Selective Evolution Of Ligands Research Articles

Aptasensors and Advancement in Molecular Recognition Technology

AbstractSynthetic oligonucleic acids known as aptamers exhibit remarkable selectivity and affinity for target recognition and binding. Selected via an iterative process known as “selective evolution of ligands by exponential enrichment” (SELEX), aptamers fold into defined 3D conformations to interact with their targets. The incorporation of aptamers as recognition elements has driven notable progress in biosensors, giving rise to the development of aptasensors. Here, the process of aptamer discovery and the development of various types of aptasensors are summarized. The fundamental design principles of aptasensors are elaborated along with the superiority of aptamers compared to antibodies. The various modes employed by aptasensors, such as structure‐switching design, hybridization chain reaction amplification, enzyme‐assisted recycling, and split aptamer design are examined. Further light is shed on the diverse landscape of aptasensors, their adaptability to different analytes aptasensors as well as their potential to propel advancements in modern biosensor technology. As a nucleic acids‐based biosensor platform, aptasensors poise to become a next generation of sensitive and cost‐effective technology to shape the future of molecular recognition in biosensing.

Generation and identification of novel DNA aptamers with antiviral activities against largemouth bass virus (LMBV)

Largemouth bass virus (LMBV) causes high mortality in largemouth bass, and results in serious economic loses in the aquaculture industry. However, there is no effective treatment to control LMBV infection. Aptamers are single-stranded oligonucleotides with high specificity and affinity to various targets, including viruses, viral components, and virus-infected cells. In this study, three novel DNA aptamers (LA38, LB49, and LA13), which specifically targeted LMBV, were identified by selective evolution of ligands by exponential enrichment. These aptamers formed stable stem-loop structures identified by secondary structures and minimum free energy predictions. Moreover, enzyme-linked apta-adsorption assays, dissociation constant (Kd) measurements, and flow cytometry analyses showed that these aptamers specifically bound to LMBV with high affinity at the nanomolar level. Furthermore, these aptamers were nontoxic, and significantly inhibited LMBV infection in vitro and in vivo. The mortality of largemouth bass was reduced approximately 40% after 10 days of infection by LMBV preincubated with LA38 or LB49, compared to that infected with wild or random ssDNA pretreated LMBV. In addition, confocal imaging and flow cytometry analyses indicated that these aptamers only entered cells along with LMBV, suggesting their potential as a delivery system. Presently, this is the first report of specific aptamers targeting iridovirus from freshwater fish. These aptamers have great potential in diagnosis and therapy, and in delivery agents for detecting LMBV infection.

An electrochemical aptamer-based biosensor targeting Plasmodium falciparum histidine-rich protein II for malaria diagnosis

Malaria is an infectious disease caused by parasitic protozoans from the genus Plasmodium, with the species P. falciparum causing the highest number of deaths worldwide. Rapid diagnostic tests (RDTs) have become critical in the management of malaria, but current RDTs that detect P. falciparum are primarily antibody-based, which can have drawbacks in cost and robustness. Here, we report the development of an electrochemical aptamer-based (E-AB) biosensing alternative. Through selective evolution of ligands by exponential enrichment, we identify DNA aptamers that bind specifically to P. falciparum histidine-rich protein II (PfHRP2). The aptamer is modified with a methylene blue reporter and attached to a gold sensor surface for square-wave voltammetry interrogation. Through this method we are able to quantify PfHRP2 in human serum with an LOD of 3.73 nM. We further demonstrate the biosensor is stable in serum buffers and reusable for multiple detection rounds. These findings provide a promising alternative to conventional PfHRP2 detection for malaria diagnosis, while also expanding the capabilities of E-AB biosensors.

