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

Because of their easily modified chemical structures and wide range of targets, aptamers are ideal candidates for various applications, such as biomarker discovery, target diagnosis, molecular imaging, and drug delivery. Aptamers are oligonucleotide sequences that can bind to their targets specifically via unique three dimensional (3-D) structures. Usually, aptamers are obtained from repeated rounds of in vitro or in vivo selection termed SELEX (Systematic Evolution of Ligands by EXponential enrichment), which can generate aptamers with high affinity and specificity for many kinds of targets, such as biomedically important proteins and even cancer cells. In this review, some basic principles and recent developments in the design of SELEX process are discussed, hopefully to provide some guidelines towards performing more efficient aptamer isolation procedures. Moreover, the biomedical and bioanalytical applications of aptamers are further reviewed, based on some smart biochemical modifications of these oligonucleotide structures.     

SELEX技术及寡核苷酸适配体的近期研究进展

指数富集的配体系统进化（SELEX）技术是一类具备蓬勃发展前景的体外筛选技术,在生物学、药学及化学领域已引起广泛关注。本文即针对2004年以来SELEX技术的发展特点,主要介绍两类新型SELEX策略,即毛细管电泳-SELEX和针对复杂靶标的SELEX方法,并简要总结了寡核苷酸适配体在生物医学和药学相关方面的最新应用进展。     

Improving the stability of aptamers by chemical modification

Ever since the invention of SELEX (systematic evolution of ligands by exponential enrichment), there has been rapid development for aptamers over the last two decades, making them a promising approach in therapeutic applications as either drug candidates or diagnostic tools. For therapeutic purposes, a durable performance of aptamers in biofluids is required, which is, however, hampered by the lack of stability of most aptamers. Not only are the nucleic acid aptamers susceptible to nucleases, the peptide aptamers are also subjective to degradation by proteases. With the advancement of chemical biology, numerous attempts have been made to overcome this obstacle, many resulting in significant improvements in stability. In this review, chemical modifications to increase the stability of three main types of aptamers, DNA, RNA and peptide are comprehensively summarized. For nucleic acid aptamers, development of modified SELEX coupled with mutated polymerase is discussed, which is adaptive to a number of modifications in aptamers and in a large extent facilitates the research of aptamer-modifications. For peptide aptamers, approaches in molecular biology with introduction of stabilizing protein as well as the switch of scaffold protein are included, which may represent a future direction of chemical conjugations to aptamers.     

Cell-based aptamer selection for diagnosing cancer and predicting cancer progression

Antibodies are excellent molecular recognition agents for a wide range of applications therefore they have been used heavily in clinical assays such as disease diagnosis. More recently, aptamers have emerged as alternative capturing agents in a variety of applications including medical diagnosis, environmental toxicity detection, targeted drug delivery and viral therapeutics. Aptamers are ssDNA or RNA that form three dimensional structures and bind to the target molecules such as peptide, protein or small molecules. Aptamers are generated by in vitro process called “SELEX (Systematic Evolution of Ligands by Exponential Enrichment)”. Conventionally, SELEX is performed with immobilized target molecules such as proteins in column, filter or beads. However, for some targets like membrane proteins, it is very difficult or almost impossible to immobilize the target proteins in their active conformation. However, cell-based aptamer selection technology explain how it can be better than standard immobilization methods in brief. Here, we described the cell-specific aptamers selecting technology, called cell-based SELEX, for diagnosing disease and predicting disease progression, especially in the case of complex disease, like cancer.     

Aptamer-based strategies for stem cell research

Aptamers have been introduced to analytical applications, target validation, and drug discovery processes and, recently, applied directly as therapeutic agents. Aptamers can be generated by a method called SELEX (Systematic Evolution of Ligands by Exponential Enrichment). This is quite remarkable for such a young technology, which is only created in the early 1990s. This paper reviews recent new applications of aptamers in stem cell research and tissue engineering.     

基于SELEX技术的疾病标志物发现新策略研究进展

生物标志物(Biomarker)是指可以标记生物体结构或功能改变的生化指标.在疾病研究中,生物标志物可供客观测定和评价机体所处的生理或病理状态,为疾病的诊断、鉴定提供辅助手段.指数富集的配体系统进化(Systematic evolution of ligands by exponential enrichment,SE...     

