Generation Of Aptamers Research Articles

CD28 Aptamers as Powerful Immune Response Modulators

CD28 is one of the main costimulatory receptors responsible for the proper activation of T lymphocytes. We have isolated two aptamers that bind to the CD28 receptor. As a monomer, one of them interfered with the binding of CD28 to its ligand (B7), precluding the costimulatory signal, whereas the other one was inactive. However, dimerization of any of the anti-CD28 aptamers was sufficient to provide an artificial costimulatory signal. No antibody has featured a dual function (i.e., the ability to work as agonist and antagonist) to date. Two different agonistic structures were engineered for each anti-CD28 aptamer. One showed remarkably improved costimulatory properties, surpassing the agonistic effect of an anti-CD28 antibody. Moreover, we showed in vivo that the CD28 agonistic aptamer is capable of enhancing the cellular immune response against a lymphoma idiotype and of prolonging survival of mice which receive the aptamer together with an idiotype vaccine. The CD28 aptamers described in this work could be used to modulate the immune response either blocking the interaction with B7 or enhancing vaccine-induced immune responses in cancer immunotherapy.

Pan‐Selective Aptamers for the Family of Small GTPases

Pan‐Selective Aptamers for the Family of Small GTPases

One round of SELEX for the generation of DNA aptamers directed against KLK6

Kallikrein-related peptidase 6 (KLK6) is an active serine protease that has been implicated in common pathologies, including neurodegenerative disorders such as Parkinson and Alzheimer disease and certain types of cancer. Antibodies, either polyclonal or monoclonal, that exhibit specificity for distinct members of the extended kallikrein family, including KLK6, were developed. With the exception of KLK3/PSA, the identification and generation of aptamers, as potential new tools with improved characteristics demanded for therapeutic and diagnostic applications, has not been explored for KLKs. Here, we report for the first time the identification of novel DNA aptamers against KLK6 that were isolated using a modified systemic evolution of ligands by exponential enrichment technique. The identified aptamers were characterized using fluorescence spectroscopy, competition ELISA, and quartz crystal microbalance, and two aptamers (008 and 022) were found to exhibit high affinity (K(d) in the low nanomolar range) for KLK6. Aptamers were tested for their ability to bind to serum albumin, to demonstrate their specificity for their target, and the possible involvement of such proteins in the transport of aptamers into the bloodstream. The developed aptamers are expected to assist the development of novel diagnostic, biosensing, and therapeutic strategies.

Single-stranded DNA (ssDNA) production in DNA aptamer generation

The discovery that synthetic short chain nucleic acids are capable of selective binding to biological targets has made them to be widely used as molecular recognition elements. These nucleic acids, called aptamers, are comprised of two types, DNA and RNA aptamers, where the DNA aptamer is preferred over the latter due to its stability, making it widely used in a number of applications. However, the success of the DNA selection process through Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments is very much dependent on its most critical step, which is the conversion of the dsDNA to ssDNA. There is a plethora of methods available in generating ssDNA from the corresponding dsDNA. These include asymmetric PCR, biotin-streptavidin separation, lambda exonuclease digestion and size separation on denaturing-urea PAGE. Herein, different methods of ssDNA generation following the PCR amplification step in SELEX are reviewed.

Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels.

The generation of nucleic acid aptamers with high affinity typically entails a time-consuming, iterative process of binding, separation, and amplification. It would therefore be beneficial to develop an efficient selection strategy that can generate these high-quality aptamers rapidly, economically, and reproducibly. Toward this goal, we have developed a method that efficiently generates DNA aptamers with slow off-rates. This methodology, called VDC-MSELEX, pairs the volume dilution challenge process with microfluidic separation for magnetic bead-assisted aptamer selection. This method offers improved aptamer selection efficiencies through the application of highly stringent selection conditions: it retrieves a small number (<10(6)) of magnetic beads suspended in a large volume (>50 mL) and concentrates them into a microfluidic chamber (8 μL) with minimal loss for continuous washing. We performed three rounds of the VDC-MSELEX using streptavidin (SA) as the target and obtained new DNA aptamer sequences with low nanomolar affinity that specifically bind to the SA proteins.

