived growth factor detection

In the development of disease diagnoses, rapid responses to and accurate selectivity for target analytes are critical aspects. As one diagnostic approach, biosensors with high sensitivity and selectivity are investigated to detect disorder factors (e.g., endocrine disruptors and cancer oncoproteins). In this report, we demonstrate an aptamer-functionalized multidimensional hybrid conducting-polymer (3-carboxylated polypyrrole) plate (A_MHCPP) based field-effect transistor (FET) sensor to detect a platelet-derived growth factor (PDGF-BB). The multidimensional hybrid conducting-polymer plates (MHCPPs) are formed on the graphene surface by using electrodeposition and vapor deposition polymerization (VDP) steps. The amine-functionalized PDGF-B binding aptamers are then immobilized on the carboxylated polypyrrole surface by means of covalent bond formation (-CONH). The prepared FET sensors present high sensing ability toward PDGF-BB - as low as 1.78 fM among interfering biomolecules at room temperature.

Nicking endonuclease-assisted signal amplification of a split molecular aptamer beacon for biomolecule detection using graphene oxide as a sensing platform

Sensitive and selective detection of ultralow concentrations of specific biomolecules is important in early clinical diagnoses and biomedical applications. Many types of aptasensors have been developed for the detection of various biomolecules, but usually suffer from false positive signals and high background signals. In this work, we have developed an amplified fluorescence aptasensor platform for ultrasensitive biomolecule detection based on enzyme-assisted target-recycling signal amplification and graphene oxide. By using a split molecular aptamer beacon and a nicking enzyme, the typical problem of false positive signals can be effectively resolved. Only in the presence of a target biomolecule, the sensor system is able to generate a positive signal, which significantly improves the selectivity of the aptasensor. Moreover, using graphene oxide as a super-quencher can effectively reduce the high background signal of a sensing platform. We select vascular endothelial growth factor (VEGF) and adenosine triphosphate (ATP) as model analytes in the current proof-of-concept experiments. It is shown that under optimized conditions, our strategy exhibits high sensitivity and selectivity for the quantification of VEGF and ATP with a low detection limit (1 pM and 4 nM, respectively). In addition, this biosensor has been successfully utilized in the analysis of real biological samples.

Electrochemical aptamer scaffold biosensors for detection of botulism and ricin toxins

Protein toxins present considerable health risks, but detection often requires laborious analysis. Here, we developed electrochemical aptamer biosensors for ricin and botulinum neurotoxins, which display robust and specific signal at nanomolar concentrations and function in dilute serum. These biosensors may aid future efforts for the rapid diagnosis of toxins.

Protein-Protein Communication and Enzyme Activation Mediated by a Synthetic Chemical Transducer

The design and function of a synthetic "chemical transducer" that can generate an unnatural communication channel between two proteins is described. Specifically, we show how this transducer enables platelet-derived growth factor to trigger (in vitro) the catalytic activity of glutathione-s-transferase (GST), which is not its natural enzyme partner. GST activity can be further controlled by adding specific oligonucleotides that switch the enzymatic reaction on and off. We also demonstrate that a molecular machine, which can regulate the function of an enzyme, could be used to change the way a prodrug is activated in a "programmable" manner.

Interaction of gallic acid with trypsin analyzed by spectroscopy

The interactions between trypsin and gallic acid (GA) were investigated by means of fluorescence spectroscopy, UV-vis absorption spectroscopy, resonance light scattering (RLS) spectroscopy, synchronous fluorescence spectroscopy, and enzymatic inhibition assay. It was found that GA can cause the fluorescence quenching of trypsin during the process of formation of GA-trypsin complex, resulting in inhibition of trypsin activity (IC₅₀ = 3.9 × 10⁻⁶ mol/L). The fluorescence spectroscopic data showed that the quenching efficiency can reach about 80%. The binding constants were 1.9371 × 10⁴ L/mol, 1.8192 × 10⁴ L/mol, and 1.7465 × 10⁴ L/mol at three temperatures, respectively. The thermodynamic parameters revealed that hydrogen bonds, van der Waals, hydrophobic, and electrostatic interactions were involved in the binding process of GA to trypsin. Molecular modeling studies illustrated a specific display of binding information and explained most of the experiment phenomena. The microenvironments of tryptophan and tyrosine residue in trypsin were changed by the GA. Results indicated that GA was a strong quencher and inhibitor of trypsin.

