用SELEX技术筛选环孢霉素A适体

目的：运用指数富集的配体系统进化（SELEX）技术筛选并鉴定环孢霉素A（CsA）特异性适体。方法：合成全长78个核苷酸中间含35个随机序列的随机单链DNA（ssDNA）文库,通过SELEX方法,以CsA为靶标、磁珠为筛选介质,利用生物素-链亲和素-辣根过氧化物酶系统检测每轮ssDNA文库与CsA的亲和力,筛选针对CsA的适体,将最后一轮筛选产物克隆测序,并运用相关软件进行一级结构和二级结构分析。结果：经过10轮筛选,ssDNA文库与CsA的亲和力呈上升趋势,随机挑选的19个克隆适体根据一级结构的同源性可分为5个家族,二级结构预测以茎环（发夹）为主。结论：通过改良SELEX方法筛选得到了CsA特异性的适体。     

金黄色葡萄球菌外毒素B特异性适体的筛选及其应用

目的:利用指数富集配基的系统进化(SELEX)技术,筛选能与金黄色葡萄球菌外毒素B(SEB)特异、高亲和力结合的单链DNA(ssDNA)适体,并将该适体应用于患者血清标本的检测。方法:从体外合成的96核苷酸随机ss-DNA文库中,以羧基磁珠作为筛选介质,经逐步PCR扩增、筛选,获得针对SEB的高亲和力、高特异性适体;利用荧光素标记适体测定筛选过程中各轮结合力;利用酶连接适体方法检测适体特异性和结合力。结果:经过13轮筛选,ssDNA文库与SEB的结合百分率从1.1%提高到39.8%,增加了36倍;获得的ssDNA适体(A11)针对SEB的特异性强,与金黄色葡萄球菌表面蛋白A(SPA)结合低,并能初步识别患者血清。结论:利用SELEX技术筛选获得了特异结合SEB的高亲和力的ssDNA适体,为金黄色葡萄球菌的临床诊断与治疗奠定了基础。     

SELEX法体外筛选胃癌细胞适配子方法的建立

目的:建立SELEX技术筛选胃癌细胞SGC-7901适配子的方法,并初步鉴定获得的SGC-790 1细胞适配子.方法:体外合成全长88bp中间含52bp随机序列的ssDNA文库 ,通过优化PCR扩 增条件,利用地高辛-抗地高辛抗体-碱性磷酸酶系统测定亲和力,经SELEX反复筛选获得胃 癌SGC-7901细胞的特异性适配子.将最后一轮筛选产物克隆、测序并用相关软件分析适配子 序列的一级结构和二级结构.结果:经12轮SELEX筛选,ssDNA文库与SGC- 7901细胞的亲和力由0.16上升至1.14,表明特异性适配子得到逐步富集.22个克隆子测序, 有4个序列完全一致,二级结构预测茎环可能是适配子与胃癌细胞作用的结构基础.结论:成功建立了SELEX技术体外筛选胃癌细胞SGC-7901高亲和性适配子的方法.     

灭活铜绿假单胞菌适体的筛选

利用指数富集配基的系统进化(SELEX)技术,以灭活的铜绿假单胞菌为靶标,从体外合成的96 nt随机ssDNA文库中筛选与铜绿假单胞菌特异结合的适体.在第12轮和第14轮与其它假单胞菌属进行反筛策略,并进行了适体的结合亲和力的测定,再分别利用ClustalX、Mega2和Mfold sever软件分析适体的一级和二级结构.研究结果表明,经过15轮筛选,随机ssDNA文库与铜绿假单胞菌结合的A值从0.022上升到0.448.反筛与未反筛的结合A比值最高比为53倍.经过第15轮反筛后的24个阳性克隆子测序,根据软件分析,其可分成10个家族.每个家族都有其共同的保守序列（除第10个家族）,其中有2条序列几乎完全一致(F23和F47),同源性达到97%,A值分别高达1.598和1.508,Kd为14.55和77.46 nmol/L,间接说明适体与铜绿假单胞菌的结合力明显增高.     