RNA Aptamers Targeting Integrin α5β1 as Probes for Cyto- and Histofluorescence in Glioblastoma

Nucleic acid aptamers are often referred to as chemical antibodies. Because they possess several advantages, like their smaller size, temperature stability, ease of chemical modification, lack of immunogenicity and toxicity, and lower cost of production, aptamers are promising tools for clinical applications. Aptamers against cell surface protein biomarkers are of particular interest for cancer diagnosis and targeted therapy. In this study, we identified and characterized RNA aptamers targeting cells expressing integrin α5β1. This αβ heterodimeric cell surface receptor is implicated in tumor angiogenesis and solid tumor aggressiveness. In glioblastoma, integrin α5β1 expression is associated with an aggressive phenotype and a decrease in patient survival. We used a complex and original hybrid SELEX (selective evolution of ligands by exponential enrichment) strategy combining protein-SELEX cycles on the recombinant α5β1 protein, surrounded by cell-SELEX cycles using two different cell lines. We identified aptamer H02, able to differentiate, in cyto- and histofluorescence assays, glioblastoma cell lines, and tissues from patient-derived tumor xenografts according to their α5 expression levels. Aptamer H02 is therefore an interesting tool for glioblastoma tumor characterization.

DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection: Sequence-Affinity Relation.

Native DNA strongly adsorbs to citrate-coated gold nanoparticles (AuNPs). The resulting composites (DNA/AuNPs) are valuable materials in many fields, especially in biomedicine. For this reason, the process of adsorption is a focus for intensive research. In this work, DNA adsorption to gold nanoparticles was studied using a molecular selection procedure followed by high-throughput DNA sequencing. The chemically synthesized DNA library containing a central N26 randomized fragment was sieved through four cycles of adsorption to AuNPs in a tree-like selection-amplification scheme (SELEX (Selective Evolution of Ligands by EXponential enrichment)). The frequencies of occurrence of specific oligomeric DNA motifs, k-mers ( k = 1-6), in the initial and selected pools were calculated. Distribution of secondary structures in the pools was analyzed. A large set of diverse A, T, and G enriched k-mers undergo a pronounced positive selection, and these sequences demonstrate faster and strong binding to the AuNPs. For facile binding, such structural motifs should be located in the loop regions of weak intramolecular complexes-hairpins with imperfect stem, or other portion of the structure, which is unpaired under selection conditions. Our data also show that, under the conditions employed in this study, cytosine is significantly depleted during the selection process, although guanine remains unchanged. These regularities were confirmed in a series of binding experiments with a set of synthetic DNA oligonucleotides. The detailed analysis of DNA binding to AuNPs shows that the sequence specificity of this interaction is low due to its nature, although the presence and the number of specific structural motifs in DNA affect both the rate of formation and the strength of the formed noncovalent associates with AuNPs.

SAT-LB040 Measuring LH Pulsatility in Patients with Reproductive Disorders Using a Novel Robotic Aptamer-Enabled Electrochemical Reader (RAPTER)

Normal reproductive functioning is critically dependent on pulsatile secretion of LH. Assessment of LH pulsatility is important for the clinical diagnosis of patients with reproductive disorders, but this is not routinely available in the clinic because of the need for frequent blood sampling coupled with expensive serial immunochemical analysis. The emerging technology of electrochemical aptamer-based (E-AB) sensing could potentially offer a generalizable approach for LH pulsatility measurement in humans. E-AB sensors take advantage of the intrinsic properties of nucleic acid aptamers to specifically bind to a molecular target and undergo a reversible conformational change. The conformational change can be measured through the electrochemical signal response. Aptamers, unlike antibodies, can facilitate low-cost repeat analytical measurements. However, there is currently no aptamer-based LH sensing technology. Here, we report the development and application of a novel antibody-free DNA aptamer-mediated electrochemical analysis to accurately assess LH pulsatility in patients with reproductive disorders. Through selective evolution of ligands by exponential enrichment (SELEX), single-stranded DNA oligonucleotides (aptamers) were identified that bind specifically to LH (and that do not bind to the closely related FSH). The aptamers were integrated into E-AB sensors on a robotic platform (which we term RAPTER) to enable sensitive, rapid and repeatable detection of LH. We next determined if the RAPTER system could measure LH pulsatility in clinical samples from patients with reproductive disorders. We obtained 441 serum samples from 3 patient cohorts - young females with regular menstrual cycles (normal LH pulsatility), menopausal women (disordered LH pulsatility, high LH), and women with hypothalamic amenorrhoea (suppressed/ absent LH pulsatility, low LH). Blood sampling was performed every 10 minutes for 8 hours in these patients and samples were analysed using both the current gold standard LH immunochemical assay and RAPTER. We performed a Bland-Altman analysis and plotted the linear regression to compare the results obtained. The RAPTER assay showed an almost perfect correlation with the clinical immunochemical assay (R2= 0.94). Bayesian Spectrum Analysis was used to determine the effective LH pulse interval from both datasets (clinical assay and RAPTER assay). We are able to distinguish 3 patient cohorts based on the time interval ranges. Taken together, the RAPTER system provides a new approach for LH pulsatility determination by reliably and immediately calculating varying LH concentrations within distinct patient cohorts. This has the potential to transform the clinical care of patients with reproductive disorders as LH pulsatility could be measured easily in clinical practice to aid correct diagnosis. Unless otherwise noted, all abstracts presented at ENDO are embargoed until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. s presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.

