Aptamer-based affinity labeling of proteins

A most able label: Labeled aptamers can be cross-linked to their target structures in a light-dependent and highly specific manner as a result of a new strategy termed aptamer-based affinity labeling (ABAL) of proteins. The aptamer-protein complexes can be enriched in?vitro, from a cellular lysate and from the surface of living cells, opening new ways to study aptamer interactions in biological contexts.     

Selection of aptamers for signal transduction proteins by capillary electrophoresis

High‐affinity aptamers for important signal transduction proteins, i.e. Cdc42‐GTP, p21‐activated kinase1 (PAK1) and MRCK (myotonic dystrophy kinase‐related Cdc42‐binding kinase) α were successfully selected in the low micro‐ to nanomolar range using non‐systematic evolution of ligands by exponential enrichment (SELEX) with at least three orders of magnitude enhancement from their respective bulk affinity of naïve DNA library. In the non‐SELEX procedure, CE was used as a highly efficient affinity method to select aptamers for the desired molecular target through a process that involved repetitive steps of partitioning, known as non‐equilibrium CE of equilibrium mixtures with no PCR amplification between successive steps. Various non‐SELEX conditions including the type, concentration and pH of the run buffer were optimized. Other considerations such as salt composition of selection buffer, protein concentration and sample injection size were also studied for high stringency during selection. After identifying the best enriched aptamer pool, randomly selected clones from the aptamer pool were sequenced to obtain the individual DNA sequences. The dissociation constants (K_d) of these sequences were in the low micromolar to nanomolar range, indicating high affinity to the respective proteins. The best binders were also subjected to sequence alignment to generate a phylogenetic tree. No significant consensus region based on approximately 50 sequences for each protein was observed, suggesting the high efficiency of non‐SELEX for the selection of numerous unique sequences with high selectivity.     

Selection and analytical applications of aptamers binding microbial pathogens

DNA aptamers specifically recognizing microbial cells and viruses have a range of analytical and therapeutic applications. This article describes recent advances in the development of aptamers targeting specific pathogens (e.g., live bacteria, whole viral particles, and virally-infected mammalian cells). Specific aptamers against pathogens have been used as affinity reagents to develop sandwich assays, to label and to image cells, to bind with cells for flow-cytometry analysis, and to act as probes for development of whole-cell biosensors. Future applications of aptamers to pathogens will benefit from recent advances in improved selection and new aptamers containing modified nucleotides, particularly slow off-rate modified aptamers (SOMAmers).     

DNA酶: 筛选、 生物传感及展望

综述了脱氧核糖核酸酶(DNA酶)的起源及分离富集策略, 对比了DNA酶与核糖核酸酶(RNA酶)及蛋白酶的相似点和不同之处, 并重点讨论了产物捕获和对冲抵消等策略对筛选获得DNA酶的独到之处; 同时系统回顾了近年来分离出的可特异感应各种金属离子或生物样本(包括细菌、 细胞等), 从而能在特定位点切割RNA底物的DNA酶探针; 阐述了DNA酶领域现存的挑战, 总结和展望了新思路和新方向.     

Two-Dimensional Electrophoresis-Based Selection of Aptamers Against an Unidentified Protein in a Tissue Sample

A fully automated two-dimensional electrophoresis (2DE) system was employed for DNA aptamer selection against an unidentified protein in a mouse liver tissue extract as a model target. A 2DE-based systematic evolution of ligands by exponential enrichment (2DE-SELEX) was demonstrated for aptamer selection against a single protein spot that was separated on a nitrocellulose membrane. After four iterative 2DE-SELEX cycles, the oligonucleotide pool was sequenced and aptamer sequences were identified. A blotting assay showed that an identified aptamer with a stable stem–loop structure had specific binding activity against the target protein. The 2DE-SELEX was shown to be promising for the development of aptamers against unidentified proteins in complex samples for proteomic analysis and biomarker discovery.

Supplemental materials are available for this article. Go to the publisher's online edition of Analytical Letters to view the supplemental file.     

