Recent developments in protein and cell-targeted aptamer selection and applications

Efficiency of electrochemical immuno- vs. apta(geno)sensors for multiple cancer biomarkers detection

The interest in biosensors technology has been constantly growing over the last few years. It is still the biggest challenge to design biosensors able to detect two or more analytes in a single measurement. Electrochemical methods are frequently used for this purpose, mainly due to the possibility of applying two or more different redox labels characterized by independent and distinguished electrochemical signals. In addition to antibodies, nucleic acids (aptamers) have been increasingly used as bioreceptors in the construction of such sensors. Within this review paper, we have collected the examples of electrochemical immuno- and geno(apta)sensors for simultaneous detection of multiple analytes. Based on many published literature examples, we have emphasized the recent application of multiplexed platforms for detection of cancer biomarkers. It has allowed us to compare the progress in design strategies, including novel nanomaterials and amplification of signals, to get as low as possible limits of detection. We have focused on multi-electrode and multi-label strategies based on redox-active labels, such as ferrocene, anthraquinone, methylene blue, thionine, hemin and quantum dots, or metal ions such as Ag+, Pb2+, Cd2+, Zn2+, Cu2+ and others. We have finally discussed the possible way of development, challenges and prospects in the area of multianalyte electrochemical immuno- and geno(apta)sensors.

New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers

Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches.

Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis

The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.

Novel Nanotherapeutics for Cancer Immunotherapy by PD-L1-Aptamer-Functionalized and Fexofenadine-Loaded Albumin Nanoparticles

Immune checkpoint blockade (ICB) is an important strategy for cancer treatment and has achieved remarkable clinical results. Further enhancement of the efficacy of ICB therapy with a new technical approach is of potential medical importance. In this study, we constructed a novel nanotherapeutic agent (PDL1-NP-FEXO) for cancer immunotherapy by attaching PD-L1 aptamers to albumin nanoparticles that were loaded with H1-antihitamine fexofenadine (FEXO). FEXO has been reported to enhance the immunotherapy response by reducing the immunosuppressive M2-like macrophages in the tumor microenvironment. The albumin nanoparticle was fabricated using a self-assembly method. A dynamic light scattering (DLS) study revealed that the average size of PD-L1 aptamer-modified nanoparticle without FEXO (PDL1-NP) was 135.5 nm, while that of PDL1-NP-FEXO was 154.6 nm. Similar to free PD-L1 aptamer, PDL1-NP could also bind with PD-L1-expressing tumor cells (MDA-MB-231). Of note, compared with free PD-L1 aptamer, PDL1-NP significantly boosted tumor inhibition in CT26-bearing mice. Moreover, PDL1-NP-FEXO further enhanced the antitumor efficacy vs. PDL1-NP in an animal model, without raising systemic toxicity. These results indicate that PDL1-NP-FEXO represents a promising strategy to improve ICB efficacy and may have application potential in cancer immunotherapy.

Aptamer-based rapid diagnosis for point-of-care application

Aptasensors have attracted considerable interest and widespread application in point-of-care testing worldwide. One of the biggest challenges of a point-of-care (POC) is the reduction of treatment time compared to central facilities that diagnose and monitor the applications. Over the past decades, biosensors have been introduced that offer more reliable, cost-effective, and accurate detection methods. Aptamer-based biosensors have unprecedented advantages over biosensors that use natural receptors such as antibodies and enzymes. In the current epidemic, point-of-care testing (POCT) is advantageous because it is easy to use, more accessible, faster to detect, and has high accuracy and sensitivity, reducing the burden of testing on healthcare systems. POCT is beneficial for daily epidemic control as well as early detection and treatment. This review provides detailed information on the various design strategies and virus detection methods using aptamer-based sensors. In addition, we discussed the importance of different aptamers and their detection principles. Aptasensors with higher sensitivity, specificity, and flexibility are critically discussed to establish simple, cost-effective, and rapid detection methods. POC-based aptasensors' diagnostic applications are classified and summarised based on infectious and infectious diseases. Finally, the design factors to be considered are outlined to meet the future of rapid POC-based sensors.

Aptamers as Smart Ligands for Targeted Drug Delivery in Cancer Therapy

Undesirable side effects and multidrug tolerance are the main holdbacks to the treatment of cancer in conventional chemotherapy. Fortunately, targeted drug delivery can improve the enrichment of drugs at the target site and reduce toxicity to normal tissues and cells. A targeted drug delivery system is usually composed of a nanocarrier and a targeting component. The targeting component is called a "ligand". Aptamers have high target affinity and specificity, which are identified as attractive and promising ligands. Therefore, aptamers have potential application in the development of smart targeting systems. For instance, aptamers are able to efficiently recognize tumor markers such as nucleolin, mucin, and epidermal growth factor receptor (EGFR). Besides, aptamers can also identify glycoproteins on the surface of tumor cells. Thus, the aptamer-mediated targeted drug delivery system has received extensive attention in the application of cancer therapy. This article reviews the application of aptamers as smart ligands for targeted drug delivery in cancer therapy. Special interest is focused on aptamers as smart ligands, aptamer-conjugated nanocarriers, aptamer targeting strategy for tumor microenvironment (TME), and aptamers that are specified to crucial cancer biomarkers for targeted drug delivery.

