Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food

Aptamers as a kind of biological recognition element have shown great potential in monitoring and the rapid quantification of organophosphorus pesticides(OPPs). However, molecules of OPPs are structurally similar and original aptamers selected by systematic evolution of ligands by exponential enrichment are usually long-chain bases, which hamper the further application under OPPs-aptamer recognition. The aim of the research was to develop a new strategy to design oligonucleotide sequences for binding OPPs by combination of experimental and molecular modeling methods. 3D models of aptamers binding OPPs were constructed, and binding energy and the most probable binding site for the OPPs were then determined by molecular docking, and the binding sites were further confirmed by the results of 2-AP replaced experiments. Based on the docking results, a new aptamer for detection 4 representative OPPs with only 29 bases was designed by reasonable truncation and mutation of the reported aptamer(named S4-29). The interaction between this new aptamer and OPPs were analyzed by molecular docking, microscale thermophoresis, circular dichroism and fluorometric analysis. The results revealed that the new aptamer exhibit more superior recognition performance to OPPs, which can be promote the monitoring ability of OPPs contaminations in food.

Electrochemical Biosensor for Detection of Staphylococcus aureus Based on Nucleic Acid Aptamers

Staphylococcus aureus is a gram-staining positive cocci bacillus baterium and also one of the foodborne pathogens, which is a serious potential hazard to human health and food safety. We constructed an electrochemical biosensor for the detection of S. aureus based on nucleic acid aptamers to achieve highly specific detection of S. aureus. The detection of S. aureus was realized by using Aptamer (Apt) to capture S. aureus, which resulted in a change in the spatial conformation of Apt and a decrease in the electrochemical signal. Under the optimized experimental conditions, the detected electrochemical signals were positively correlated with the concentration of S. aureus with a linear range of 1 × 101 - 1 × 105 CFU/mL, a detection limit of 4.76 CFU/mL, and an experimental recovery of 97.43% - 99.37%. Therefore, we successfully constructed an electrochemical biosensor for the specific detection of S. aureus, which has the advantages of high specificity, sensitive detection and convenient operation.

Aptamers Against Viral Hepatitis:from Rational Design to Practical Application

Aptamers are short nucleic acids or peptides that strongly bind to a protein of interest and functionally inhibit a given target protein at the intracellular level. Besides high affinity and specificity, aptamers have several advantages over traditional antibodies. Hence, they have been broadly selected to develop antiviral agents for therapeutic applications against hepatitis B and C viruses (HBV, HCV). This review provides a summary of in vitro selection and characterization of aptamers against viral hepatitis, which is of practical significance in drug discovery.

In vitro Selection of DNA Aptamers and Fluorescence-Based Recognition for Rapid Detection Listeria monocytogenes

Aptamers are specific nucleic acid sequences that can bind to a wide range of nucleic acid and non-nucleic acid targets with high affinity and specificity. Nucleic acid aptamers are selected in vitro from single stranded DNA or RNA ligands containing random sequences of up to a few hundred nucleotides. Systematic evolution of ligands by exponential enrichment （SELEX） was used to select and PCR amplify DNA sequences （aptamers） capable of binding to and detecting Listeria monocytogenes, one of the major food-borne pathogens. A simplified affinity separation approach was employed, in which L. monocytogenes in exponential （log） phase of growth was used as the separation target. A fluorescently-labeled aptamer assay scheme was devised for detecting L. monoeytogenes. This report described a novel approach to the detection of L. monocytogenes using DNA aptamers. Aptamers were developed by nine rounds of SELEX. A high affinity aptamer was successfully selected from the initial random DNA pool, and its secondary structure was also investigated. One of aptamers named e01 with the highest affinity was further tested in aptamer-peroxidase and aptamer-fluorescence staining protocols. This study has proved the principle that the whole-cell SELEX could be a promising technique to design aptamer-based molecular probes for dectection of pathogenic microorganisms without tedious isolation and purification of complex markers or targets.