Bioanalytical chemistry of cytokines--a review

Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.

Nucleic acid aptamer-guided cancer therapeutics and diagnostics: the next generation of cancer medicine

Conventional anticancer therapies, such as chemo- and/or radio-therapy are often unable to completely eradicate cancers due to abnormal tumor microenvironment, as well as increased drug/radiation resistance. More effective therapeutic strategies for overcoming these obstacles are urgently in demand. Aptamers, as chemical antibodies that bind to targets with high affinity and specificity, are a promising new and novel agent for both cancer diagnostic and therapeutic applications. Aptamer-based cancer cell targeting facilitates the development of active targeting in which aptamer-mediated drug delivery could provide promising anticancer outcomes. This review is to update the current progress of aptamer-based cancer diagnosis and aptamer-mediated active targeting for cancer therapy in vivo, exploring the potential of this novel form of targeted cancer therapy.

Facile and Cost-Effective Detection of Saxitoxin Exploiting Aptamer Structural Switching

A simple method to detect saxitoxin (STX), one of the main components of the paralytic shellfish poison from red tide, has been developed. By using a next generation dye for double-stranded DNA we were able to differentiate fluorescence from STX-binding aptamers when exposed to different concentrations of STX, suggesting a change in aptamer folding upon target binding. The developed method is extremely rapid, only requiring small sample volumes, with quantitative results in the concentration range of 15 ng/mL to 3 µg/mL of STX, with a detection limit of 7.5 ng/mL.

Background eliminated signal-on electrochemical aptasensing platform for highly sensitive detection of protein

Using platelet-derived growth factor B chain dimer (PDGF-BB) as the model target, a background current eliminated electrochemical aptameric sensing platform for highly sensitive and signal-on detection of protein is proposed in this paper. Successful fabrication of the biosensor depends on ingenious design of aptamer probe, which contains the aptamer sequence for PDGF-BB and the recognition sequence for EcoRI endonuclease. In the absence of PDGF-BB, the ferrocene labeled aptamer probe folds into a hairpin structure and forms a recognition site for EcoRI. By treatment with endonuclease, the specific and cleavable double-stranded region is cut off and redox-active ferrocene molecule is removed from the electrode surface, and almost no peak current is observed. When binding with target protein, the designed aptamer probe changes its conformation and dissociates the recognition double strand. The integrated aptamer probe is maintained when exposing to EcoRI endonuclease, resulting in obvious peak current. Therefore, a signal-on and sensitive sensing strategy for PDGF-BB detection is fabricated with eliminated background current. Under the optimized experimental conditions, a wide linear response range of 4 orders of magnitude from 20pgmL(-1) to 200ngmL(-1) is achieved with a detection limit of 10pgmL(-1). Moreover, the present aptameric platform is universal for the analysis of a broad range of target molecules of interest by changing and designing the sequence of aptamer probe.

Diagnostic applications of gastric carcinoma cell aptamers in vitro and in vivo

Gastric carcinoma is the most malignant tumor. Due to lacking of efficient means to diagnose the cancer at the early stage, it is necessary to develop effective molecular probes for early diagnosis and treatment. We have selected aptamers with high specificity and affinity against SGC7901 cells by cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) method, which shown important clinical applications: (1) Specific recognize human gastric tumor tissues compared to the normal tissues. (2)When used to capture cancerous cells, the aptamer-functionalized fluorescent-magnetic nanospheres (FMNS) could specifically capture 93% target cancer cells and about 70% target cells can be released. (3) The aptamer probe displayed a quenched fluorescence in the absence of target cancer cells and went through a conformational transformation upon binding to target cancer cells that induced fluorescence. (4) The aptamer probe could target gastric tumors transplanted into mice with obvious fluorescence. The newly generated aptamers hold great potential in early cancer diagnosis.