Recent Advances in Solid-Phase Extraction as a Platform for Sample Preparation in Biomarker Assay

Low levels of biomarkers and the complexity of bio sample make the analytical assay of several biomarkers a challenging issue. Suitable sample preparation run remain a vital part of the puzzle of diagnostic level. Enhancing the detection limit of bioanalytical methods start during the sample preparation procedure. A robust sample preparation method is needed to evaluate the number of biomarkers. As worldwide environmental issues attract expanding consideration, all the more harmless to the ecosystem investigations are liked. Solid-phase extraction (SPE) is an appealing strategy among the sample treatment methods due to the versatility of sorbent materials, less solvent consumption, and compatibility with analytical devices. Miniaturization of the SPE gives the chance to integrate the other analytical steps in a single run, known as an easy-to-use and effective method. SPE utilizes various SPE sorbent beds such as packed beads, porous polymer monoliths, molecularly imprinted polymers, membranes, or other magnetic form microstructures to achieve high surface-to-volume ratio and appropriate chemical properties effective extraction. Also, SPE is the methodology of interest to fulfill high recovery and efficiency demands. In this review, we intend to explain more recent methods for the rational design of SPE and miniaturized SPE to determine biomarkers from biological media. The headlines are subdivided into (1) packing materials in SPE, (2) setups for sample preparation by magnetic SPE, and (3) and future perspective for the application of SPE in sample preparation for analysis of biomarkers.

Novel Complex of PD-L1 Aptamer and Albumin Enhances Antitumor Efficacy In Vivo

The PD-1/PD-L1 pathway blockade can generate a good clinical response by reducing immunosuppression and provoking durable antitumor immunity. In addition to antibodies, aptamers can also block the interaction between PD-1 and PD-L1. For the in vivo application, however, free aptamers are usually too small in size and quickly removed from blood via glomerular filtration. To avoid renal clearance of aptamer, we conjugated the PD-L1 aptamer to albumin to form a larger complex (BSA-Apt) and evaluated whether BSA-Apt would enhance the in vivo antitumor efficacy. The PD-L1 aptamer was thiol-modified and conjugated to the amino group of BSA via a SMCC linker. The average size of BSA-Apt was 11.65 nm, which was above the threshold for renal clearance. Functionally, BSA-Apt retained the capability of the PD-L1 aptamer to bind with PDL1-expressing tumor cells. Moreover, both the free aptamer and BSA-Apt augmented the PBMC-induced antitumor cytotoxicity in vitro. Furthermore, BSA-Apt generated a significantly stronger antitumor efficacy than the free PD-L1 aptamer in vivo without raising systemic toxicity. The results indicate that conjugating the PD-L1 aptamer to albumin may serve as a promising strategy to improve the in vivo functionality of the aptamer and that BSA-Apt may have application potential in cancer immunotherapy.

Molecular probes for cellular imaging of post-translational proteoforms

Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.

ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes

We demonstrate early progress toward constructing a high-throughput, single-molecule protein sequencing technology utilizing barcoded DNA aptamers (binders) to recognize terminal amino acids of peptides (targets) tethered on a next-generation sequencing chip. DNA binders deposit unique, amino acid-identifying barcodes on the chip. The end goal is that, over multiple binding cycles, a sequential chain of DNA barcodes will identify the amino acid sequence of a peptide. Toward this, we demonstrate successful target identification with two sets of target-binder pairs: DNA-DNA and Peptide-Protein. For DNA-DNA binding, we show assembly and sequencing of DNA barcodes over six consecutive binding cycles. Intriguingly, our computational simulation predicts that a small set of semi-selective DNA binders offers significant coverage of the human proteome. Toward this end, we introduce a binder discovery pipeline that ultimately could merge with the chip assay into a technology called ProtSeq, for future high-throughput, single-molecule protein sequencing.