Evolution of specific RNA aptamers via SELEX targeting recombinant human CD36 protein:A candidate therapeutic target in severe malaria

Objective:To isolate and characterize RNA aptamers that are specific to human CD36 protein using systematic evolution of ligands by exponential enrichment(SELEX)technology to identify candidates for adjunct therapy to reverse the binding of Plasmodiuminfected erythrocytes.Methods:RNA aptamers were isolated using nitrocellulose membrane-based SELEX and binding analysis was screened using an electrophoretic mobility shift assay and enzyme-linked oligonucleotide assay.Results:Thirteen cycles of nitrocellulose membrane-based SELEX yielded three aptamers(RC60,RC25,RC04)exhibiting high binding against CD36 protein as shown on electrophoretic mobility shift assay.The sequence analysis revealed a G-quadruplex sequence within all the isolated aptamers that might contribute to aptamer binding and thermodynamic stability.The specificity assay further showed that RC60 and RC25 were highly specific to CD36.The competitive inhibition assay demonstrated that RC60 and RC25 shared a similar binding epitope recognized by m Ab FA6-152,a specific monoclonal antibody against CD36.Conclusions:RC60 and RC25 are promising candidates as anticytoadherence for severe malaria adjunct therapy.

Aptamers—A Promising Approach for Sensing of Biothreats Using Different Bioinformatics Tools

Intentional release of pathogens or biotoxin against humans, plants, or animals is an impending threat all over the world. Continuous monitoring of environment is required for their detection. These signals can help to distinguish whether the bioattack has occurred or not. Biosensors utilise biological response including different biochemical reactions, antigen antibody reactions, electrochemical reactions, aptameric reactions etc. The currently available biosensors have a limit of detection, specificity and less linearity which affect their sensitivity. Aptamers are single stranded oligonucleotides binding species which are capable of tightly binding to their distinguishing targets. They are evolved from random oligonucleotides pools by using different strategies. These are capable of conscientiously distinguishing their target ligands. They have high sensitivity and a wide range of detection limit. The versatility of nucleic acid based methods allowed for the design of specific aptamer sequences, typically on the order of 10 to 30 base pairs in length, identifying the different biothreat agents in the environment. By using different bioinformatics tools we can design RNA aptamers for toxins of lectin family.

Screening of aptamers and their potential application in targeted diagnosis and therapy of liver cancer

Aptamers are a class of single oligonucleotide molecules(DNA or RNA)that are screened from random DNA or RNA oligonucleotide chain libraries by the systemic evolution of ligands by exponential enrichment technology.The selected aptamers are capable of specifically binding to different targeting molecules,which is achieved by the three-dimensional structure of aptamers.Aptamers are similar in function to monoclonal antibodies,and therefore,they are also referred to as"chemical antibodies".Due to their high affinity and specificity and low immunogenicity,aptamers are topics of intense interest in today's biological targeting research especially in tumor research.They not only have high potential for clinical advances in tumor targeting detection but also are highly promising as targeted tumor drug carriers for use in tumor therapy.Various experimental studies have shown that aptamer-based diagnostic and therapeutic methods for liver cancer have great potential for application.This paper summarizes the structure,characteristics,and screening methods of aptamers and reviews the recent research progress on nucleic acid aptamers in the targeted diagnosis and treatment of liver cancer.

Development of HBsAg-Binding Aptamers that bind HepG2.2.15 cells via HBV surface antigen

Hepatitis B virus surface antigen （HBsAg）, a specific antigen on the membrane of Hepatitis B virus （HBV）-infected cells, provides a perfect target for therapeutic drugs. The development of reagents with high affinity and specificity to the HBsAg is of great significance to the early-stage diagnosis and treatment of HBV infection. Herein, we report the selection of RNA aptamers that can specifically bind to HBsAg protein and HBsAg-positive hepatocytes. One high affinity aptamer, HBs-A22, was isolated from an initial 115 met library of -1.1 ×10^15 random-sequence RNA molecules using the SELEX procedure. The selected aptamer HBs-A22 bound specifically to hepatoma cell line HepG2.2.15 that expresses HBsAg but did not bind to HBsAg-devoid HepG2 cells. This is the first reported RNA aptamer which could bind to a HBV specific antigen. This newly isolated aptamer could be modified to deliver imaging, diagnostic, and therapeutic agents targeted at HBV-infected cells.

Nucleic Acid Aptamers as Potential Therapeutic and Diagnostic Agents for Lymphoma

Lymphomas are cancers that arise from white blood cells and usually present as solid tumors. Treatment of lymphoma often involves chemotherapy, and can also include radiotherapy and/or bone marrow transplantation. There is an unquestioned need for more effective therapies and diagnostic tool for lymphoma. Aptamers are single stranded DNA or RNA oligonucleotides whose three-dimensional structures are dictated by their sequences. The immense diversity in function and structure of nucleic acids enable numerous aptamers to be generated through an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers have several biochemical properties that make them attractive tools for use as potential diagnostic and pharmacologic agents. Isolated aptamers may directly inhibit the function of target proteins, or they can also be formulated for use as delivery agents for other therapeutic or imaging cargoes. More complex aptamer identification methods, using whole cancer cells (Cell-SELEX), may identify novel targets and aptamers to affect them. This review focuses on recent advances in the use of nucleic acid aptamers as diagnostic and therapeutic agents and as targeted delivery carriers that are relevant to lymphoma. Some representative examples are also discussed.

