Aptamers: Features,Synthesis and Applications

Aptamers have become a topic of interest among the researchers and scientists since they not only possess all of the benefits of antibodies but also possess special qualities including heat stability, low cost, and limitless uses⋅ Here we give a review about the features, applications, and challenges of aptamers and also how they are beneficial over the antibodies for biomedical applications. Their unique features make aptamers a prominent tool in therapeutics, diagnostics, biosensors and targeted drug delivery. In conclusion, aptamers represent exciting materials for a variety of applications and can be modified to improve their properties and to extend their applications in biomedical field.     

信号适体的设计策略及应用

信号适体兼具有分子识别和信号转导的功能.从随机寡核苷酸库中筛选出的适体,要经过合理设计和筛选后修饰,才具备信号转导功能.信号适体可分为标记和非标记两大类.本文着重介绍荧光标记信号适体的设计策略,包括基于荧光偏振分析标记一个荧光基团,及基于荧光共振能量转移同时标记荧光基团、淬灭基团,或两个荧光基团的信号适体(包括分子信标适体、结构转换和原位标记信号适体).非标记信号适体的设计,有嵌合法、置换法、光转换复合物法,及适体－多聚物偶联法.此外,亦可直接从体外筛选出信号适体.信号适体的诸多优点利于其用于生物传感器及均相液相中实时蛋白识别与定量分析.     

研究报告: 基于分子对接和步进序列群的蓖麻毒素核酸适配体序列优化

目的 有效结合分子对接预测和表面等离子体共振实验评价技术，获得亲和力更强、序列最短的最优适配体。方法 针对前期筛选出的靶向蓖麻毒素的3条80 nt单链DNA适配体（L14、P3、L7），在明确各自二维随机区茎环序列与靶蛋白结合能力的基础上，以H-DOCK分子对接为指导，分别确定蓖麻毒素适配体随机区的最短结合单元，从而构建两端延长步进序列群，以表面等离子体共振技术测定序列群序列的亲和力和动力学参数，明确适配体的结合关键结构，从而筛选得到最优适配体。结果 3条全长适配体的随机区适配体L14r、P3r、L7r均可形成一定的茎环结构，其中L14r较L14的亲和力增强9倍、L7r增强2倍、P3r基本不变。对随机区适配体和蓖麻毒素进行分子对接，结果显示，L14r、P3r、L7r的对接分数值皆优于阴性序列40T，结合关键氨基酸个数分别为11、8、9个，存在距离小于5 ?的预测结合位点分别为20、12、15个，具有良好的与蓖麻毒素的结合能力。进一步明确了蓖麻毒素活性口袋所容纳的适配体最短结合单元L14rm、P3rm、L7rm的序列构成，在此基础上构建出两端延长步进序列群。针对该步进群，基于结合关键氨基酸个数、结合位点个数、对接得分等参数的变化和表面等离子体共振测定结果筛选出最优适配体。所获得的最优适配体L14rm、L7rm-2亲和力继续增强了1~2倍。结论 随机区适配体能有效地与蓖麻毒素结合，较之全长适配体亲和力更强，分子对接结合步进序列群设计，仅使用17条序列，便有效获得了3条最优适配体并明确其结合作用。3条结合蓖麻毒素的最优适配体——L14rm、P3r、L7rm-2的K_D值分别为（64±30）、（167±19）、（120±1）nmol/L，亲和力提高到全长适配体的14、1、4倍。     