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Designed ProtSeq protein sequencing method compatible with widely used NGS technology

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Built Target-Switch SELEX to isolate aptamers specific to N-terminal amino acids (AAs)

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Showed binding, ligation, cleavage, and NGS of six DNA binders in ordered barcode chain

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Developed pipeline to deconvolve AAs from DNA barcodes to identify putative proteins

Advances in Design Strategies of Multiplex Electrochemical Aptasensors

In recent years, the need for simple, fast, and economical detection of food and environmental contaminants, and the necessity to monitor biomarkers of different diseases have considerably accelerated the development of biosensor technology. However, designing biosensors capable of simultaneous determination of two or more analytes in a single measurement, for example on a single working electrode in single solution, is still a great challenge. On the other hand, such analysis offers many advantages compared to single analyte tests, such as cost per test, labor, throughput, and convenience. Because of the high sensitivity and scalability of the electrochemical detection systems on the one hand and the specificity of aptamers on the other, the electrochemical aptasensors are considered to be highly effective devices for simultaneous detection of multiple-target analytes. In this review, we describe and evaluate multi-label approaches based on (1) metal quantum dots and metal ions, (2) redox labels, and (3) enzyme labels. We focus on recently developed strategies for multiplex sensing using electrochemical aptasensors. Furthermore, we emphasize the use of different nanomaterials in the construction of these aptasensors. Based on examples from the existing literature, we highlight recent applications of multiplexed detection platforms in clinical diagnostics, food control, and environmental monitoring. Finally, we discuss the advantages and disadvantages of the aptasensors developed so far, and debate possible challenges and prospects.

Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection

The coronavirus disease 2019 (COVID-19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for distinct viral proteins are critical components for rapid diagnostics and targeted therapeutics. In this work, we demonstrate the selection of novel DNA aptamers that bind to the SARS-CoV-2 spike glycoprotein with high specificity and affinity (<80 nM). Through binding assays and high resolution cryo-EM, we demonstrate that SNAP1 (SARS-CoV-2 spike protein N-terminal domain-binding aptamer 1) binds to the S N-terminal domain. We applied SNAP1 in lateral flow assays (LFAs) and ELISAs to detect UV-inactivated SARS-CoV-2 at concentrations as low as 5×105  copies mL-1 . SNAP1 is therefore a promising molecular tool for SARS-CoV-2 diagnostics.

A DNA Aptameric Ligand of Human Transferrin Receptor Generated by Cell-SELEX

General cancer-targeted ligands that can deliver drugs to cells have been given considerable attention. In this paper, a high-affinity DNA aptamer (HG1) generally binding to human tumor cells was evolved by cell-SELEX, and was further optimized to have 35 deoxynucleotides (HG1-9). Aptamer HG1-9 could be taken up by live cells, and its target protein on a cell was identified to be human transferrin receptor (TfR). As a man-made ligand of TfR, aptamer HG1-9 was demonstrated to bind at the same site of human TfR as transferrin with comparable binding affinity, and was proved to cross the epithelium barrier through transferrin receptor-mediated transcytosis. These results suggest that aptamer HG1-9 holds potential as a promising ligand to develop general cancer-targeted diagnostics and therapeutics.

Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles

The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.

An ultra-sensitive optical aptasensor based on gold nanoparticles/poly vinyl alcohol hydrogel as acceptor/emitter pair for fluorometric detection of digoxin with on/off/on strategy

A novel nanobiosensor was prepared by aptamer and gold nanoparticles conjugate in poly vinyl alcohol hydrogel for sensitive detection of digoxin in human plasma samples. The developed nanobiosensor was characterized by Fourier transform infrared spectroscopy, transmission electron microscopy, and dynamic light scattering instrument. In this sensor the hydrogel acted as a fluorescent probe. The fluorescence intensity of the hydrogel was quenched by aptamer stabilized gold nanoparticles as energy acceptor. Upon addition of digoxin, the aptamer/drug complex was formed and the fluorescence of the hydrogel was restored because of destabilization and aggregation of gold nanoparticles in the presence of salt. The affecting parameters on the nanobiosensor performance were assessed and under the optimized conditions the external and in plasma calibration curves were linear in the 10-1000 ng L^-1 digoxin concentration range with detection limits of 2.9 and 3.1 ng L^-1, respectively. The relative standard deviations for 5 replicate determinations of 50, 250, and 500 ng L^-1 of digoxin, were 7.3, 5.1, and 3.8%, respectively. This nanofluoroprobe was successfully applied for determination of digoxin in spiked plasma samples without any pretreatment procedure.

Single-Strand DNA-Like Oligonucleotide Aptamer Against Proprotein Convertase Subtilisin/Kexin 9 Using CE-SELEX: PCSK9 Targeting Selection

BACKGROUND

Proprotein convertase subtilisin/kexin 9 (PCSK9) serves a key regulatory function in the metabolism of low-density lipoprotein (LDL)-cholesterol (LDL-C) through interaction with the LDL receptor (LDLR) followed by its destruction that results in the elevation of the plasma levels of LDL-C. The aims of the present study were to separate and select a number of single-stranded DNA (ssDNA) aptamers against PCSK9 from a library pool (n > 10¹²) followed by their characterization.