Bi-specific Aptamers Mediating Tumor Cell Lysis

Antibody-dependent cellular cytotoxicity plays a pivotal role in antibody-based tumor therapies and is based on the recruitment of natural killer cells to antibody-bound tumor cells via binding of the Fcγ receptor III (CD16). Here we describe the generation of chimeric DNA aptamers that simultaneously bind to CD16α and c-Met, a receptor that is overexpressed in many tumors. By application of the systematic evolution of ligands by exponential enrichment (SELEX) method, CD16α specific DNA aptamers were isolated that bound with high specificity and affinity (91 pm-195 nm) to their respective recombinant and cellularly expressed target proteins. Two optimized CD16α specific aptamers were coupled to each of two c-Met specific aptamers using different linkers. Bi-specific aptamers retained suitable binding properties and displayed simultaneous binding to both antigens. Moreover, they mediated cellular cytotoxicity dependent on aptamer and effector cell concentration. Displacement of a bi-specific aptamer from CD16α by competing antibody 3G8 reduced cytotoxicity and confirmed the proposed mode of action. These results represent the first gain of a tumor-effective function of two distinct oligonucleotides by linkage into a bi-specific aptamer mediating cellular cytotoxicity.

Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery

BackgroundThe interrogation of proteomes (“proteomics”) in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine.Methodology/Principal FindingsWe present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma). Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (∼100 fM–1 µM), and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states.Conclusions/SignificanceWe describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.

A Novel Unstructured Scaffold Based on 4EBP1 Enables the Functional Display of a Wide Range of Bioactive Peptides

Target validation using protein aptamers enables the characterization of a specific function of a target protein in an environment that resembles native conditions as closely as possible. A major obstacle to the use of this technology has been the generation of bioactive aptamers, which is dependent on the choice of scaffold. Constraining binding peptides within a particular scaffold does not necessarily result in binding aptamers, as suboptimal presentation of peptides can occur. It is therefore understandable that different peptides might require different scaffolds for optimal presentation. In this article, we describe a novel scaffold protein that bypasses the conventional requirement for scaffolds to have known rigid structures and yet successfully presents several peptides that need to adopt a wide range of conformations for binding to their target protein. Using an unstructured protein, 4EBP1, as scaffold, we successfully construct binding aptamers to three different target proteins: Mdm2, proliferating cell nuclear antigen, and cyclin A. The Mdm2-binding aptamer constructed using 4EBP1 as scaffold demonstrates better stability and bioactivity compared to that constructed using thioredoxin as scaffold. This new scaffold protein, which makes it relatively easy to create bioactive aptamers based on known interaction sequences, will greatly facilitate the aptamer approach to target validation.

Selection of aptamers for a non-DNA binding protein in the context of cell lysate

Aptamer-facilitated Protein Isolation from Cells (AptaPIC) is a recently introduced method that allows, in particular, generation of aptamers for a protein target in a context of a crude cell lysate. The approach enables efficient, tag-free, affinity purification of target proteins which are not available in a pure form a priori, and for which no affinity ligands are available. In the proof-of-principle work, AptaPIC was used to develop aptamers for and purify MutS, a DNA mismatch repair protein. The DNA-binding nature of MutS raised concerns that AptaPIC was not a generic technique and could be inapplicable to protein targets that do not possess native nucleic acid-binding properties. Here we prove that these concerns are invalid. We used AptaPIC to generate pools of aptamers for human Platelet-Derived Growth Factor chain B (PDGF-B) protein, a non-DNA binding protein, in the context of a bacterial cell lysate, and subsequently purify it from the same lysate. Within a small number of rounds, the efficiencies of aptamer selection were similar in conventional Systematic Evolution of Ligands by Exponential Enrichment (SELEX) for pure protein and in AptaPIC for protein in the cell lysate. The conventional selection approach resulted in an aptamer pool with an EC 50 value of 2.0 ± 0.1 μM, while the AptaPIC selection approach resulted in a pool with an EC 50 value of 3.9 ± 0.4 μM. Our results clearly demonstrate that selection of aptamers for proteins in the cell lysate is not only realistic but also efficient.

Conditions optimized for the preparation of single-stranded DNA (ssDNA) employing lambda exonuclease digestion in generating DNA aptamer

The generation of DNA aptamer by Systematic Evolution of Ligands by Exponential Enrichment requires a good method of ssDNA generation. There are various methods developed to generate ssDNA such as streptavidin-biotin based separation techniques, asymmetric PCR and strand separation of the PCR product containing primer with a terminator and an extension of 20 nucleotides on denaturing urea-polyacrylamide gel. In the present investigation, we have shown the possible improvements for the regular lambda nuclease digestion under optimized conditions. Optimization of the PCR cycles, time course studies on lambda nuclease digestion and purification of the ssDNA from the lambda exonuclease digestion mixture was found to be able to recover ssDNA amounting up to 39.19 ± 2.48 % of the starting amount of dsDNA. These strategies can be applied to the techniques involving essential usage of ssDNA.