Aptamer technology for tracking cells' status & function

In fields such as cancer biology and regenerative medicine, obtaining information regarding cell bio-distribution, tropism, status, and other cellular functions are highly desired. Understanding cancer behaviors including metastasis is important for developing effective cancer treatments, while assessing the fate of therapeutic cells following implantation is critical to validate the efficacy and efficiency of the therapy. For visualization purposes with medical imaging modalities (e.g. magnetic resonance imaging), cells can be labeled with contrast agents (e.g. iron-oxide nanoparticles), which allows their identification from the surrounding environment. Despite the success of revealing cell biodistribution in vivo, most of the existing agents do not provide information about the status and functions of cells following transplantation. The emergence of aptamers, single-stranded RNA or DNA oligonucleotides of 15 to 60 bases in length, is a promising solution to address this need. When aptamers bind specifically to their cognate molecules, they undergo conformational changes which can be transduced into a change of imaging contrast (e.g. optical, magnetic resonance). Thus by monitoring this signal change, researchers can obtain information about the expression of the target molecules (e.g. mRNA, surface markers, cell metabolites), which offer clues regarding cell status/function in a non-invasive manner. In this review, we summarize recent efforts to utilize aptamers as biosensors for monitoring the status and function of transplanted cells. We focus on cancer cell tracking for cancer study, stem cell tracking for regenerative medicine, and immune cell (e.g. dendritic cells) tracking for immune therapy.

Aptamer-functionalized hybrid carbon nanofiber FET-type electrode for a highly sensitive and selective platelet-derived growth factor biosensor

Precise selectivity and rapid responses to target biomolecules are important in the development of biosensors. In particular, highly sensitive and selective biosensors have been used in clinical treatment to detect factors such as cancer oncoproteins and endocrine disruptors. Herein, highly sensitive liquid electrolyte field-effect transistor (FET) system biosensors were fabricated to detect platelet-derived growth factor (PDGF) using a PDGF-B binding aptamer conjugated with carboxylic polypyrrole-coated metal oxide-decorated carbon nanofibers (CPMCNFs) as the signal transducer. First, CPMCNFs were fabricated using vapor deposition polymerization (VDP) of the carboxylic pryrrole monomer (CPy) on metal oxide-decorated carbon nanofiber (MCNF) surfaces with no treatment for carbon surface functionalization. Furthermore, a 3 nm thick uniformly coated carboxylic polypyrrole (CPPy) layer was formed without aggregation. The CPMCNFs were integrated with the PDGF-B binding aptamer and immobilized on the interdigitated array substrate by covalent anchoring to produce a FET-type biosensor transducer. The PDGF-B binding aptamer conjugated CPMCNF (CPB-Apt) FET sensor was highly sensitive (5 fM) and extremely selective for isoforms of PDGFs. Additionally, the CPB-Apt FET sensor could be reused over a few weeks.

High-throughput bead-based identification of structure-switching aptamer beacons

We describe a new platform to identify structure-switching DNA beacon aptamers, which detect small molecules in a specific manner. By clonally amplifying a DNA library designed to fluoresce in response to binding events onto microbeads, aptamer beacons can be selected by stringent fluorescence-assisted sorting. We validated this method by isolating known and novel anti-steroid aptamers from two separate DNA libraries that were structurally enriched with three-way junctions. Importantly, aptamers were retrieved in only a few (three) rounds of selection by this approach and did not require further optimization, significantly streamlining the process of beacon development.

Nucleic acid aptamers for living cell analysis

Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as "chemical antibodies," have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.

Is less more? Lessons from aptamer selection strategies

Aptamers have many inherent advantages originating from their in vitro selection and tailored chemical synthesis that makes them appealing alternatives of antibodies in bioaffinity assays. However, what ultimately matters, and that is the prerequisite to give way to all these advantages, is how well, and how selectively the aptamers bind to their targets. With the aptamer selection largely in the hand of life scientists, analytical chemists focused mostly on methodological development of aptamer-based assays using a fairly restricted number of aptamers to prove their concepts. However, ideally the development of an aptamer-based assay should start from the selection of aptamers to ensure their proper functionality in real samples. For instance information on the sample matrix can be implemented within counter-selection steps to discard aptamer candidates that show cross-reactivity to matrix components or critical interferents. In general, a larger consideration of the analytical use during selection and characterization of aptamers have been shown to increase the applicability of aptamers. Therefore, this review is a short, subjective view on trends in aptamer development highlighting factors to consider during their selection for a successful analytical application.