Probing the Effects of Androgen and Glucocorticoid Receptor Sequences on DNA Binding Preferences

Prostate cancer is the second leading cause of cancer among men and although survival rates are high for regional tumors, it is estimated that almost 30,000 men will succumb to their diagnosis in 2018. Androgen hormones fuel prostate tumor growth by signaling through the androgen receptor (AR), a member of the nuclear receptor superfamily of transcription factors. Blocking androgen signaling through administration of antagonists (e.g bicalutamide, enzalutamide) or halting production of androgens through chemical or surgical castration arrests progression of the disease. Patients often relapse with castration resistant prostate cancer (CRPC) that continues to grow despite the lack of androgens. One mechanism of resistance is due to upregulation of a related nuclear receptor, the glucocorticoid receptor (GR). Because AR and GR have overlapping DNA binding specificities, GR is able to functionally substitute for AR at key disease genes. We have shown previously, using SELEX (Selective Evolution of Ligands by Exponential Enrichment) coupled with a novel computational algorithm (SelexGLM), that although AR and GR bind similar sequences, they recognize DNA differently. GR is less specific than AR, allowing it to accommodate predominantly AR sequences. To better understand the selectivity of AR and GR, and to identify the determinants of their specificity, we are measuring the sequence preference of AR and GR mutants using the No Read Left Behind (NRLB) method. As opposed to traditional SELEX, NRLB yields high resolution models of specificity with a single round of selection, which allows rapid screening of our mutants. We have over‐expressed and purified both the AR and GR DNA binding domains, and have designed hybrid mutants. Comparison of the DNA binding preferences of AR, GR and the hybrid molecules by NRLB should help uncover how GR might be playing a role in CRPC.Support or Funding InformationThis work was supported in part by the FUTURE program of the University of Iowa Carver College of Medicine.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Measuring luteinising hormone pulsatility with a robotic aptamer-enabled electrochemical reader

Normal reproductive functioning is critically dependent on pulsatile secretion of luteinising hormone (LH). Assessment of LH pulsatility is important for the clinical diagnosis of reproductive disorders, but current methods are hampered by frequent blood sampling coupled to expensive serial immunochemical analysis. Here, we report the development and application of a Robotic APTamer-enabled Electrochemical Reader (RAPTER) electrochemical analysis system to determine LH pulsatility. Through selective evolution of ligands by exponential enrichment (SELEX), we identify DNA aptamers that bind specifically to LH and not to related hormones. The aptamers are integrated into electrochemical aptamer-based (E-AB) sensors on a robotic platform. E-AB enables rapid, sensitive and repeatable determination of LH concentration profiles. Bayesian Spectrum Analysis is applied to determine LH pulsatility in three distinct patient cohorts. This technology has the potential to transform the clinical care of patients with reproductive disorders and could be developed to allow real-time in vivo hormone monitoring.

Selection of Nucleic Acid Aptamers Targeting Tumor Cell-Surface Protein Biomarkers.