Aptamer-based multiplexed proteomic technology for biomarker discovery

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.

Low efficient generation of ssDNA aptamer using chemical modified spacer primer

Aptamers are oligonucleotides (ssDNA or RNA) with an appropriate size of 100 bps that bind with high affinity and specificity to a wide range of target molecules, including virtually any class of protein, drugs or small organic/inorganic molecules. The in vitro selection process referred to as SELEX provides a powerful tool to identify specific aptamers with high affinity and even discriminate between closely related targets. Aptamers have various applications such as analytical tools, disease diagnosis and prediction, pharmaceutical research, drug development, therapy and even for environmental monitoring. Nowadays, with the development of SELEX methods, generation of aptamer becomes more efficient, less time consuming and even automatically. The whole SELEX process includes binding, separation, and nucleic acid amplification. As amplification of nucleotides is an important process in successive SELEX, we will compare several methods for generation of aptamer in this report.

Changing the scope of preventative and therapeutic approaches in atherothrombosis

Major recent advances in the development of preventative and therapeutic approaches in atherothrombotic disease has prompted this Theme Issue of Thrombosis and Haemostasis. We are currently witnessing a fascinating introduction of novel antithrombotic agents into clinical practice, which will probably result in the disappearance of some drugs, which generations of physicians and patients have learned to live with, including all their advantages and disadvantages. Indeed, warfarin has been synonymous with oral anticoagulation as is heparin for intravenous anticoagulation. Hopefully, both may soon be replaced by new agents – broadly the oral direct thrombin inhibitors or oral factor Xa inhibitors – that provide major benefits for patients. Also anti-platelet therapy will change with the availability of a plethora of different agents already approved or currently in clinical trials or in development, including prasugrel or ticagrelor. Finally, the therapeutic potential of stem cell therapy (see upcoming Theme Issue by Guest Editor H. F. Tse) for the clinical consequences of atherothrombosis, myocardial infarction, has attracted major interest but also major controversy. Freudenberger et al. start off this Theme Issue with a systematic assessment of the clinical data available for anticoagulation therapy in patients with heart failure (1). The latter is commonly seen in clinical practice, and many complications associated with heart failure can be thrombosisrelated. Oral anticoagulation with warfarin or other vitamin K antagonists are associated with a high rate of bleeding complications as well as therapeutic failures. For decades, these shortcomings have initiated major drug development programs in the pharmaceutical industry. However, only recently advances in the understanding of serine protease biology and sophisticated drug development tools have resulted in long soughtafter successful drug development programs. Of the drugs in development, the direct thrombin inhibitor dabigatran and the direct factor Xa inhibitors rivaroxaban and apixaban are amongst those most advanced. In this issue, Ufer et al. provide a thorough comparison of these agents (2). One of the most fascinating drug developments in the field of anticoagulation is the generation of nucleid acid aptamers as described in a detailed review by Becker et al. (3). Specific three-dimensional structures of small RNA or DNA single-stranded molecules allow the blockade of enzyme function. Using a powerful screening technology, nucleic acid combinatorial libraries are incubated with the coagulation protease to be targeted. High-affinity blockers are then amplified by repeated screening rounds. The first aptamer developed for humans targets factor IXa and indeed this aptamer has successfully passed a phase 1 trial and overall looks promising. One of the biggest advantages of the aptamer technology is the technology-inherent availability of an antidote, which is composed of the antisense strand of the respective DNA or RNA sequence. In this, the aptamer technology is clearly superior to other drug developments in the field of anticoagulation or anti-platelet therapy where an antidote is typically not available. Personalised pharmacotherapy has long been discussed but rarely performed in Correspondence to: Prof. Karlheinz Peter Baker Heart Research Institute Centre for Thrombosis & Myocardial Infarction PO Box 6492, St Kilda Road Melbourne, 8008 Victoria, Australia Fax: +61 3 8532 1160 E-mail: Karlheinz.Peter@bakeridi.edu.au