特异性结合白色念珠菌（1，3）-β-D-葡聚糖单链 DNA 适配子的筛选及其应用

目的：通过指数富集的配基系统进化技术（systematic evolution of ligands by exponential enrichment ,SELEX）筛选能与高亲和力（1,3）‐β‐D‐葡聚糖特异性结合的适配子,并用该适配子建立双适配子夹心酶联寡聚核苷酸吸附试验（enzyme‐linked oligonucleotide assay ,ELONA）来对深部真菌感染血浆进行辅助诊断。方法提取白色念珠菌 ATCC10231株细胞壁（1,3）‐β‐D‐葡聚糖,通过 SELEX 筛选获得能与（1,3）‐β‐D‐葡聚糖特异性结合的高亲和力单链 DNA 适配子,并用该适配子建立双适配子夹心ELONA 来检测深部真菌感染血浆中的（1,3）‐β‐D‐葡聚糖。结果从白色念珠菌细胞壁中成功提取了高聚合度（1,3）‐β‐D‐葡聚糖,并通过体外酶解获得可溶性低聚合度（1,3）‐β‐D‐葡聚糖作为筛选靶标。用SELEX 进行12轮筛选后,从初始单链 DNA 文库中获得2个高亲和力适配子 AU1和 AD1,检测发现它们并非结合于（1,3）‐β‐D‐葡聚糖的同一表位。双适配子夹心 ELONA 检测深部真菌感染血浆中（1,3）‐β‐D‐葡聚糖的特异性和敏感度分别为91．94％和92．31％。结论从初始单链 DNA 文库中成功获得可与（1,3）‐β‐D‐葡聚糖特异结合的高亲和力适配子,为深部真菌感染新型诊断试剂的研发奠定了基础。     

Derivation of RNA aptamer inhibitors of human complement C5.

Specific aptamer inhibitors of the human complement C5 component were produced by the SELEX methodology of directed evolution of nucleic acid ligands. The SELEX procedure started with a pool of random-sequence, 2'F-pyrimidine-modified nuclease-stabilized RNA, and after twelve rounds of iterative C5 binding and nucleic acid amplification an evolved RNA pool was obtained which contained the highest affinity binders to the C5 protein. The evolved RNA pool was then cloned and sequenced, and individual clones were analyzed for binding and function. Twenty-eight clones (out of sixty) were identified which bound C5 (termed aptamers). Seven of these aptamers formed a closely related sequence homology family; these aptamers bound C5 with a Kd 20-40 nM and also inhibited human serum hemolytic activity. In addition, these aptamers inhibited zymosan-induced generation of C5a. Aptamer inhibition of both C5b and C5a suggests that aptamer binding inhibits cleavage of C5 by the C5 convertase of both pathways. One of the inhibitory aptamer sequences was truncated to yield a 38-mer 2'F RNA aptamer which retained C5 binding and inhibitory activity. The structure of this aptamer is predicted to be a stem-loop containing thirteen base pairs, and also containing two bulges. The affinity of this aptamer was improved by performing a second biased SELEX experiment, where the randomized starting RNA pool uses a template where the individual base compositions are biased toward a specific sequence. This second SELEX experiment produced an aptamer with a Kd of 2-5 nM which retained functional activity. Another SELEX to rat C5 produced an aptamer with binding and inhibitory properties virtually identical with the human aptamer. The human and rat aptamers are being evaluated for complement inhibition in vitro and in vivo as potential therapeutics for treatment of human disease.     

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.     

Low efficient immobilization of active chloramphenicol for SELEX

Chloramphenicol is an antibacterial antibiotic which interferes with the protein synthesis of microorganisms. However, the use of chloramphenicol should be limited in humans and food products, because it is known to have side effects such as genotoxicity and aplastic anemia in humans. Therefore, it is important to monitor the amount of chloramphenicol in food products. Instead of using conventional analytical methods or antibodies, using aptamers can be a good alternative for measuring the amount of chloramphenicol in food. Aptamers are nucleic acids within 100 base pairs that can bind to target with high specificities and sensitivities, and are derived through a process called SELEX. Here, we report that the immobilization efficiency of chloramphenicol is low with SELEX, which can lead to the low amount of active chloramphenicol immobilized to epoxy resin. This result may be applicable to general SELEX process, especially for negative SELEX during which aptamers that are not bound to targets are removed to increase the amount of aptamers that can bind specifically to targets.     

Aptamers as therapeutics in cardiovascular diseases

With many advantages over other therapeutic agents such as monoclonal antibodies, aptamers have recently emerged as a novel and powerful class of ligands with excellent potential for diagnostic and therapeutic applications. Typically generated through Systematic Evolution of Ligands by EXponential enrichment (SELEX), aptamers have been selected against a wide range of targets such as proteins, phospholipids, sugars, nucleic acids, as well as whole cells. DNA/RNA aptamers are single-stranded DNA/RNA oligonucleotides (with a molecular weight of 5-40 kDa) that can fold into well-defined 3D structures and bind to their target molecules with high affinity and specificity. A number of strategies have been adopted to synthesize aptamers with enhanced in vitro/in vivo stability, aiming at potential therapeutic/diagnostic applications in the clinic. In cardiovascular diseases, aptamers can be developed into therapeutic agents as anti-thrombotics, anti-coagulants, among others. This review focuses on aptamers that were selected against various molecular targets involved in cardiovascular diseases: von Willebrand factor (vWF), thrombin, factor IX, phospholamban, P-selectin, platelet-derived growth factor, integrin α(v)β(3), CXCL10, vasopressin, among others. With continued effort in the development of aptamer-based therapeutics, aptamers will find their niches in cardiovascular diseases and significantly impact clinical patient management.     