Isolation and characterization of a new class of DNA aptamers specific binding to Singapore grouper iridovirus (SGIV) with antiviral activities

The Singapore grouper iridovirus (SGIV), a member of the genus Ranavirus, is a major viral pathogen that has caused heavy economic losses to the grouper aquaculture industry in China and Southeast Asia. No efficient method of controlling SGIV outbreaks is currently available. Systematic evolution of ligands by exponential enrichment (SELEX) is now widely used for the in vitro selection of artificial ssDNA or RNA ligands, known as aptamers, which bind to targets through their stable three-dimensional structures. In our current study, we generated ssDNA aptamers against the SGIV, and evaluated their ability to block SGIV infection in cultured fish cells and cultured fish in vivo. The anti-SGIV DNA aptamers, LMB-761, LMB-764, LMB-748, LMB-439, LMB-755, and LMB-767, were selected from a pool of oligonucleotides randomly generated using a SELEX iterative method. The analysis of the secondary structure of the aptamers revealed that they all formed similar stem-loop structures. Electrophoretic mobility shift assays showed that the aptamers bound SGIV specifically, as evidenced by a lack cross-reactivity with the soft shell turtle iridovirus. The aptamers produced no cytotoxic effects in cultured grouper spleen cells (GS). Assessment of cytopathic effects (CPE) and viral titer assays showed that LMB-761, LMB-764, LMB-748, LMB-755, and LMB-767 significantly inhibited SGIV infection in GS cells. The in vivo experiments showed that LMB-761 and LMB-764 reduced SGIV-related mortality, and no negative effects were observed in orange-spotted grouper, Epinephelus coioides, indicating that these DNA aptamers may be suitable antiviral candidates for controlling SGIV infections in fish reared in marine aquaculture facilities.

A universal electrochemical sensing system for small biomolecules using target-mediated sticky ends-based ligation-rolling circle amplification

A novel versatile electrochemical platform for ultrasensitive detection of small biomolecules was developed using ligation-rolling circle amplification (L-RCA) with analyte-mediated sticky ends. In order to achieve DNA cyclization, we designed two ss-DNA probes: the leftpart probe could form a "hairpin" structure by denaturing; the rightpart probe could also form a "hairpin" structure based on analyte-activated conformation change. Then the two probes with the same sticky ends (G-AATTC) could be ligated in the presence of Escherichia coli DNA ligase, forming a circular template for rolling circle amplification (RCA), which could be triggered by adding the primer probe and Phi29 DNA polymerase. Electrochemical impedance spectroscopy (EIS) was employed as the detection method. Overall, the proposed L-RCA-based sensing system not only exhibits excellent analytical characteristics with a detection limit of 320 pM and a linear range of 5 orders of magnitude (1 nM-10 μM), but also provides a universal design idea of L-RCA, which broadens the use of DNA amplification method and holds great promise in ultrasensitive bioassay in the future.

Aptamers: molecules of great potential

Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.

An electrochemiluminescence strategy based on aptamers and nanoparticles for the detection of cancer cells

A PCR (polymerase chain reaction)-free electrochemiluminescence (ECL) strategy based on aptamers and ECL nanoprobes was developed for rapid collection and detection of Ramos cells. The ECL nanoprobes consisted of gold nanoparticles (AuNPs), linker DNA and tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled signal DNA. The linker DNA and signal DNA were modified on the surface of the AuNPs through AuS bonds. The linker DNA can hybridize partly with the aptamers loaded on the magnetic beads to construct the magnetic biocomplex. In the presence of the cancer cells, the aptamers conjugated with the cancer cells with higher affinity. The ECL nanoprobe released from the biocomplex and subsequently hybridized with the capture DNA modified on the Au electrode. The ECL intensity of the TBR loaded on the nanoprobes directly reflected the amount of the cancer cells. With the use of the developed ECL probe, a limit of detection as low as 50 Ramos cells per mL could be achieved. The proposed methods based on ECL should have wide applications in the diagnosis of cancers due to their high sensitivity, simplicity and low cost.

Platelet-derived growth factor oncoprotein detection using three-dimensional carbon microarrays

The potential of aptamers as ligand binding molecule has opened new avenues in the development of biosensors for cancer oncoproteins. In this paper, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor (PDGF-BB) oncoprotein detection is reported. The detection mechanism is based on the release of fluorophore (TOTO intercalating dye) from the target binding aptamer's stem structure when it captures PDGF. Amino-terminated three-dimensional carbon microarrays fabricated by pyrolyzing patterned photoresist were used as a detection platform. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5pmol. This detection strategy is promising in a wide range of applications in the detection of cancer biomarkers and other proteins.