METHODS

The aptamers obtained from the DNA-PCSK9 complexes which presented the highest affinity against PCSK9 were separated and selected using capillary electrophoresis evolution of ligands by exponential enrichment (CE-SELEX). The selected aptamers were amplified and cloned into a T/A vector. The plasmids from the positive clones were extracted and sequenced. The Mfold web server was used to predict the secondary structure of the aptamers.

RESULTS

Following three rounds of CE-SELEX, the identified anti-PCSK9 ssDNA aptamers, namely aptamer 1 (AP-1) and aptamer 2 (AP-2), presented half maximal inhibitory concentrations of 325 and 327 nM, lowest dissociation constants of 294 and 323 nM, and most negative Gibbs free energy values of - 9.17 and - 8.28 kcal/mol, respectively.

CONCLUSION

The results indicated that the selected aptamers (AP-1 and AP-2) induced potent inhibitory effects against PCSK9. Further in vivo studies demand to find out AP-1 and AP-2 aptamers as suitable candidates, instead of antibodies, for using in therapeutic purposes in patients with hypercholesterolemia and cardiovascular disease.

Identification and Application of an Aptamer Targeting Papillary Thyroid Carcinoma Using Tissue-SELEX

Aptamers, short DNA or RNA oligonucleotides, which evolved from systematic evolution of ligands by exponential enrichment (SELEX), can perform specific target recognition. Papillary thyroid carcinoma (PTC) is of high incidence worldwide, and the prognosis of advanced PTC is poor. Up to now, there is no specific biomarker that can identify PTC and defects still remain in existing diagnostic methods. Here we report an aptamer, termed TC-6, which is generated from tissue-SELEX by using sections of papillary thyroid carcinoma and a normal thyroid gland. TC-6 could specifically target intracellular components of papillary thyroid cells with high affinity ( K_d = 57.66 ± 5.93 nmol/L) and have performed excellent biocompatibility both in vivo and in vitro. Moreover, fluorescence imaging of PTC tumor-bearing mice revealed that TC-6 was able to accumulate in tumor sites and could distinguish thyroid carcinoma from other benign thyroid diseases efficiently. In addition, TC-6d, a truncated aptamer of TC-6, maintained its affinity toward PTC with K_d of 39.20 ± 8.20 nmol/L. Overall, these results indicate that TC-6 is a potential candidate for developing novel tools for diagnosis and targeted therapy of PTC.

Selection of a novel DNA aptamer against OFA/iLRP for targeted delivery of doxorubicin to AML cells

The standard treatment for most acute myeloid leukemia (AML) is chemotherapy, which is often associated with severe adverse effects. One strategy to reduce the adverse effects is targeted therapy that can selectively deliver anticancer drugs to tumor cells. Immature laminin receptor protein (OFA/iLRP) is a potential target for AML treatment, because it is over-expressed on the surface of AML cells but under-expressed in normal tissue. In this study, we developed the first aptamer for OFA/iLRP and explored its potential as a targeting ligand for delivery of doxorubicin (Dox) to AML cells in vitro. The selected aptamer (AB3) was a 59-base DNA oligonucleotides. It bound to OFA/iLRP structure with a K_d of 101 nM and had minimal cross-reactivity to albumin, trypsin, or ovalbumin. Moreover, AB3 could bind to OFA/iLRP-positive AML cells but not the OFA/iLRP-negative control cells. An aptamer-doxorubicin (Apt-Dox) complex was formed by intercalating doxorubicin into the DNA structure of AB3. Apt-Dox selectively delivered Dox to OFA/iLRP-positive AML cells but notably decreased the drug intake by OFA/iLRP-negative control cells. In addition, cytotoxicity study revealed that Apt-Dox efficaciously destroyed the OFA/iLRP-positive AML cells, but significantly reduced the damage to control cells. The results indicate that the OFA/iLRP aptamer AB3 may have application potential in targeted therapy against AML.

A DNA aptamer recognizing MMP14 for in vivo and in vitro imaging identified by cell-SELEX

A key challenge for the management of various types of cancer, including pancreatic cancer and hepatocellular carcinoma, is accurate diagnosis at an early stage. Matrix metalloproteinase 14 (MMP14) is overexpressed in numerous types of cancer and is associated with poor prognosis. Therefore, MMP14-specific imaging probes have potential use in the diagnosis of MMP14-positive cancer. Aptamers are short oligonucleotide sequences that can bind to molecular targets with a high specificity and affinity. Aptamers are typically obtained from an in vitro library; this process is usually termed systematic evolution of ligands by exponential enrichment (SELEX). In the present study, a DNA aptamer targeting MMP14 was obtained by cell-SELEX and termed M17, which specifically recognizes MMP14-positive cells. Aptamer M17 selectively binds to membrane proteins of MMP14-transfected 293T cells (Kd, 4.98±1.26 nM). Pancreatic cancer cell imaging suggested that aptamer M17 can bind to the cell membranes of two pancreatic cancer cell lines (MIA PaCa-2 and PANC-1). In vivo tumor imaging demonstrated that the targeting recognition of MIA PaCa-2 tumor cells in mice could be visualized using Cy5-labeled aptamer M17. Aptamer M17-conjugated polyethylene glycol-Fe3O4 can specifically bind to MIA PaCa-2 and PANC-1 cells, and reduce MRI T2-weighted imaging signal intensity. The DNA aptamer M17 has the advantages of simplicity of synthesis, small size, low immunogenicity, high penetrability and high affinity. Therefore, aptamer M17 is a potential molecular probe for the diagnosis and treatment of MMP14-positive cancer.