Upgrading SELEX Technology by Using Lambda Exonuclease Digestion for Single-Stranded DNA Generation

The generation of single-stranded DNA (ssDNA) molecules plays a key role in the SELEX (Systematic Evolution of Ligands by EXponential enrichment) combinatorial chemistry process and numerous molecular biology techniques and applications, such as DNA sequencing, single-nucleotide polymorphism (SNP) analysis, DNA chips, DNA single-strand conformation polymorphism (SSCP) analysis and many other techniques. The purity and yield of ssDNA can affect the success of each application. This study compares the two ssDNA production methods, the strand separation by streptavidin-coated magnetic beads and alkaline denaturation and the lambda exonuclease digestion, in regard to the purity of generated ssDNA and the efficiency. Here, we demonstrate the considerable benefits of ssDNA production by lambda exonuclease digestion for in vitro selection of DNA aptamers. We believe that the generation of ssDNA aptamers using this method will greatly improve the success rate of SELEX experiments concerning the recovery of target-specific aptamers.

Effect of PAI-1 Specific RNA Aptamers On Cell Adhesion and Motility.

Abstract 2135Poster Board II-112 Introduction:The serine protease inhibitor (serpin), plasminogen activator inhibitor-1 (PAI-1) binds to and inhibits the plasminogen activators tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA). This results in both a decrease in plasmin production, as well as a decrease in the dissolution of fibrin clots. PAI-1 is also associated with the pathophysiology of several diseases, including cancer and cardiovascular disease. Both experimental and clinical studies have shown that increasing the plasma and vessel wall PAI-1 levels positively correlates with an increased risk of cardiovascular-related events. Consequently, the pharmacological suppression of PAI-1 might prevent or treat vascular disease. Unfortunately, since PAI-1 is a multifunctional protein, complete inhibition of PAI-1 might hinder its ability to regulate fibrinolysis, which can provoke bleeding. However, eliminating the pathological functions of PAI-1 without hindering its physiological functions might be beneficial in treating a variety of diseases. Extracellular matrix vitronectin (VN) increases at sites of vessel injury and is also present in fibrin clots. In response to injury, vitronectin facilitates cell adhesion, thereby increasing vascular cell migration by binding to integrins and to surface-bound uPA. PAI-1 competes with integrins and the urokinase-type plasminogen activator receptor (uPAR) for VN binding, resulting in the detachment of cells from the extracellular matrix. The binding of PAI-1 to VN prevents integrins from binding to VN, and inhibits cell adhesion and migration. Objective:The goal of this study was to develop RNA aptamers to interfere with a single PAI-1 function, without obstructing its other functions. The present study concentrated on developing PAI-1 aptamers to the vitronectin binding site of PAI-1. Aptamers are single-stranded nucleic acids, either DNA or RNA, that bind to their target protein with high affinity and specificity. Methods:Our aptamers were generated by the systematic evolution of ligands by exponential enrichment (SELEX). Adopting the SELEX in vitro selection technique ensures creation of nuclease-resistant RNA molecules that will bind to target proteins. We used in vitro assays to determine the effect of the aptamers on the adhesion and migration of smooth muscle (SM) and human umbilical vein endothelial cells (EC). Results:Recently, we published a paper that showed the generation of PAI-1 specific RNA aptamers that bind to the heparin/vitronectin binding site of PAI-1 (Blake et al., 2009). We showed that PAI-1 specific aptamers prevented the detachment of cancer cells from vitronectin in the presence of PAI-1, resulting in an increase in cell adhesion. We have expanded these studies to include smooth muscle (SMC) and human umbilical vein endothelial cells (EC). We demonstrated that the PAI-1 specific aptamers (SM-20 and WT-15) dose dependently increase SMC and EC attachment in the presence of vitronectin (compared to the control aptamer). Interestingly, SM-20 (the aptamer to stable PAI-1) was more effective than WT-15 (aptamer to wild-type PAI-1). Whereas PAI-1 significantly inhibited cell migration (in the presence of vitronectin), the PAI-1 specific aptamers were able to restore migration of both SMC and EC cells. Additionally, the PAI-1 aptamers were unable to bind to the PAI-1 vitronectin binding mutant, further suggesting that these aptamers bind to the PAI-1's vitronectin binding site. Importantly, these aptamers did not affect the antiprotease activity of PAI-1. Conclusions:We have shown that we are able to inhibit one of PAI-1's functions without hindering its other functions. By promoting smooth muscle and endothelial cell migration, these aptamers can potentially eliminate the adverse effects of elevated PAI-1 levels in the pathogenesis of vascular disease. Disclosures:Sullenger:Regado Biosciences Inc.: Equity Ownership, Scientific Founder.