基于分子模拟的河鲀毒素核酸适配体的连续优化*

河鲀毒素(tetrodotoxin, TTX)是一种生物碱类神经毒素,其中毒事件在世界范围内广泛发生,严重危害到人类健康,但尚无特效解毒剂,因此TTX的检测对食品安全领域有重大意义。为了得到更高效的TTX识别元件,在分子模拟指导下对SELEX筛选所得的核酸适配体TTX-27进行了连续优化。首先,使用Mini-hairpin结构替换阻碍TTX结合的茎环结构,使TTX更易与截短型适配体结合,然后将T39、C40碱基突变为C39、T40碱基,并对C39进行了2'-OH修饰,以增强结合区域碱基与TTX的氢键作用和范德瓦耳斯相互作用。微量热泳动(microscale thermophoresis, MST)实验证实,经截短、碱基突变和化学修饰的各适配体变体的亲和力均有提高,其中化学修饰变体TTX-D2-X-R结合TTX的解离平衡常数K_d为1.08 nmol/L,相较于TTX-27的亲和力提高了75.5倍。表明基于分子模拟的截短-突变-化学修饰是核酸适配体post-SELEX优化的有效途径,所得的适配体变体TTX-D2-X-R在TTX检测领域有着潜在的应用价值。     

Rational Design and Biophysical Characterization of Thioredoxin-Based Aptamers: Insights into Peptide Grafting

Peptide aptamers are simple structures, often made up of a single-variable peptide loop constrained within a constant scaffold protein. Aptamers were rationally designed by inserting peptides into a solvent-exposed loop on thioredoxin (Trx). They were designed to interact with the proteins elongation initiation factor 4E (eIF4E) and mouse double minute 2 (MDM2) and were then validated by competitive fluorescence anisotropy experiments. The constructed aptamers interacted with eIF4E and MDM2 with apparent K_d values of 1.25 ± 0.06 μM and 0.09 ± 0.01 μM, respectively, as determined by isothermal titration calorimetry (ITC). The MDM2 aptamer (SuperTIP) interacted ∼ 2-fold more tightly with MDM2 than the free linear peptide (12.1 peptide), while the eIF4E aptamer elongation initiation factor 4GI-SG interacted ∼ 5-fold less strongly than the free linear peptide (elongation initiation factor 4GI). These differences in binding with respect to each aptamer's free peptide reveal that there are more factors involved than just constraining a peptide in a scaffold that lead to tighter binding. ITC studies of aptamer interactions reveal an enthalpic component more favorable than that for the free linear peptides, as well as a larger unfavorable entropic component. These results indicated that stapling of the free peptide in the scaffold increases the favorable enthalpy of the interaction with the target protein. Thermostability studies also revealed that peptide insertion significantly destabilized the Trx scaffold by ∼ 27 °C. It is this destabilization that leads to an increase in the flexibility of the Trx scaffold, which presumably is lost upon the aptamer's interaction with the target protein and is the cause of the increase in unfavorable entropy in the ITC studies. The precise origin of the enthalpic effect was further studied using molecular dynamics for the MDM2-SuperTIP system, which revealed that there were also favorable electrostatic interactions between the Trx scaffold and the MDM2 protein itself, as well as with the inserted peptide. This work reveals that any increase in the binding affinity of an aptamer over a free peptide is dependent on the increase in the favorable enthalpy of binding, which is ideally caused by stapling of the peptide or by additional interactions between the aptamer protein and its target. These need to be sufficient to compensate for the destabilization of the scaffold by peptide insertion. These observations will be useful in future aptamer designs.     

Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP

Summary

A poly (A)-binding protein from Leishmania infantum (LiPABP) has been recently cloned and characterized in our laboratory. Although this protein shows a very high homology with PABPs from other eukaryotic organisms including mammals and other parasites, exist divergences along the sequence that convert them in potential diagnostic markers and/or therapeutics targets. Aptamers are oligonucleotide ligands that are selected in vitro by their affinity and specificity for the target as a consequence of the particular tertiary structure that they are able to acquire depending on their sequence. Development of high-affinity molecules with the ability to recognize specifically Leishmania proteins is essential for the progress of this kind of study.