随机单链DNA文库SELEX筛选寡核苷酸适配子方法的建立

指数富集配基的系统进化(SELEX)技术是一种新的组合化学技术.体外构建了一个长度为81 nt、含有35个随机序列的单链DNA(ssDNA)文库,优化了ssDNA文库扩增为双链DNA (dsDNA)文库的PCR反应条件.通过对比不对称PCR和生物素-链亲和素磁珠分离方法制备ssDNA文库的效果,确定了以生物素-链亲和素磁珠分离方法制备ssDNA.由于脱氧核糖核酸的疏水性导致ssDNA文库与硝酸纤维素滤膜的结合背景过高,因此选择以微孔板为介质,分离与靶蛋白结合的适配子.经过9轮循环筛选,随机ssDNA文库与丙型肝炎病毒(HCV)核心蛋白(C蛋白)的结合率从0.5%上升到32.5%.     

CP4- EPSPS转基因蛋白的适体筛选与亲和性分析

目的:通过筛选获得CP4 - EPSPS转基因蛋白的最优适体,为应用于检测作准备.方法:体外合成长度为78个碱基的随机ssDNA文库,应用指数富集配基的系统进化(SELEX)技术,以CP4 - EPSPS转基因蛋白为靶目标进行15轮筛选,将筛选到的适体群进行克隆、测序,用DNAMAN软件对每个适体的保守序列和二级结构进行分析并应用生物素-抗地高辛碱性磷酸酶显色系统进行亲和性分析.结果:成功获得靶目标的最优适体,即D04号适体,结合率最高(2.2745)为最低的5.9倍.结论:筛选流程合理、可行,实验结果较理想.     

基于Cell-SELEX的核酸适体在肿瘤中的应用研究进展

核酸适体是运用指数富集的配体系统进化(systematic evolution of ligand and byexponential enrichment,SELEX)技术从人工体外合成的随机寡核苷酸序列库中,经过多轮筛选后得到的单链DNA或RNA,具有识别靶标范围广、亲和力高和稳定性好等优势。Cell-SELEX技术是指将整个细胞作为靶标筛选特异性核酸适体的技术,近年来已经广泛应用于肿瘤细胞特异的核酸适体筛选。本研究综述了Cell-SELEX技术的筛选过程以及通过cell-SELEX技术产生的核酸适体在肿瘤标志物、肿瘤靶向治疗和循环肿瘤细胞的识别与检测等方面的应用研究进展。     

哈维氏弧菌适配子的SELEX筛选及其亲和特异性研究

哈维氏弧菌是水产养殖中的重要条件致病菌,对其进行快速、准确地检测和鉴定是相关病害防治的基础和关键.适配子具有亲和力高、特异性强、稳定性好等优点,在微生物的检测和鉴定方面呈现出广泛的应用前景.本研究以哈维氏弧菌为靶目标,采用SELEX技术,即指数级富集配体的系统进化技术,筛选其特异性适配子.经15轮筛选后,随机ssDNA文库的亲和力从3.51上升到58.95,提高了15.8倍.筛选出的适配子富集库经克隆、测序后得到52条不同序列,根据同源性将这些序列分成8个家族,其中第1和第2家族的适配子数量最多,超过总数的50%.通过深入分析,筛选出6个对哈维氏弧菌有显著亲和特异性(P0.01)的高频适配子,其中5个高频适配子(S1、S25、S26、S27、S35)对哈维氏弧菌有较高的亲和力,相应的亲和常数Kd值分别为(32.6±7.1)、(45.3±10.1)、(24.7±5.8)、(34.8±5.6)、(12.9±4.0)nmol/L.本文还对高频适配子的产生机制及其应用价值进行了探讨.本文首次筛选出了对哈维氏弧菌具有较高亲和特异性的适配子,为后续利用适配子进行哈维氏弧菌的检测和鉴定奠定了基础.     