Kinetic capillary electrophoresis-based affinity screening of aptamer clones

DNA aptamers are single stranded DNA (ssDNA) molecules artificially selected from random-sequence DNA libraries for their specific binding to a certain target. DNA aptamers have a number of advantages over antibodies and promise to replace them in both diagnostic and therapeutic applications. The development of DNA aptamers involves three major stages: library enrichment, obtaining individual DNA clones, and the affinity screening of the clones. The purpose of the screening is to obtain the nucleotide sequences of aptamers and the binding parameters of their interaction with the target. Highly efficient approaches have been recently developed for the first two stages, while the third stage remained the rate-limiting one. Here, we introduce a new method for affinity screening of individual DNA aptamer clones. The proposed method amalgamates: (i) aptamer amplification by asymmetric PCR (PCR with a primer ratio different from unity), (ii) analysis of aptamer-target interaction, combining in-capillary mixing of reactants by transverse diffusion of laminar flow profiles (TDLFP) and affinity analysis using kinetic capillary electrophoresis (KCE), and (iii) sequencing of only aptamers with satisfying binding parameters. For the first time we showed that aptamer clones can be directly used in TDLFP/KCE-based affinity analysis without an additional purification step after asymmetric PCR amplification. We also demonstrated that mathematical modeling of TDLFP-based mixing allows for the determination of K_d values for the in-capillary reaction of an aptamer and a target and that the obtained K_d values can be used for the accurate affinity ranking of aptamers. The proposed method does not require the knowledge of aptamer sequences before screening, avoids lengthy (3-5 h) purification steps of aptamer clones, and minimizes reagent consumption to nanoliters.     

化学修饰提高核酸适体结合亲和力的研究进展

核酸适体(Aptamer)是通过体外筛选得到的短单链DNA或RNA寡核苷酸, 具有与抗体相当或更优异的特异性及亲和力, 且具有靶标范围广、 易制备和灵活可控修饰、 免疫原性低、 批次差异性小以及易于运输保存等优势, 为食品、 环境和生物医学等领域提供了全新的分子识别工具, 获得了研究者的广泛关注. 但是目前其商业应用的数量仍有限. 为了增强核酸适体的应用性能, 研究者对核酸适体进行了大量的改性研究. 本文系统总结了核酸适体筛选前、 后采用非共价或共价方式对其进行化学修饰, 以增加核酸适体与靶标的结合亲和力的相关研究进展, 并对未来发展前景进行了展望.     

Selection of a DNA aptamer for the development of fluorescent aptasensor for carbaryl detection

An improved ssDNA library immobilized systematic evolution of ligands by enrichment(SELEX) was applied to select aptamers against carbaryl.After nine selection rounds,a highly enriched ssDNA pool was obtained.The Apta3 was demonstrated as the optimal aptame r.In order to facilitate the modification of aptamer,the Apta3 was further truncated with the dissociation constant(K_d) of 0.3 64 ± 0.055 μmol/L and a fluorescent aptasensor was developed.The linear range for carbaryl was from 100 nmol/L to1500 nmol/L,with the limit of detection was as low as 15.23 nmol/L.Besides,the biosensor was validated for the carbaryl spiked real samples,and the recoveries were between 97.7% and 107.3%.     

In vitro selection methodologies to probe RNA function and structure

Summary In vitro selection, or SELEX, has been used both to characterize the interaction of natural nucleic acids with proteins and to generate novel nucleic acid-binding species, or aptamers. Although numerous reports have demonstrated the power of the technique, they have not expanded on the methodologies that can be used for selection. This review focuses on the considerations and problems involved in selecting protein-binding aptamers from a random-sequence RNA pool. As an illustration, we describe two approaches to selecting aptamers to a particular target, the HTLV-I Rex protein. In the first, complete randomization is used to find an artificial, high-affinity RNA binding site. In the second, the contributions of individual nucleotides and/or base pairs to the natural Rex-binding element are determined by mutating the wild-type sequence and selecting active binding variants.