Electrochemical biosensors and logic devices based on aptamers

Aptamers are molecular recognition elements with high specificity that are selected from deoxyribonucleic acid/ribonucleic acid (DNA/RNA) library. Compared with the traditional protein recognition elements,aptamers have excellent properties such as cost-effective,stable,easy for synthesis and modification. In recent years,electrochemistry plays an important role in biosensor field because of its high sensitivity,high stability, fast response and easy miniaturization. Through the combination of these two technologies and our rational design,we constructed a series of biosensors and biochips that are simple,fast,cheap and miniaturized. Firstly,we designed an adenosine triphosphate (ATP) electrochemical biosensor based on the strand displacement strategy. We can detect as low as 10 nmol/L of ATP both in pure solution and complicated cell lysates. Secondly,we creatively split the aptamers into two fragments and constructed the sandwich assay platform only based on single aptamer sequence. We successfully transferred this design on biochips with multiple micro electrodes (6×6) and accomplished multiplex detection. In the fields of biochips and biocomputers,we designed several DNA logic gates with electric (electrochemical) signal as output which paves a new way for the development of DNA computer.

Molecular recognition of live methicillin-resistant staphylococcus aureus cells using DNA aptamers

AIM: To generate DNA-aptamers binding to Methicillinresistant Staphylococcus aureus(MRSA).METHODS: The Cell-Systematic Evolution of Ligands by Exponential Enrichment(SELEX) technology was used to run the selection against MRSA bacteria and develop target-specific aptamers. MRSA bacteria were targeted while Enterococcus faecalis bacteria were used for counter selection during that process. Binding assays to determine the right aptamer candidates as well as binding assays on clinical samples were performed through flow cytometry and analyzed using the FlowJ o software. The characterization of the aptamers was done by determination of their Kd values and determined by analysis of flow data at different aptamer concentration using Sigma Plot. Finally, the recognitionof the complex Gold-nanoparticle-aptamer to the bacteria cells was observed using transmission electron microscopy(TEM).RESULTS: During the cell-SELEX selection process, 17 rounds were necessary to generate enrichment of the pool. While the selection was run using fixed cells, it was shown that the binding of the pools with live cells was giving similar results. After sequencing and analysis of the two last pools, four sequences were identified to be aptamer candidates. The characterization of those aptamers showed that based on their Kd values, DTMRSA4 presented the best binding with a Kd value of 94.61 ± 18.82 nmol/L. A total of ten clinical samples of MRSA, S. aureus and Enterococcus faecalis were obtained to test those aptamers and determine their binding on a panel of samples. DTMRSA1 and DTMRSA3 showed the best results regarding their specificity to MRSA, DTMRSA1 being the most specific of all. Finally, those aptamers were coupled with gold-nanoparticle and their binding to MRSA cells was visualized through TEM showing that adduction of nanoparticles on the aptamers did not change their binding property.CONCLUSION: A total of four aptamers that bind to MRSA were obtained with Kd values ranking from 94 to 200 nmol/L.

Monoclonal antibodies and aptamers:The future therapeutics for Alzheimer’s disease

Alzheimer’s disease(AD)is considered the most common and prevalent form of dementia of adult-onset with characteristic progressive impairment in cognition and memory.The cure for AD has not been found yet and the treatments available until recently were only symptomatic.Regardless of multidisciplinary approaches and efforts made by pharmaceutical companies,it was only in the past two years that new drugs were approved for the treatment of the disease.Amyloid beta(Aβ)immunotherapy is at the core of this therapy,which is one of the most innovative approaches looking to change the course of AD.This technology is based on synthetic peptides or monoclonal antibodies(mAb)to reduce Ab levels in the brain and slow down the advance of neurodegeneration.Hence,this article reviews the state of the art about AD neuropathogenesis,the traditional pharmacologic treatment,as well as the modern active and passive immunization describing approved drugs,and drug prototypes currently under investigation in different clinical trials.In addition,future perspectives on immunotherapeutic strategies for AD and the rise of the aptamer technology as a non-immunogenic alternative to curb the disease progression are discussed.