Aptamers are nucleic acids referred to as chemical antibodies as they bind to their specific targets with high affinity and selectivity. They are selected via an iterative process known as ‘selective evolution of ligands by exponential enrichment’ (SELEX). Aptamers have been developed against numerous cancer targets and among them, many tumor cell-membrane protein biomarkers. The identification of aptamers targeting cell-surface proteins has mainly been performed by two different strategies: protein- and cell-based SELEX, when the targets used for selection were proteins and cells, respectively. This review aims to update the literature on aptamers targeting tumor cell surface protein biomarkers, highlighting potentials, pitfalls of protein- and cell-based selection processes and applications of such selected molecules. Aptamers as promising agents for diagnosis and therapeutic approaches in oncology are documented, as well as aptamers in clinical development.

Generation and characterization of novel DNA aptamers against coat protein of grouper nervous necrosis virus (GNNV) with antiviral activities and delivery potential in grouper cells

Nervous necrosis virus (NNV) infected larvae and juveniles of more than 50 fish species, resulting in mortality rates of greater than 95%. However, there is no efficient method to control NNV infections. Aptamers generated by selective evolution of ligands by exponential enrichment (SELEX) are short, single-stranded nucleic acid oligomers. They display a high degree of affinity and specificity for many targets, such as viruses and viral proteins. In this study, three novel DNA aptamers (A5, A10, and B11) that specifically target the coat protein (CP) of grouper nervous necrosis virus (GNNV) were selected using SELEX. Secondary structures and minimum free energy (ΔG) predictions indicated that these aptamers could form stable, secondary stem-loop structures. Electrophoretic mobility shift assays, enzyme-linked immunosorbent assays, Kd measurements, the co-localization of tetramethylrhodamine (TAMRA) labeled-aptamers with the CP and flow cytometry analysis revealed that these aptamers could specifically bind the CP with high (nanomolar) affinities. In addition, competition analysis suggested the aptamers shared some common CP binding sites with the anti-CP antibody. Moreover, all three aptamers did not show any cytotoxic effects in vitro or in vivo, and anti-viral analysis indicated the selected aptamers could inhibit NNV infection in vitro and in vivo. Compared with controls, mortality of GNNV-infected fish decreased by 40% and 80% after 10 days infection, when the GNNV was pre-incubated with the 1000 nM A10 and B11, respectively. TAMRA-labeled aptamers could bind to NNV virions and directly enter NNV-infected cells, suggesting they could be used as tracers to study the mechanism of viral infection, as well as for targeted therapy. This is the first time that aptamers targeting a viral protein of marine fish have been generated and characterized. These aptamers hold promise as diagnostic, therapeutic, and targeted drug delivery agents for controlling NNV infections.

Inhibition of hepatitis C virus infection by NS5A-specific aptamer

To increase efficacy of hepatitis C treatment, future regiments will incorporate multiple direct-acting antiviral drugs. HCV NS5A protein was expressed and purified. Aptamers against NS5A were screened and obtained by the selective evolution of ligands by exponential enrichment approach and the antiviral actions of the aptamers were tested. The mechanisms through which the aptamers exert their antiviral activity were explored. The aptamers NS5A-4 and NS5A-5 inhibit HCV RNA replication and infectious virus production without causing cytotoxicity in human hepatocytes. The aptamers do not affect hepatitis B virus replication in HepG2.2.15 cells. Interferon beta (IFN-β) and interferon-stimulated genes (ISGs) are not induced by the aptamers in HCV-infected hepatocytes. Further study shows that domain I and domain III of NS5A protein are involved in the suppression of HCV RNA replication and infectious virus production by NS5A-4. Y2105H within NS5A is the major resistance mutation identified. NS5A aptamer disrupts the interaction of NS5A with core protein. The data suggest that the aptamers against NS5A protein may exert antiviral effects through inhibiting viral RNA replication, preventing the interaction of NS5A with core protein. Aptamers for NS5A may be used to understand the mechanisms of virus replication and assembly and served as potential therapeutic agents for hepatitis C.

Selective Evolution of Ligands by Exponential Enrichment to Identify RNA Aptamers against Shiga Toxins.