Results

We have selected a ssDNA aptamer population against a recombinant 6xHIS–LiPABP protein (rLiPABP) that is able to recognize the target with a low Kd. Cloning, sequencing and in silico analysis of the aptamers obtained from the population yielded three aptamers (ApPABP#3, ApPABP#7 and ApPABP#11) that significantly bound to PABP with higher affinity than the naïve population. These aptamers were analyzed by ELONA and slot blot to establish affinity and specificity for rLiPABP. Results demonstrated that the three aptamers have high affinity and specificity for the target and that they are able to detect an endogenous LiPABP (eLiPABP) protein amount corresponding to 2500 L. infantum promastigotes in a significant manner. The functional analysis of the aptamers also revealed that ApPABP#11 disrupts the binding of both Myc-LiPABP and eLiPABP to poly (A) in vitro. On the other hand, these aptamers are able to bind and purify LiPABP from complex mixes.

Conclusion

Results presented here demonstrate that aptamers represent new reagents for characterization of LiPABP and that they can affect LiPABP activity. At this respect, the use of these aptamers as therapeutic tool affecting the physiological role of PABP has to be analyzed.     

Aptamers: A promising tool for cancer imaging,diagnosis, and therapy

Aptamers are a group of molecules, which can specifically bind, track, and inhibit target molecules, comprising DNA aptamers, RNA aptamers, and peptide aptamers. So far, there are much progress about developing novel aptamers and their expansile applications. This prospect systematically introduces the composition and technological evolution of aptamers, and then focuses on the application of aptamers in cancer diagnosis, imaging, and therapy. Following this, we discuss the potential to harness aptamers in discovering the biomarker of stem cells, which is favorable for us to study the normal developmental or abnormal pathological process of tissue and to deliver drugs into target cells or tissues in the future. J. Cell. Biochem. 114: 250–255, 2013. © 2012 Wiley Periodicals, Inc.     

Aptamers and riboswitches: perspectives in biotechnology

Aptamers are short, single stranded nucleic acids which bind a wide range of different ligands with extraordinary high binding affinity and specificity. The steadily increasing number of aptamers is accompanied by an expanding range of applications in biotechnology. We will describe new developments in the field including the use of aptamers for conditional gene regulation and as biosensors. In addition, we will discuss the potential of aptamers as tags to visualize RNA and protein distribution in living cells and as therapeutics. Furthermore, we will consider biotechnological applications of riboswitches for gene regulation and as drug target.     

Novel Self-Nanoemulsifying Drug Delivery Systems (SNEDDS) for Oral Delivery of Cinnarizine: Design, Optimization, and In-Vitro Assessment

Due to its extreme lipophilicity, the oral delivery of cinnarizine (CN) encounters several problems such as poor aqueous solubility and pH-dependent dissolution, which result in low and erratic bioavailability. The current study aims to design self-nanoemulsifying drug delivery systems (SNEDDS) of CN that circumvent such obstacles. Equilibrium solubility of CN was determined in a range of anhydrous and diluted lipid-based formulations. Dynamic dispersion tests were carried out to investigate the efficiency of drug release and magnitude of precipitation that could occur upon aqueous dilution. Droplet sizes of selected formulations, upon (1:1,000) aqueous dilution, were presented. The optimal formulations were enrolled in subsequent dissolution studies. The results showed that increasing lipid chain length and surfactant lipophilicity raised the formulation solvent capacity, while adding co-solvents provoked a negative influence. The inclusion of mixed glycerides and/or hydrophilic surfactants improved the drug release efficiency. Generally, no significant precipitation was observed upon aqueous dilution of the formulations. Five formulations were optimal in terms of their superior self-emulsifying efficiency, drug solubility, dispersion characteristics, and lower droplet size. Furthermore, the optimal formulations showed superior dissolution profile compared to the marketed (Stugeron®) tablet. Most importantly, they could resist the intensive precipitation observed with the marketed tablet upon shifting from acidic to alkaline media. However, SNEDDS containing medium-chain mixed glycerides showed the highest drug release rate and provide great potential to enhance the oral CN delivery. Accordingly, the lipid portion seems to be the most vital component in designing CN self-nanoemulsifying systems.     