A novel aptamer-based online magnetic solid phase extraction method for simultaneous determination of urinary 8-hydroxy-2'-deoxyguanosine and monohydroxylated polycyclic aromatic hydrocarbons

In this work, an innovative aptamer-based magnetic adsorbent (Fe₃O₄@PDA-aptamer MNPs) was prepared by hydrothermal synthesis method followed by the surface functionalization of nanoparticles. After fixing in a steel stainless tube as sorbent of magnetic solid phase extraction (MSPE), an online magnetic solid phase extraction-high performance liquid chromatography-mass spectrometry (online-MSPE-HPLC-MS) method was developed and applied for the determination of 8-hydroxy-2'-deoxyguanosine (8-OHdG) and monohydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) simultaneously in urine. The synthesized sorbent presented outstanding features, including large specific surface area, high enrichment capacity and excellent stability. High throughput analysis can be achieved by affinity-specific adsorption of 8-OHdG and non-specific adsorption of OH-PAHs at the same time. In addition, online MSPE can greatly simplify the analysis process, reduce human errors and enhance the sensitivity. When compared with offline MSPE, a sensitivity enhancement of 30-400 times was obtained for the online method. Some experimental parameters such as the amount of the sorbent, sampling flow rate and sample volume, were optimized systematically. Under the optimal conditions, the limits of detection (LOD) were in the range of 0.028-0.114 ng mL^-1, and the correlation coefficients (R²) were higher than 0.9962. The relative standard deviations (RSDs) were less than 16.1% (n = 5) and the recoveries ranged from 71% to 116%. The above results show that the rapid, sensitive and automated online-MSPE-HPLC-MS method has potential application in the simultaneous determination of 8-OHdG and PAHs in complex sample matrix to assess the environmental exposure level.

Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development

Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.

In vitro selection of DNA aptamers recognizing drug-resistant ovarian cancer by cell-SELEX

Ovarian cancer is regarded as the most lethal gynecologic malignancy with poor prognosis and high mortality rate. Drug-resistance was thought to be the main obstacle to improving overall survival rate of ovarian cancer. New ligands for drug-resistant ovarian cancer cells have potential for the development of diagnosis and therapy of ovarian cancer. In present work, we reported two aptamers, HF3-58 and HA5-68 generated by cell-SELEX, against a paclitaxel-resistant ovarian cancer cell line (A2780T). Both two aptamers exhibited high selectivity and strong affinity to target cells with low nanomolar dissociation constants. The binding of aptamers to target cells was independent of divalent ions, and was tolerant of incubation temperature and nucleases in serum. Molecular targets of the two aptamers were preliminarily demonstrated to be two different glycoproteins on cell surface of A2780T cells. Owing to the structure stability and high resistance to nuclease, these two aptamers had good performance in the detection of drug-resistant ovarian cancer cells in human serum.

Competition-Enhanced Ligand Selection to Identify DNA Aptamers

Competition-enhanced ligand screening (CompELS) was employed to rapidly screen through large DNA libraries to identify single-stranded, oligonucleotide-based ligands called aptamers that bind to a nonbiological target. This previously unreported aptamer screening approach involves the repeated introduction of unenriched random sequence populations during the biopanning process, but avoids iterative elution and polymerase chain reaction (PCR) amplification steps inherent to traditional SELEX (systematic evolution of ligands by exponential enrichment) screening. In this study, 25 aptamers were identified against a gold surface via CompELS and evaluated to identify patterns in primary structures and predicted secondary structures. Following a final one-round competition experiment with the 25 identified aptamers, one particular aptamer sequence (1N) emerged as the most competitive adsorbate species for the gold substrate. Binding analysis indicated at least an order of magnitude difference in the binding affinity of 1N ( K_d = 5.6 × 10^-10 M) compared to five other high affinity aptamer candidates ( K_d = 10^-8-10^-9 M) from identical secondary structure families. Collectively, these studies introduce a rapid, reliable screening and ranking platform along with a classification scheme well-suited for identifying and characterizing aptamers for nonbiological as well as biological targets.