Automated screening of primary cell-based aptamers for targeting and therapy of pancreatic cancer

Although it has been developed for many years, nucleic acid aptamer screening technology still fails to be widely used, a considerable part of it is due to the variability of tumor cell morphology, which leads to the use of immortalized cell lines in the laboratory to screen nucleic acid aptamers for recognition ability of tumor cells in the diseased body.To address this, primary cells that can be stably passaged were isolated and extracted from spontaneous tumors of genetically engineered pancreatic ductal adenocarcinoma model mice in this study.Next, an automated screening instrument for nucleic acid aptamers developed autonomously by our group was used to perform efficient aptamer screening using a limited number of cells, and the obtained nucleic acid aptamers were affinity verified at the cellular level.Finally, to answer the question of the cell growth environment difference on the recognition ability of nucleic acid aptamers, we verified its targeting ability to tumors in vivo on a nude mice xenograft tumor model, and further used a common antitumor drug doxorubicin combined with nucleic acid aptamers to verify the drug loading ability of this aptamer combined with the targeting therapeutic ability.

Selecting small molecule DNA aptamers with significant conformational changes for constructing transcriptional switches and biosensors

Small molecule aptamers discovered by traditional selection methods usually lack conformational changes upon target binding.This limits the use of aptamers as molecular probes for small molecule detection and regulatory elements of genetic circuits.Here,we report a new method called capture and in vitro transcription-systematic evolution of ligands by exponential enrichment(CIVT-SELEX)to select DNA aptamers that can not only bind to small molecule ligands but also undergo significant conformational changes.Through this method,we select a structure-switching aptamer of uridine-5′-diphosphate(UDP).Taking advantage of its conformational changes,we first construct a UDP-responsive transcriptional switch by inserting the aptamer in a genetic circuit and demonstrate that it can respond to the addition of UDP and regulate the transcription of downstream genes.We also build a UDP aptamer-based biosensor that can be used for active glycosyltransferase screening.We believe this method can provide a universal platform for selecting small molecule aptamers with conformational changes and expand the use of aptamers in small molecule detection and genetic regulation.

Capture-SELEX for Chloramphenicol Binding Aptamers for Labeled and Label-Free Fluorescence Sensing

Chloramphenicol(CAP)is a potent antibiotic.Due to its side effects,CAP is currently banned in most countries,but it is still found in many food products and in the environment.Developing aptamer-based biosensors for the detection of CAP has interested many researchers.While both RNA and DNA aptamers were previously reported for CAP,they were all obtained by immobilization of the CAP base,which omitted the two chlorine atoms.In this work,DNA aptamers were selected using the libraryimmobilized method and free unmodified CAP.Three families of aptamers were obtained,and the best one named CAP1 showed a dissociation constant(K_(d))of 9.8μM using isothermal titration calorimetry(ITC).A fluorescent strand-displacement sensor showed a limit of detection(LOD)of 14μM CAP.Thioflavin T(ThT)staining allowed label-free detection of CAP with a LOD of 1μM in buffer,1.8μM in Lake Ontario water,and 3.6μM in a wastewater sample.Comparisons were made with previously reported aptamers,and ITC failed to show binding of a previously reported 80-mer aptamer.Due to the small size and well-defined secondary structures of CAP1,this aptamer will find analytical applications for environmental and food monitoring.

High Mannose-Specific Aptamers for Broad-Spectrum Virus Inhibition and Cancer Targeting

High mannose oligosaccharides are characteristic and essential for immune evasion of many viruses and cancer cells.They are potential targets for viral inhibition and cancer diagnosis/therapy.Particularly,high mannose-binding reagents may be a unique asset for fighting the ongoing and mutating SARSCoV-2 virus.Lectins are prevailing reagents for saccharide binding but suffer from inadequate specificity and apparent immunogenicity.Meanwhile,other reagents for the same purpose,such as antibodies and aptamers,have rarely been reported.Herein,using molecularly imprinted magnetic nanoparticles as a potent platform,we report a smart selection method for fine screening of high mannose-specific aptamers.Monovalent aptamers were first effectively screened within eight rounds of selection.Multivalent aptamers,in the forms of dendritic polymer or tetrahedral DNA nanostructure(TDN),were further engineered.The aptamers exhibited high affinity toward the spike protein of SARS-CoV-2 and the envelope protein GP120 of HIV.Both the monovalent aptamer and its TDN form exhibited a certain inhibition effect to the SARS-CoV-2 pseudovirus.On the other hand,both the monovalent aptamer and its dendritic form permitted the recognition of cancer cells over normal cells.Therefore,as unprecedented reagents for broad-spectrum viral inhibition and cancer targeting,these aptamers hold great promise for clinical treatment and diagnosis.