Aptamers: Molecules of great potential

Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.     

核酸适配体及其在病原微生物学中的应用

核酸适配体指利用指数富集配体系统进化技术筛选出的寡聚核苷酸片段,它可以特异性地识别靶标并与之结合,已经广泛应用于基础研究、临床诊断、纳米技术等。以下综述了适配体在微生物学方面的应用。     

Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins

Aptamers are single stranded oligonucleotides, comparable to monoclonal antibodies (mAbs) in selectivity and affinity and have significant strategic properties in design, development and applications more than mAbs. Ease of design and development, simple chemical modification and the attachment of functional groups, easily handling and more adaptability with analytical methods, small size and adaptation with nanostructures are the valuable characteristics of aptamers in comparison to large protein based ligands. Among a broad range of targets that their specific aptamers developed, proteins and peptides have significant position according to the number of related studies performed so far. Since proteins control many of important physiological and pathological incidents in the living organisms, particularly human beings and because of the benefits of aptamers in clinical and analytical applications, aptamer related technologies in the field of proteins and peptides are under progress, exclusively. Currently, there is only one FDA approved therapeutic aptamer in the pharmaceutical market, which is specific to vascular endothelial growth factor and is prescribed for age related macular degenerative disease. Additionally, there are several aptamers in the different phases of clinical trials. Almost all of these aptamers are specific to clinically important peptide or protein targets. In addition, the application of protein specific aptamers in the design and development of targeted drug delivery systems and diagnostic biosensors is another intersting field of aptamer technology. In this review, significant efforts related to development and applications of aptamer technologies in proteins and peptides sciences were considered to emphasis on the importance of aptamers in medicinal and clinical applications.     

Aptamers: versatile probes for flow cytometry

Aptamers are nucleic acid oligomers with distinct conformational shapes that allow them to bind targets with high affinity and specificity. Aptamers are selected from a random oligonucleotide library by their capability to bind a certain molecular target. A variety of targets ranging from small molecules like amino acids to complex targets and whole cells have been used to select aptamers. These characteristics and the ability to create specific aptamers against virtually any cell type in a process termed “systematic evolution by exponential enrichment” make them interesting tools for flow cytometry. In this contribution, we review the application of aptamers as probes for flow cytometry, especially cell-phenotyping and detection of various cancer cell lines and virus-infected cells and pathogens. We also discuss the potential of aptamers combined with nanoparticles such as quantum dots for the generation of new multivalent detector molecules with enhanced affinity and sensitivity. With regard to recent advancements in aptamer selection and the decreasing costs for oligonucleotide synthesis, aptamers may rise as potent competitors for antibodies as molecular probes in flow cytometry.     

研究报告: 基于遗传算法的计算机辅助策略优化孕酮适配体

目的 本研究致力于优化孕酮（progesterone,P4）适配体的亲和力和选择性。方法 基于遗传算法（genetic algorithm,GA）的计算机辅助优化策略（in silico maturation,ISM）,进行了4轮GA操作（含交叉变异、单点突变和双点突变操作）,构建了初始文库和G1、G2、G3代ssDNA作为新的候选适配体库,采用分子对接对候选适配体进行筛选和分析,并使用迭代策略不断优化适配体。此外,还提出了一种较为准确预测ssDNA三级结构的方法,首先使用Mfold预测二级结构,继而使用RNAComposer建立与ssDNA相对应的RNA三级结构,输出的PDB文件使用Discovery Studio将RNA修改为DNA,最后使用Molecular Operating Environment对结构进行能量最小化处理。结果 到G2代,在局部搜索空间对P4S-0进行优化,筛选出P4G1-14、P4G2-20、P4G1-6、P4G1-7和P4G2-14这5条适配体作为P4的最佳候选适配体。采用AuNPs比色法初步验证优化后适配体的亲和力,继而构建了基于适配体结构开关的荧光法测定适配体的解离常数（equilibrium dissociation constant,K_D）,并以此方法对适配体的选择性（对双酚A、雌二醇、睾酮和皮质醇）进行了评估。结论 通过ISM优化后的适配体,对P4的亲和力较原适配体有了较大提升,仍保留着识别结构类似分子的选择性。     