A novel aptamer-based online magnetic solid phase extraction method for the selective determination of 8-hydroxy-2'-deoxyguanosine in human urine

In this work, an innovative magnetic aptamer adsorbent (Fe₃O₄-aptamer MNPs) was synthesized for the selective extraction of 8-hydroxy-2'-deoxyguanosine (8-OHdG). Amino-functionalized-Fe₃O₄ was crosslinked with 8-OHdG aptamer by glutaraldehyde and fixed into a steel stainless tube as the sorbent of magnetic solid phase extraction (MSPE). After selective extraction by the aptamer adsorbent, the adsorbed 8-OHdG was desorbed dynamically and online analyzed by high performance liquid chromatography-mass spectrometry (HPLC-MS). The synthesized sorbent presented outstanding features, including specific selectivity, high enrichment capacity, stability and biocompatibility. Moreover, this proposed MSPE-HPLC-MS can achieve adsorption and desorption operation integration, greatly simplify the analysis process and reduce human errors. When compared with offline MSPE, a sensitivity enhancement of 800 times was obtained for the online method. Some experimental parameters such as the amount of the sorbent, sample flow rate and sample volume, were optimized systematically. Under the optimal conditions, low limit of detection (0.01 ng mL^-1, S/N = 3), limit of quantity (0.03 ng mL^-1, S/N = 10) and wide linear range with a satisfactory correlation coefficient (R² ≥ 0.9992) were obtained. And the recoveries of 8-OHdG in the urine samples varied from 82% to 116%. All these results revealed that the method is simple, rapid, selective, sensitive and automated, and it could be expected to become a potential approach for the selective determination of trace 8-OHdG in complex urinary samples.

Selection and characterization of DNA aptamer against glucagon receptor by cell-SELEX

Excessive secretion of glucagon, a functional insulin antagonist, significantly contributes to hyperglycemia. Glucagon exerts its physiological functions through activation of the glucagon receptor (GCGR). Inhibition of GCGR activity represents a potential therapeutic approach for reducing excess glucose production in diabetes mellitus. Aptamers are short DNA or RNA oligonucleotides evolved from systematic evolution of ligands by exponential enrichment (SELEX). Here, we have successfully selected a DNA aptamer against GCGR by cell-SELEX, which can specifically bind membrane protein of CHO-GCGR cells with a K_d of 52.7 ± 5.1 nM. Aptamer-mediated pull-down and gcgr knockdown assay verified that GCGR was the target of aptamer GR-3. Binding analysis revealed that GR-3 could recognize other cells with different affinity according to the level of GCGR protein expressed in these cells. Hepatic tissue imaging suggested that GR-3 could bind the cell membrane of hepatic tissues. With the advantages of small size, high binding affinity, good stability, lack of immunogenicity, and easy synthesis, aptamer GR-3 against GCGR can be a promising tool with the potential to attenuate hyperglycemia in diabetes mellitus.

Versatile aptasensor for electrochemical quantification of cell surface glycan and naked-eye tracking glycolytic inhibition in living cells

Quantifying the glycan expression status on cell surfaces is of vital importance for insight into the glycan function in biological processes and related diseases. Here we developed a versatile aptasensor for electrochemical quantification of cell surface glycan by taking advantage of the cell-specific aptamer, and the lectin-functionalized gold nanoparticles acting as both a glycan recognition unit and a signal amplification probe. To construct the aptasensor, amine-functionalized mucin 1 protein (MUC1) aptamer was first covalently conjugated to carboxylated-magnetic beads (MBs) using the succinimide coupling (EDC-NHS) method. On the basis of the specific recognition between aptamer and MUC1 protein that overexpressed on the surface of MCF-7 cells, the aptamer conjugated MBs showed a predominant capability for cell capture with high selectivity. Moreover, a lectin-based nanoprobe was designed by noncovalent assembly of concanavalin A (ConA) on gold nanoparticles (AuNPs). This nanoprobe incorporated the abilities of both the specific carbohydrate recognition and the signal amplification based on the gold-promoted reduction of silver ions. By coupling with electrochemical stripping analysis, the proposed sandwich-type cytosensor showed an excellent analytical performance for the ultrasensitive detection of MCF-7 cells and quantification of cell surface glycan. More importantly, taking advantage of Con A-gold nanoprobe catalyzed silver enhancement, the proposed method was further used for naked-eye tracking glycolytic inhibition in living cells. This aptasensor holds great promise as a new point-of-care diagnostic tool for analyzing glycan expression on living cells and further helps cancer diagnosis and treatment.