系统进化指数富集法筛选抑制人乙酰胆碱酯酶的RNA分子

目的：获得针对人红细胞乙酰胆碱酯酶(AChE)的特异性核酸配基．方法：利用微孔板法筛选人红细胞膜AChE的核酸配基．利用凝胶阻滞实验检测核酸配基与AChE特异性的结合．微量碱羟胺比色法测定AChE的活性．结果：经过9轮筛选得到针对人红细胞AChE的核酸配基．在相同浓度(2．25μmol/L)下,它们不与人重组丁酰胆碱酯酶(rhBChE)作用,而与人RBCAChE特异结合并抑制AChE的活性．结论：用SELEX技术可以高效地从大容量寡核苷酸组合文库中得到AChE特异性抑制剂．     

Aptamer-based fluorescent biosensors

Selected from random pools of DNA or RNA molecules through systematic evolution of ligands by exponential enrichment (SELEX), aptamers can bind to target molecules with high affinity and specificity, which makes them ideal recognition elements in the development of biosensors. To date, aptamer-based biosensors have used a wide variety of detection techniques, which are briefly summarized in this article. The focus of this review is on the development of aptamer-based fluorescent biosensors, with emphasis on their design as well as properties such as sensitivity and specificity. These biosensors can be broadly divided into two categories: those using fluorescently-labeled aptamers and others that employ label-free aptamers. Within each category, they can be further divided into "signal-on" and "signal-off" sensors. A number of these aptamer-based fluorescent biosensors have shown promising results in biological samples such as urine and serum, suggesting their potential applications in biomedical research and disease diagnostics.     

Cell SELEX技术筛选巨噬细胞源性泡沫细胞适配子的初步研究

目的利用Cell SELEX技术筛选巨噬细胞源性泡沫细胞适配子。方法通过80mg/L氧化性低密度脂蛋白诱导THP-1巨噬细胞为泡沫细胞;聚合酶链反应扩增文库;生物素-链霉亲和素磁珠分离法构建单链DNA文库;以巨噬细胞源性泡沫细胞为靶细胞,巨噬细胞和血管平滑肌细胞为反筛细胞,利用Cell SELEX技术筛选与巨噬细胞源性泡沫细胞结合的寡核苷酸序列,并对最后一轮筛选结果进行克隆测序。结果 PCR的退火温度对PCR产物的量有显著的影响,退火温度由65℃提高为72℃时的产物量明显增加。利用生物素-链霉亲和素磁珠分离法获得了纯度高、产量大的ssDNA文库;经过18轮筛选后,成功获得了28个与预期大小相同的ssDNA序列。结论利用Cell SELEX技术筛选出了巨噬细胞源性泡沫细胞的适配子,为研发用于动脉粥样硬化的早期无创诊断试剂和靶向治疗药物奠定了基础。     

Nucleic Acid Aptamers: New Methods for Selection,Stabilization, and Application in Biomedical Science

The adoption of oligonucleotide aptamer is well on the rise, serving an ever increasing demand for versatility in biomedical field. Through the SELEX (Systematic Evolution of Ligands by EXponential enrichment), aptamer that can bind to specific target with high affinity and specificity can be obtained. Aptamers are single-stranded nucleic acid molecules that can fold into complex threedimensional structures, forming binding pockets and clefts for the specific recognition and tight binding of any given molecular target. Recently, aptamers have attracted much attention because they not only have all of the advantages of antibodies, but also have unique merits such as thermal stability, ease of synthesis, reversibility, and little immunogenicity. The advent of novel technologies is revolutionizing aptamer applications. Aptamers can be easily modified by various chemical reactions to introduce functional groups and/or nucleotide extensions. They can also be conjugated to therapeutic molecules such as drugs, drug containing carriers, toxins, or photosensitizers. Here, we discuss new SELEX strategies and stabilization methods as well as applications in drug delivery and molecular imaging.     

Aptamers: new arrows to target dendritic cells

Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the “systematic evolution of ligands by exponential enrichment” (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.     

核酸适配体在抗肿瘤药物主动靶向传递中的应用

核酸适配体是通过指数级富集的配体系统进化技术(systematic evolution of ligands by exponential enrichment,SELEX)从合成的大容量单链随机寡核苷酸文库中筛选并富集的对某些靶点具有高特异性和高结合率的小分子DNA或RNA片段.核酸适配体具有直接抑制肿瘤细胞增殖的作用,通过结构修饰可增强在体内的稳定性.此外,它可与载药纳米结构键合,用于肿瘤诊断和治疗.本文综述了核酸适配体的肿瘤靶点、筛选方法及其在肿瘤诊断和治疗中的应用.     

Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy

Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures.     

Aptamers: potential applications to pancreatic cancer therapy

There is an unquestionable need for more effective therapies for pancreatic cancer. Aptamers are single-stranded DNA or RNA oligonucleotide ligands whose 3-dimensional structures are dictated by their sequences. Aptamers have been generated against numerous purified protein targets using an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Several biochemical properties make them attractive tools for use in an array of biological research applications and as potential pharmacologic agents. Isolated aptamers may directly affect target protein function, or they may also be modified for use as delivery agents for other therapeutic cargo or as imaging agents. More complex selections, using whole cancer cells or tumor tissue, may simultaneously identify novel or unexpected targets and aptamers to inhibit them. This review summarizes recent advances in the field of aptamers and discusses aptamer targets that have relevance to pancreatic cancer.