Infection with Shiga toxin- (Stx-) producing E. coli causes life threatening hemolytic uremic syndrome (HUS), a leading cause of acute renal failure in children. Of the two antigenically distinct toxins, Stx1 and Stx2, Stx2 is more firmly linked with the development of HUS. In the present study, selective evolution of ligands by exponential enrichment (SELEX) was used in an attempt to identify RNA aptamers against Stx1 and Stx2. After 5 rounds of selection, significant enrichment of aptamer pool was obtained against Stx2, but not against Stx1, using a RNA aptamer library containing 56 random nucleotides (N56). Characterization of individual aptamer sequences revealed that six unique RNA aptamers (mA/pC, mB/pA, mC, mD, pB, and pD) recognized Stx2 in a filter binding assay. None of these aptamers bound Stx1. Aptamers mA/pC, mB/pA, mC, and mD, but not pB and pD, partially blocked binding of Alexa 488-labeled Stx2 with HeLa cells in a flow cytometry assay. However, none of the aptamers neutralized Stx2-mediated cytotoxicity and death of HeLa cells.

Inhibition of Hepatitis C Virus Production by Aptamers against the Core Protein

Hepatitis C virus (HCV) core protein is essential for virus assembly. HCV core protein was expressed and purified. Aptamers against core protein were raised through the selective evolution of ligands by the exponential enrichment approach. Detection of HCV infection by core aptamers and the antiviral activities of aptamers were characterized. The mechanism of their anti-HCV activity was determined. The data showed that selected aptamers against core specifically recognize the recombinant core protein but also can detect serum samples from hepatitis C patients. Aptamers have no effect on HCV RNA replication in the infectious cell culture system. However, the aptamers inhibit the production of infectious virus particles. Beta interferon (IFN-β) and interferon-stimulated genes (ISGs) are not induced in virally infected hepatocytes by aptamers. Domains I and II of core protein are involved in the inhibition of infectious virus production by the aptamers. V31A within core is the major resistance mutation identified. Further study shows that the aptamers disrupt the localization of core with lipid droplets and NS5A and perturb the association of core protein with viral RNA. The data suggest that aptamers against HCV core protein inhibit infectious virus production by disrupting the localization of core with lipid droplets and NS5A and preventing the association of core protein with viral RNA. The aptamers for core protein may be used to understand the mechanisms of virus assembly. Core-specific aptamers may hold promise for development as early diagnostic reagents and potential therapeutic agents for chronic hepatitis C.

Aptamers: An in vitro Evolution of Therapeutic and Diagnostic Applications in Medicine

Aptamers are nucleic acid oligomers with distinct conformational shapes that allow binding targets with high affinity and specificity. Selective Evolution of Ligands by Exponential Enrichment (SELEX); an in vitro selection process to develop aptamers, has been invented in 1990. Despite more than 20 years have passed after its discovery, products of SELEX technology are in use in medicine. In this review we discuss why we need aptamers not only in therapeutic but also in diagnostic applications; and also critical points in SELEX technology. Finally; we present the aptamers in use and some patented aptamers awaiting approval.

A DNA Aptamer Prevents Influenza Infection by Blocking the Receptor Binding Region of the Viral Hemagglutinin

Influenza A virus infection is a major source of morbidity and mortality worldwide. Current means of control for influenza are based on prophylaxis by vaccines and on treatment by the available specific influenza neuraminidase inhibitor drugs. The approach taken in the present study is to prevent and/or ameliorate influenza infection by site-specific blocking of the viral binding to host cell receptors. We describe a novel oligonucleotide, known also as an aptamer, which has been designed to complement the receptor-binding region of the influenza hemagglutinin molecule. It was constructed by screening a DNA library and processing by the selective evolution of ligands by exponential enrichment (SELEX) procedure. We show that this DNA aptamer is indeed capable of inhibiting the hemagglutinin capacity of the virus, as well as in the prevention of viral infectivity in vitro, in tissue culture. Furthermore, it inhibits viral infection by different influenza strains in an animal model, as manifested by 90-99% reduction of virus burden in the lungs of treated mice. The mode of action of this aptamer is by blocking the binding of influenza virus to target cell receptors and consequently prevention of the virus invasion into the host cells.