Applications of aptamers in targeted imaging: state of the art

Aptamers are single-stranded oligonucleotides with high affinity and specificity to the target molecules or cells, thus they can serve as an important category of molecular targeting ligand. Since their discovery, aptamers have been rapidly translated into clinical practice. The strong target affinity/selectivity, cost-effectivity, chemical versatility and safety of aptamers are superior to traditional peptides- or proteins-based ligands which make them unique choices for molecular imaging. Therefore, aptamers are considered to be extremely useful to guide various imaging contrast agents to the target tissues or cells for optical, magnetic resonance, nuclear, computed tomography, ultrasound and multimodality imaging. This review aims to provide an overview of aptamers' advantages as targeting ligands and their application in targeted imaging. Further research in synthesis of new types of aptamers and their conjugation with new categories of contrast agents is required to develop clinically translatable aptamer-based imaging agents which will eventually result in improved patient care.

Label-free aptamer biosensor for thrombin detection based on functionalized graphene nanocomposites

A label-free and amplified electrochemical impedimetric aptasensor based on functionalized graphene nanocomposites (rGO-AuNPs) was developed for the detection of thrombin, which played a vital role in thrombosis and hemostasis. The thiolated aptamer and dithiothreitol (TBA15-DTT) were firstly immobilized on the gold electrode to capture the thrombin molecules, and then aptamer functionalized graphene nanocomposites (rGO-TBA29) were used to fabricate a sandwich sensing platform for amplifying the impedimetric signals. As numerous negative charges of TBA29 on the electrode repelled to the [Fe(CN)6](4-/3-) anions, resulting in an obvious amplified charge-transfer resistance (Rct) signal. The Rct increase was linearly proportional to the thrombin concentration from 0.3 to 50nM and a detection limit of 0.01nM thrombin was achieved. In addition, graphene could also be labeled with other probes via electrostatic or π-π stacking interactions to produce signals, therefore different detection methods expanding wide application could be used in this model.

Electrogenerated chemiluminescence aptasensor for ultrasensitive detection of thrombin incorporating an auxiliary probe

A novel electrogenerated chemiluminescence (ECL) aptasensor for ultrasensitive detection of thrombin incorporating an auxiliary probe was designed by employing specific anti-thrombin aptamer as a capture probe and a ruthenium(II) complex-tagged reporter probe as an ECL probe and an auxiliary probe to assist the ECL probe close to the surface of the electrode. The ECL aptasensor was fabricated by self-assembling a thiolated capture probe on the surface of gold electrode and then hybridizing the ECL probe with the capture probe, and further self-assembling the auxiliary probe. When analyte thrombin was bound with the capture probe, the part of the dehybridized ECL probe was hybridized with the neighboring auxiliary probe, led to the tagged ruthenium(II) complex close to the electrode surface, resulted in great increase in the ECL intensity. The results showed that the increased ECL intensity was directly related to the logarithm of thrombin concentrations in the range from 5.0 × 10(-15)M to 5.0 × 10(-12)M with a detection limit of 2.0 × 10(-15)M. This work demonstrates that employing an auxiliary probe which exists nearby the capture probe can enhance the sensitivity of the ECL aptasensor. This promising strategy will be extended to the design of other biosensors for detection of other proteins and genes.

Selection of aptamers for mature white adipocytes by cell SELEX using flow cytometry

BACKGROUND

Adipose tissue, mainly composed of adipocytes, plays an important role in metabolism by regulating energy homeostasis. Obesity is primarily caused by an abundance of adipose tissue. Therefore, specific targeting of adipose tissue is critical during the treatment of obesity, and plays a major role in overcoming it. However, the knowledge of cell-surface markers specific to adipocytes is limited.

METHODS AND RESULTS

We applied the CELL SELEX (Systematic Evolution of Ligands by EXponential enrichment) method using flow cytometry to isolate molecular probes for specific recognition of adipocytes. The aptamer library, a mixture of FITC-tagged single-stranded random DNAs, is used as a source for acquiring molecular probes. With the increasing number of selection cycles, there was a steady increase in the fluorescence intensity toward mature adipocytes. Through 12 rounds of SELEX, enriched aptamers showing specific recognition toward mature 3T3-L1 adipocyte cells were isolated. Among these, two aptamers (MA-33 and 91) were able to selectively bind to mature adipocytes with an equilibrium dissociation constant (Kd) in the nanomolar range. These aptamers did not bind to preadipocytes or other cell lines (such as HeLa, HEK-293, or C2C12 cells). Additionally, it was confirmed that MA-33 and 91 can distinguish between mature primary white and primary brown adipocytes.

CONCLUSIONS

These selected aptamers have the potential to be applied as markers for detecting mature white adipocytes and monitoring adipogenesis, and could emerge as an important tool in the treatment of obesity.