从噬菌体随机肽库中筛选流感病毒神经氨酸酶的抑制多肽

目的:从噬菌体呈现12肽库中筛选与流感病毒神经氨酸酶特异性结合的肽。方法:以甲三型流感病毒裂解疫苗原液为靶分子,经过3轮生物淘选,从噬菌体随机肽库中筛选与之结合的噬菌体。用ELISA方法鉴定噬菌体克隆与靶分子的结合力,用荧光方法测定噬菌体克隆对流感病毒A/Sydney/5/97(H3N2)神经氨酸酶的抑制活性。对筛选到的阳性克隆进行DNA序列测定并推导出相应的氨基酸序列。结果:经过3轮筛选后,42个噬菌体克隆与靶分子有高度亲和力,23个噬菌体克隆对流感病毒A/Sydney/5/97(H3N2)神经氨酸酶有抑制活性。对27个噬菌体克隆的测序结果表明,分别有10个和2个克隆的序列是一致的,其氨基酸序列分别为KSLSRHDHIHHH和WPRHHHSASVQT。结论:通过噬菌体肽库筛选到抑制流感病毒神经氨酸酶的12肽,为进一步研究对流感病毒神经氨酸酶有抑制活性的分子药物奠定了基础。     

丙型肝炎病毒 NS3 螺旋酶寡核苷酸 适配子的筛选与鉴定

为筛选和鉴定抗丙型肝炎病毒 (HCV) NS3 螺旋酶 (NS3h) 的寡核苷酸适配子 (aptamers). 利用 SELEX 技术,以 HCV NS3h 为靶分子,从体外合成的 81 bp 随机单链 DNA 文库中筛选与 HCV NS3h 特异结合的寡核苷酸适配子 . 克隆测序后,进行了解离常数 (K_d) 测定和 Clustal W 软件包分析适配子一级结构 . 经过 8 轮循环筛选,随机 ssDNA 库与 HCV NS3h 的结合率从 0.45% 上升到 29.5%. 所有的一级结构没有共同的同源序列,但可分 5 个家族,其中 4 个家族具有共同的保守序列 . 解离常数测定表明,寡核苷酸适配子 H2 与 HCV NS3h 特异结合的亲和力最高,K_d值为 140 nmol/L. 适配子 H2 (10 μmol/L) 在体外对 HCV NS3h 的活性具有一定的抑制作用,抑制率达 44%. 利用随机寡核苷酸文库获得了抗 HCV NS3h 的寡核苷酸适配子 .     

In vitro selection of a DNA aptamer targeted against Shigella dysenteriae

To identify DNA aptamers demonstrating binding specificity for Shigella dysenteriae, a whole-bacterium Systemic Evolution of Ligands by Exponential enrichment (SELEX) method was applied to a combinatorial library of single-stranded DNA (ssDNA) molecules. After several rounds of selection using S. dysenteriae as the target, the highly enriched oligonucleotide pool was sequenced and then grouped into different families based on primary sequence homologies and similarities in the secondary structures. Aptamer S 1, which showed particularly high binding affinity in preliminary studies, was chosen for further characterisation. This aptamer displayed a dissociation constant (K_d value) of 23.47 ± 2.48 nM. Binding assays to assess the specificity of aptamer S 1 showed high binding affinity for S. dysenteriae and low apparent binding affinity for other bacteria. The ssDNA aptamers generated may serve as a new type of molecular probe for microbial pathogens, as it has the potential to overcome the tedious isolation and purification requirements for complex targets.     