Electrochemiluminescent determination of cancer cells based on aptamers, nanoparticles, and magnetic beads

Herein we report a polymerase chain reaction (PCR)-free electrochemiluminescence (ECL) approach that uses ECL nanoprobes for the determination of cancer cells with high sensitivity. The ECL nanoprobe consists of gold nanoparticles (AuNPs), linker DNA, and tris(2,2'-bipyridyl)ruthenium (TBR)-labeled signal DNA. The linker DNA and signal DNA were modified on the surface of the AuNPs through Au-S bonds. The linker DNA can partly hybridize with the aptamers of cancer cells loaded onto the magnetic beads (MB1) to construct the magnetic biocomplexes. In the presence of the cancer cells, the aptamers conjugated with the cancer cells with higher affinity. The ECL nanoprobe was released from the biocomplexes and subsequently hybridized with the capture DNA loaded onto another magnetic bead (MB2) to form the magnetic nanocomposite. The nanocomposites can be easily separated and firmly attached to an electrode on account of their excellent magnetic properties. The ECL intensity of the TBR loaded onto the nanocomposites directly reflected the amount of cancer cells. By using cell lines of Burkitt's lymphoma (Ramos cells) as a model, the ECL response was proportional to the cell concentration in the range from 5 to 100 cells ml(-1); a limit of detection as low as 5 cells ml(-1) of Ramos cells could be achieved. The proposed method described here is ideal for the diagnosis of cancers due to its high sensitivity, simplicity, and low cost.

Highly sensitive detection of platelet-derived growth factor on a functionalized diamond surface using aptamer sandwich design

Aptamer-based fluorescence detection of platelet-derived growth factor (PDGF) on a functionalized diamond surface was demonstrated. In this work, a sandwich design based on the ability of PDGF to bind with aptamers at its two available binding sites was employed. It was found that this sandwich design approach significantly increases the fluorescence signal intensity, and thereby a very low detection limit of 4 pM was achieved. The effect of the ionic strength of MgCl(2) buffer solution was also investigated, and the most favourable binding for PDGF-BB occurred at a Mg(2+) concentration of 5.5 mM. Since the aptamers bind to the target PDGF with high affinity, fluorescence detection exhibited high selectivity towards different biomolecules. The high reproducibility of detection was confirmed by performing three cycles of measurements over a period of three days.

Assays for aptamer-based platforms

Aptamers are single stranded DNA or RNA oligonucleotides that have high affinity and specificity towards a wide range of target molecules. Aptamers have low molecular weight, amenable to chemical modifications and exhibit stability undeterred by repetitive denaturation and renaturation. Owing to these indispensable advantages, aptamers have been implemented as molecular recognition element as alternative to antibodies in various assays for diagnostics. By amalgamating with a number of methods that can provide information on the aptamer-target complex formation, aptamers have become the elemental tool for numerous biosensor developments. In this review, administration of aptamers in applications involving assays of fluorescence, electrochemistry, nano-label and nano-constructs are discussed. Although detection strategies are different for various aptamer-based assays, the core of the design strategies is similar towards reporting the presence of specific target binding to the corresponding aptamers. It is prognosticated that aptamers will find even broader applications with the development of new methods of transducing aptamer target binding.

Highly sensitive chemiluminescence technology for protein detection using aptamer-based rolling circle amplification platform

A robust, selective and highly sensitive chemiluminescent (CL) platform for protein assay was presented in this paper. This novel CL approach utilized rolling circle amplification (RCA) as a signal enhancement technique and the 96-well plate as the immobilization and separation carrier. Typically, the antibody immobilized on the surface of 96-well plate was sandwiched with the protein target and the aptamer–primer sequence. This aptamer–primer sequence was then employed as the primer of RCA. Based on this design, a number of the biotinylated probes and streptavidin–horseradish peroxidase (SA–HRP) were captured on the plate, and the CL signal was amplified. In summary, our results demonstrated a robust biosensor with a detection limit of 10 fM that is easy to be established and utilized, and devoid of light source. Therefore, this new technique will broaden the perspective for future development of DNA-based biosensors for the detection of other protein biomarkers related to clinical diseases, by taking advantages of high sensitivity and selectivity.