Blocking interaction of viral gp120 and CD4-expressing T cells by single-stranded DNA aptamers

To investigate the potential clinical application of aptamers to prevention of HIV infection, single-stranded DNA (ssDNA) aptamers specific for CD4 were developed using the systematic evolution of ligands by exponential enrichment approach and next generation sequencing. In contrast to RNA-based aptamers, the developed ssDNA aptamers were stable in human serum up to 12h. Cell binding assays revealed that the aptamers specifically targeted CD4-expressing cells with high binding affinity (Kd=1.59nM), a concentration within the range required for therapeutic application. Importantly, the aptamers selectively bound CD4 on human cells and disrupted the interaction of viral gp120 to CD4 receptors, which is a prerequisite step of HIV-1 infection. Functional studies showed that the aptamer polymers significantly blocked binding of viral gp120 to CD4-expressing cells by up to 70% inhibition. These findings provide a new approach to prevent HIV-1 transmission using oligonucleotide aptamers.

Aptamer-based therapeutics: new approaches to combat human viral diseases

Viruses replicate inside the cells of an organism and continuously evolve to contend with an ever-changing environment. Many life-threatening diseases, such as AIDS, SARS, hepatitis and some cancers, are caused by viruses. Because viruses have small genome sizes and high mutability, there is currently a lack of and an urgent need for effective treatment for many viral pathogens. One approach that has recently received much attention is aptamer-based therapeutics. Aptamer technology has high target specificity and versatility, i.e., any viral proteins could potentially be targeted. Consequently, new aptamer-based therapeutics have the potential to lead a revolution in the development of anti-infective drugs. Additionally, aptamers can potentially bind any targets and any pathogen that is theoretically amenable to rapid targeting, making aptamers invaluable tools for treating a wide range of diseases. This review will provide a broad, comprehensive overview of viral therapies that use aptamers. The aptamer selection process will be described, followed by an explanation of the potential for treating virus infection by aptamers. Recent progress and prospective use of aptamers against a large variety of human viruses, such as HIV-1, HCV, HBV, SCoV, Rabies virus, HPV, HSV and influenza virus, with particular focus on clinical development of aptamers will also be described. Finally, we will discuss the challenges of advancing antiviral aptamer therapeutics and prospects for future success.

The novel amyloid-beta peptide aptamer inhibits intracellular amyloid-beta peptide toxicity

Amyloid β peptide binding alcohol dehydrogenase (ABAD) decoy peptide (DP) can competitively antagonize binding of amyloid β peptide to ABAD and inhibit the cytotoxic effects of amyloid β peptide. Based on peptide aptamers, the present study inserted ABAD-DP into the disulfide bond of human thioredoxin (TRX) using molecular cloning technique to construct a fusion gene that can express the TRX1-ABAD-DP-TRX2 aptamer. Moreover, adeno-associated virus was used to allow its stable expression. Immunofluorescent staining revealed the co-expression of the transduced fusion gene TRX1-ABAD-DP-TRX2 and amyloid β peptide in NIH-3T3 cells, indicating that the TRX1-ABAD-DP-TRX2 aptamer can bind amyloid β peptide within cells. In addition, cell morphology and MTT results suggested that TRX1-ABAD-DP-TRX2 attenuated amyloid β peptide-induced SH-SY5Y cell injury and improved cell viability. These findings confirmed the possibility of constructing TRX-based peptide aptamer using ABAD-DP. Moreover, TRX1-ABAD-DP-TRX2 inhibited the cytotoxic effect of amyloid β peptide.

Aptamers: problems, solutions and prospects

Aptamers are short single-stranded oligonucleotides that are capable of binding various molecules with high affinity and specificity. When the technology of aptamer selection was developed almost a quarter of a century ago, a suggestion was immediately put forward that it might be a revolutionary start into solving many problems associated with diagnostics and the therapy of diseases. However, multiple attempts to use aptamers in practice, although sometimes successful, have been generally much less efficient than had been expected initially. This review is mostly devoted not to the successful use of aptamers but to the problems impeding the widespread application of aptamers in diagnostics and therapy, as well as to approaches that could considerably expand the range of aptamer application.

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 un-questioned 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.

Sensitive and antifouling impedimetric aptasensor for the determination of thrombin in undiluted serum sample

A highly sensitive and attractive antifouling impedimetric aptasensor for the determination of thrombin in undiluted serum sample was developed. The aptasensor was fabricated by co-assembling thiol-modified anti-thrombin binding aptamer, dithiothreitol and mercaptohexanol on the surface of gold electrode. The performance of aptasensor was characterized by atomic force microscopy, contact angle and electrochemical impedance spectroscopy. In the measurement of thrombin, the change in interfacial electron transfer resistance of aptasensor was monitored using a redox couple of Fe(CN)(6)(3-/4-). The increase in the electron transfer resistance was linearly proportional to the concentration of thrombin in the range from 1.0 to 20ng/mL and a detection limit of 0.3ng/mL thrombin was achieved. The fabricated aptasensor displayed attractive antifouling properties and allowed direct quantification of extrinsic thrombin down to 0.08ng/mL in undiluted serum sample. This work provides a promising strategy for clinical application with impressive sensitivity and antifouling characteristics.