抑制肿瘤坏死因子-α的DNA适配子的筛选与鉴定

应用SELEX技术筛选能与TNF结合的DNA适配子。化学合成随机寡聚DNA库,以TNF为靶蛋白,经过12轮SELEX筛选,将所得产物克隆、测序。根据所测序列化学合成寡聚DNA适配子,用生物素_亲和素_辣根过氧化物酶显色系统检测适配子与TNF的结合活性;用鼠L929细胞检测适配子拮抗TNF活性。结果显示,所筛选到的寡聚DNA能与TNF-α高亲和力结合,并能在细胞培养中拮抗TNF-α的细胞毒活性。     

A sol-gel-based microfluidics system enhances the efficiency of RNA aptamer selection

RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX often requiring many rounds of selection and amplification. Recently, we have shown the efficient binding and elution of RNA aptamers against target proteins using a microfluidic chip that incorporates 5 sol-gel binding droplets within which specific target proteins are imbedded. Here, we demonstrate that our microfluidic chip in a SELEX experiment greatly improved selection efficiency of RNA aptamers to TATA-binding protein, reducing the number of selection cycles needed to produce high affinity aptamers by about 80%. Many aptamers were identical or homologous to those isolated previously by conventional filter-binding SELEX. The microfluidic chip SELEX is readily scalable using a sol-gel microarray-based target multiplexing. Additionally, we show that sol-gel embedded protein arrays can be used as a high-throughput assay for quantifying binding affinities of aptamers.     

Selection and Identification of Aptamers Against B Cell Activating Factor

Systemic lupus erythematosus (SLE) is the most common autoimmune disease in China. B cell activating factor (BAFF) is an important target for the treatment and detection of SLE. It is of great significance to develop novel molecular recognition elements with high affinity for BAFF. In this study, artificial nucleic acid aptamers against BAFF were screened from a 78 nt single-stranded DNA random library by systematic evolution of ligands exponential enrichment (SELEX) in vitro based on several selection and amplification steps. Through ten rounds of selection, the aptamers with high specificity and affinity for BAFF were identified. After high-throughput sequencing, several aptamers were selected and further examined for binding affinity and specificity. The investigation by dot blotting, Eastern blotting analyses and enzyme-linked oligonucleotide assay (ELONA) showed that the aptamers Apt 7 and Apt 12 with dissociation constants of 241.00±19.75 nmol/L and 413.51±46.94 nmol/L were able to recognize BAFF specifically. After molecular docking analysis, Apt 7 was truncated to Apt 7～1, and the dissociation constant was 192.10±28.61 nmol/L. A sandwich ELONA using Apt 7～1 and BAFF antibodies was established to detect BAFF. The detection limit was estimated to be 0.227 nmol/L. This study provides new molecular recognition elements for the detection of BAFF and the study of antagonists.     

全细菌SELEX法筛选粪肠球菌特异性适配体

肠球菌（Enterococcus）是内源性和外源性医院感染的第二大病原菌,检出率仅次于大肠杆菌,从分子水平上发展靶标的高亲和力分子探针对肠球菌的识别和检测具有非常重要的意义。本研究以粪肠球菌为靶标,运用全细菌指数富集的配体系统进化技术（whole-bacteria systematic evolution of ligands by exponential enrichment, whole-bacteria SELEX）,从全长为79个核苷酸包含35个随机碱基序列的单链DNA文库中筛选与靶标高亲和力、高特异性结合的适配体,利用荧光分析法监控筛选过程中不同轮次所得次级文库与粪肠球菌的结合力,经12轮筛选和克隆测序,获得了39条适配体序列。进一步对筛选得到的适配体进行序列比对、二级结构分析、流式细胞分析、解离常数（Kd）测定及特异性验证,最终获得一条与粪肠球菌能特异性结合的适配体Apt 21,其Kd值为549.2 ± 147.4 nmol/L。该适配体可作为粪肠球菌检测的识别元件,为建立基于适配体的新型粪肠球菌检测方法奠定了基础。     