Generation of Highly Specific Aptamers via Micromagnetic Selection

Aptamers are nucleic acid-based reagents that bind to target molecules with high affinity and specificity. However, methods for generating aptamers from random combinatorial libraries (e.g., systematic evolution of ligands by exponential enrichment (SELEX)) are often labor-intensive and time-consuming. Recent studies suggest that microfluidic SELEX (M-SELEX) technology can accelerate aptamer isolation by enabling highly stringent selection conditions through the use of very small amounts of target molecules. We present here an alternative M-SELEX method, which employs a disposable microfluidic chip to rapidly generate aptamers with high affinity and specificity. The micromagnetic separation (MMS) chip integrates microfabricated ferromagnetic structures to reproducibly generate large magnetic field gradients within its microchannel that efficiently trap magnetic bead-bound aptamers. Operation of the MMS device is facile and robust and demonstrates high recovery of the beads (99.5%), such that picomolar amounts of target molecule can be used. Importantly, the device demonstrates exceptional separation efficiency in removing weakly bound and unbound ssDNA to rapidly enrich target-specific aptamers. As a model, we demonstrate here the generation of DNA aptamers against streptavidin in three rounds of positive selection. We further enhanced the specificity of the selected aptamers via a round of negative selection in the same device against bovine serum albumin (BSA). The resulting aptamers displayed dissociation constants ranging from 25 to 65 nM for streptavidin and negligible affinity for BSA. Since a wide spectrum of molecular targets can be readily conjugated to magnetic beads, MMS-based SELEX provides a general platform for rapid generation of specific aptamers.

A Review: Electrochemical Aptasensors with Various Detection Strategies

AbstractThe combinatorial chemical synthesis offers in vitro aptamer generation with limitless aptamer selection for various analytes. Additionally, aptamer has quite many outstanding properties as the biomolecular recognition elements, thus competing with traditional affinity ligands (enzyme, antibodies, lectins etc.) in biological and medicine employments. This article reviews the advancements in electrochemical aptasensors for biomolecule monitoring, emphasizing the efficient detection strategies of sandwich structure formation using two recognition elements to capture and label target respectively, EIS measuring the electronic transfer resistance change, the aptamer conformation change triggering the electrochemical signal on/off and target molecules displacing electroactive markers.

Aptamer evolution for array-based diagnostics

Closed loop aptameric directed evolution, (CLADE) is a technique enabling simultaneous discovery, evolution, and optimization of aptamers. It was previously demonstrated using a fluorescent protein, and here we extend its applicability with the generation of surface-bound aptamers for targets containing no natural fluorescence. Starting from a random population, in four generations CLADE produced a new aptamer to thrombin with high specificity and affinity. The best aptameric sequence was void of the set of four guanine repeats typifying thrombin aptamers and, thus, highlights the benefits of evolution performed in an environment closely mimicking the final diagnostic application.

184. In Vivo SELEX: Generation of Aptamers and Identification of Target Protein Relevant to Tumor

SELEX (systematic evolution of ligands by exponential enrichment) is an in vitro iterative selection procedure used to identify oligonucleotides (aptamers) with desired protein or complex targets, such as cells. Given that binding of aptamer depends on their target conformation which is in turn conditioned by the target's environment, and obviously in vitro SELEX is no guarantee for the selected aptamers recognizing their cognate target in vivo, we seek to develop tumor-targeting aptamers through a novel in vivo application of SELEX.

Development of aptamers specific for potential diagnostic targets in Burkholderia pseudomallei

Improved diagnostic reagents would be of considerable benefit in enhancing the specificity and sensitivity of rapid assays for Burkholderia pseudomallei, the causative agent of melioidosis. The purpose of this work is to develop aptamers, high affinity RNA-based molecular recognition molecules, which could be used as reagents for identification of the whole organism in assays of biological samples. Data are presented demonstrating the purification of recombinant B. pseudomallei secreted or surface-exposed macromolecules, which have been expressed in Escherichia coli, and the initial stages of aptamer generation using these recombinant proteins. Future studies will focus upon the expansion of this methodology to include other target macromolecules located on or near the outer membrane of this organism.