Aptamers as therapeutic and diagnostic agents

Aptamers are oligonucleotides derived from an in vitro evolution process called SELEX. Aptamers have been evolved to bind proteins which are associated with a number of disease states. Using this method, many powerful antagonists of such proteins have been found. In order for these antagonists to work in animal models of disease and in humans, it is necessary to modify the aptamers. First of all, sugar modifications of nucleoside triphosphates are necessary to render the resulting aptamers resistant to nucleases found in serum. Changing the 2'OH groups of ribose to 2'F or 2'NH2 groups yields aptamers which are long lived in blood. The relatively low molecular weight of aptamers (8000-12000) leads to rapid clearance from the blood. Aptamers can be kept in the circulation from hours to days by conjugating them to higher molecular weight vehicles. When modified, conjugated aptamers are injected into animals, they inhibit physiological functions known to be associated with their target proteins. A new approach to diagnostics is also described. Aptamer arrays on solid surfaces will become available rapidly because the SELEX protocol has been successfully automated. The use of photo-cross-linkable aptamers will allow the covalent attachment of aptamers to their cognate proteins, with very low backgrounds from other proteins in body fluids. Finally, protein staining with any reagent which distinguishes functional groups of amino acids from those of nucleic acids (and the solid support) will give a direct readout of proteins on the solid support.     

Fluorescent Muscarinic EGFP-hM1 Chimeric Receptors: Design,Ligand Binding and Functional Properties

Abstract

We describe the construction, expression and characterization of recombinant proteins comprising the enhanced green fluorescent protein (EGFP) fused to the ammo-terminal part of the muscarinic hMl receptor together or not with an additional hexahistidine tag placed at the C-terminal end of the receptor. Expression of the fluorescent proteins reaches levels identical to those of the wt hM1 receptor, provided that fusion takes place at the very N-terminal end of the receptor. Also correct protein folding and targeting to plasma membrane is obtained upon addition of a signal peptide promoting amino-terminal domain translocation through the membrane. Ligarid binding properties of –- and activation of the calcium release response by –- the fusion proteins are almost identical to those of the wild-type muscarinic receptor, indicating that such fluorescently-labelled receptors are valuable model systems for further functional, biochemical and structural studies.     

Design,Optimization, and Evaluation of Lurasidone Hydrochloride Nanocrystals

The present investigation was carried out to design, optimize, and evaluate lurasidone hydrochloride nanocrystals for improving its solubility and dissolution characteristics. Nanocrystals were prepared by media milling technique using zirconium oxide beads with 0.1 mm diameter. Various stabilizers, viz. poloxamer 188, PVP K30, SLS, HPMC E15, and PVP S 630 D, were evaluated to stabilize the nanocrystals. The Pareto chart obtained through Plackett-Burman screening design revealed that HPMC E 15 showed the highest standardized effect (p value <0.05) on percent dissolution efficiency at 2 min. In subsequent studies, a 3² factorial design was employed to quantify the effect of two independent variables, namely amount of stabilizer and milling time on predetermined response variables mean particle size, saturation solubility, and percent dissolution efficiency at 2 min. Statistical analysis of the factorial design revealed that all predetermined response variables were significantly dependent (p value <0.05) on the independent variables. The observed response of the optimized batch prepared as per the desirability function was in close agreement with predicted response, and mathematical model generated was validated. The optimized batch was lyophilized, and X-ray powder diffraction studies indicated that there was no substantial change in crystallinity of the drug. The optimized formulation showed mean particle size of 228 nm and released almost all the drug within first 5 min. Since the crystallinity of the drug is maintained, improvement in saturation solubility and dissolution efficiency could be attributed to decrease in mean particle size of the drug.