两种富集方法相结合对蓖麻毒素进行SELEX筛选研究

为了获得能特异识别具有细胞毒性的蓖麻毒素蛋白寡核苷酸适配子,体外构建了含40个随机序列全长87nt的随机ssDNA文库,采用指数富集配基的系统进化(SELEX)技术方法,结合微孔板和亲和树脂两种分离、富集方法,经过数轮筛选,文库与蓖麻毒素的结合率达到了38．5％。结果表明,以亲和树脂为分离介质进行筛选,富集效果非常明显。     

In silico selection of RNA aptamers

In vitro selection of RNA aptamers that bind to a specific ligand usually begins with a random pool of RNA sequences. We propose a computational approach for designing a starting pool of RNA sequences for the selection of RNA aptamers for specific analyte binding. Our approach consists of three steps: (i) selection of RNA sequences based on their secondary structure, (ii) generating a library of three-dimensional (3D) structures of RNA molecules and (iii) high-throughput virtual screening of this library to select aptamers with binding affinity to a desired small molecule. We developed a set of criteria that allows one to select a sequence with potential binding affinity from a pool of random sequences and developed a protocol for RNA 3D structure prediction. As verification, we tested the performance of in silico selection on a set of six known aptamer–ligand complexes. The structures of the native sequences for the ligands in the testing set were among the top 5% of the selected structures. The proposed approach reduces the RNA sequences search space by four to five orders of magnitude—significantly accelerating the experimental screening and selection of high-affinity aptamers.     

Conservative secondary structure motif of streptavidin-binding aptamers generated by different laboratories

Aptamers that are selected in vitro from random pools of DNA or RNA molecules by SELEX (Systematic evolution of ligands by exponential enrichment) technique have been extensively explored for analytical and biomedical applications. Although many aptamers with high affinity and specificity against specific ligands have been reported, there is still a lack of well characterized DNA aptamers. Here we report the selection of a group of aptamer candidates (85 mer) against streptavidin. Through comparing the predicted secondary structures of all the candidates, a conservative bulge-hairpin structure section (about 29 mer) was found, and then it was determined to be the binding motif to streptavidin. This binding motif was further discovered to also exist in streptavidin-binding aptamers (SBAs) selected by three other laboratories using different methods. The primary sequences of this secondary structure motif are very different, only several nucleotides in the loop and bulge area are critical for binding and other nucleotides are variable. The streptavidin binding of all the SBAs could be competed by biotin implying that they bind to the same site on streptavidin. These results suggest that the evolution of SBA is predominated by specific groups on streptavidin. The highly variable sequence composition of streptavidin-binding aptamer would make the design of aptameric sensor or device based on streptavidin more flexible and easy.     

RNA aptamers to S-adenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S-adenosylhomocysteine antibody

To explore the potential of RNA aptamers as small-molecule discriminating devices, we have characterized the properties of aptamers selected from a library of approximately 10(14) variants through their interaction with S-adenosylhomocysteine (SAH, AdoHcy). Competition studies with SAH and azaSAM analogues revealed that the Hoogsteen face of adenine is the main contributor to binding, whereas specificity for SAH is conferred by a secondary contact point at or near the sulfur/thioether of homocysteine (Hcy). Binding specificities were determined by both affinity chromatography and a novel method designed for the biosensor. The kinetic properties of individual aptamers, including the "classic" ATP aptamer that also emerged in our selection, were studied by biosensor analysis. Association rates were slow, but the complexes were stable, suggesting micro- to submicromolar affinities. A solution affinity of approximately 0.1 microM was found for the strongest binding variant under the conditions used for selection (5 mM Mg(2+)). Systematic studies of the effect of Mg(2+) and Mn(2+) on binding, however, revealed that the affinity of the aptamers could be substantially improved, and at optimized conditions of Mn(2+) the affinity of one of the aptamers approached that of an anti-SAH antibody with similar/identical binding specificity. Comparisons with the MAb suggest that the on rate is the limiting factor for high-affinity binding by these aptamers, and comparison with a truncated aptamer shows that shortening of RNA constructs may alter binding kinetics as well as sensitivity to ions.