Systematic bio‑fabrication of aptamers and their applications in engineering biology

Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets.Compared to antibodies,aptamers are easy to in vitro synthesize with low cost,and exhibit excellent thermal stability and programmability.With these features,aptamers have been widely used in biology and medicine-related fields.In the meantime,a variety of systematic evolution of ligands by exponential enrichment(SELEX)technologies have been developed to screen aptamers for various targets.According to the characteristics of targets,customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity.In this review,we first summarize the latest research on the systematic bio-fabrication of aptamers,including various SELEX technologies,post-SELEX optimization,and aptamer modification technology.These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers.The latter provides a new perspective for the systems bio-fabrication of aptamers.Furthermore,on this basis,we review the applications of aptamers,particularly in the fields of engineering biology,including industrial biotechnology,medical and health engineering,and environmental and food safety monitoring.And the encountered challenges and prospects are discussed,providing an outlook for the future development of aptamers.

A core-satellite self-assembled SERS aptasensor containing a“biological-silent region”Raman tag for the accurate and ultrasensitive detection of histamine

Herein,a novel interference-free surface-enhanced Raman spectroscopy(SERS)strategy based on magnetic nanoparticles(MNPs)and aptamer-driven assemblies was proposed for the ultrasensitive detection of histamine.A core-satellite SERS aptasensor was constructed by combining aptamer-decorated Fe_(3)O_(4)@Au MNPs(as the recognize probe for histamine)and complementary DNA-modified silver nanoparticles carrying 4-mercaptobenzonitrile(4-MBN)(Ag@4-MBN@Ag-c-DNA)as the SERS signal probe for the indirect detection of histamine.Under an applied magnetic field in the absence of histamine,the assembly gave an intense Raman signal at“Raman biological-silent”region due to 4-MBN.In the presence of histamine,the Ag@4-MBN@Ag-c-DNA SERS-tag was released from the Fe_(3)O_(4)@Au MNPs,thus decreasing the SERS signal.Under optimal conditions,an ultra-low limit of detection of 0.65×10^(-3)ng/mL and a linear range 10^(-2)-10^5 ng/mL on the SERS aptasensor were obtained.The histamine content in four food samples were analyzed using the SERS aptasensor,with the results consistent with those determined by high performance liquid chromatography.The present work highlights the merits of indirect strategies for the ultrasensitive and highly selective SERS detection of small biological molecules in complex matrices.

Applications of aptamers for chemistry analysis, medicine and food security

Since aptamer and its in vitro selection process called SELEX were independently described by Ellington and Gold in 1990, extensive research has been undertaken and numerous isolated aptamers for various targets have been applied. Aptamers can bind to a wide range of targets that include small organic molecules, inorganic compounds, haptens and even whole cells with high binding affinity and specificity. Aptamers for a wide range of targets have been selected currently. In addition, aptamers are thermo stable and can also be regenerated easily within a few minutes denaturation, which makes them easy to store or handle. These advantages make aptamers extremely suitable for applications based on molecular recognition as analytical, diagnostic and therapeutic tools. In this review, the recent applications of aptamers for chemistry analysis, medicine and food security, along with the future trend will be discussed.

Peptide aptamers:The versatile role of specific protein function inhibitors in plant biotechnology

In recent years, peptide aptamers have emerged as novel molecular tools that have attracted the attention of researchers in various fields of basic and applied science, ranging from medicine to analytical chemistry. These artificial short peptides are able to specifically bind, track, and inhibit a given target molecule with high affinity, even molecules with poor immunogenicity or high toxicity, and represent a remarkable alternative to antibodies in many different applications. Their use is on the rise, driven mainly by the medical and pharmaceutical sector. Here we discuss the enormous potential of peptide aptamers in both basic and applied aspects of plant biotechnology and food safety. The different peptide aptamer selection methods available both in vivo and in vitro are introduced, and the most important possible applications in plant biotechnology are illustrated. In particular, we discuss the generation of broad- based virus resistance in crops, ＂reverse genetics＂ and aptasensors in bioassays for detecting contaminations in food and feed. Furthermore, we suggest an alternative to the transfer of peptide aptamers into plant cells via genetic transformation, based on the use of cell-penetrating peptides that overcome the limits imposed by both crop transformation and Genetically Modified Organism commercialization.