识别氨基酸序列的aptamer蛋白配体研究
摘要
我们设计了一种新的蛋白配体，这种配体能够识别蛋白质的氨基酸序列并捕获蛋白。这种方法的原理是能够识别三肽的DNA aptamer可以识别蛋白内部的相同序列。我们使用小鼠Cathepsin D蛋白来验证这个方法。根据发表的Cathepsin D蛋白的氨基酸序列选择四个三肽：Leu-Ala-Ser(LAS)、Asp-Gly-Ile(DGI)、Gly-Glu-Leu(GEL)和Lys-Ala-Ile(KAI)。通过指数富集的配体系统进化(Systematic Evolution of Ligands of Exponential enrichment，SELEX)技术筛选能够结合LAS、DGI、GEL和KAI这些三肽的DNA aptamer。用structure-switch signaling aptamer的方法进行检测，结果表明这种筛选得到的aptamer能够识别Cathepsin D蛋白中的相应序列，并且Cathepsin D蛋白可以被多种aptamer包被的磁珠捕获。这四个aptamer能够通过滚环DNA复制的方法检测到fM浓度的Cathepsin D蛋白。这是一种非常有潜力的蛋白芯片配体，可以应用到蛋白芯片技术中。
筛选能够识别三肽的aptamer
LAS、DGI、GEL和KAI三肽合成后分别偶联到HiTrap NHS活化柱上。起始单链DNA随机库为96个碱基短链核苷酸的混合物，其中含有60个随机插入序列。洗脱与三肽结合的单链DNA后进行PCR扩增，再进行单链PCR，得到的单链PCR产物进一步使用三肽亲和柱筛选，这样可以生成亚库。筛选过程重复了12次后，对最后得到的产物进行克隆和测序。选择GEL-aptmer、KAI-aptmer、DGI-aptamer和LAS-aptamer四个aptamer作为配体，以此来验证根据蛋白质氨基酸序列识别和捕获蛋白的技术。
验证aptamer与蛋白之间的相互作用
我们推测能够结合三肽的aptamer同样可以结合蛋白中所含有的相同序列。采用structure-switching signaling aptamer的方法来验证aptamer与蛋白之间的相互作用。在这个实验中，当蛋白和aptamer相互作用时会产生可以被检测到的荧光信号。结果表明加入Cathepsin D蛋白可以增加荧光信号而且随浓度升高荧光增强，但是加入的BSA即使在高浓度也不会生成荧光信号。这个结果表明与三肽相互作用的aptamer可以结合蛋白中所含有的相同序列，并且它们之间的相互作用具有特异性。
Aptamer组合可以捕获Cathepsin D蛋白
我们推测四个aptamer可以与Cathepsin D蛋白上的四个三肽序列结合，所以将对Cathepsin D蛋白有最高的亲和性。依此类推，三个aptamer将会比两个aptamer的亲和性高。在部分纯化的小鼠Cathepsin D蛋白中混入大量BSA蛋白和溶菌酶形成混合蛋白溶液，将生物素标记的aptamer结合到链霉素亲和素标记的磁珠上，这个蛋白溶液与磁珠相互作用，通过盐浓度梯度洗脱后用NaOH溶液洗脱并收集蛋白。实验结果表明四个aptamer组合比其它组合富集的蛋白多。随后，我们把表达重组Cathepsin D蛋白的大肠杆菌裂解液直接与磁珠相互作用，结果三个aptamer组合与四个aptamer组合在相同的洗脱条件下具有相近的蛋白捕获效率。
利用基于滚环DNA复制的多个aptamer检测Cathepsin D蛋白
根据proximity-dependent DNA连接的原理，所有四个aptamer结合Cathepsin D蛋白后能够被连接成环状单链DNA，并且可以使用滚环DNA复制的方法扩增。我们推测根据structure-switch原理设计两臂，使两臂分别与aptamer互补，可以降低背景连接反应。合成四个根据structure-switch原理设计的aptamer进行实验，结果表明Cathepsin D蛋白能够在fM水平促进这四个aptamer连接成环状单链DNA，这样就可以通过滚环DNA复制检测。对照组为只含有三个三肽的重组Cathepsin D蛋白，即使在nM水平也没有得到扩增。表明这个检测体系的背景非常低，并且对Cathepsin D蛋白具有较高的灵敏性和特异性。
We have designed and developed a technology that could capture proteins based on the amino acid sequences (CPAS). Mouse cathepsin D was used for the proof of principle experiment. Four tripeptides, LAS, DGI, GEL, and KAI, were selected based on the published sequence of mouse cathepsin D. DNA aptamers against the tripeptides were isolated using Systematic Evolution of Ligands of Exponential enrichment method. We have demonstrated that the aptamers targeted to sythesized tripepetide was able to recognize tripeptides in protein by structure-switch signaling method. Furthermore, cathepsin D could be captured by the magnetic beads which were coated with biotin-labeled aptamers. The aptamers have also been successfully used to detect cathepsin D protein at fM level using rolling circle amplification method. This technology is potential to be applied for protein array development.Isolation of DNA aptamers against tripeptides.The tripeptides were synthesized and coupled to HiTrap NHS-activated column. The starting DNA pool was a mixture of 96-mer single-stranded DNA (ssDNA) molecules that had randomized 60-nucleotide inserts. The ssDNA molecules that bound to the tripeptides were eluted and amplified by PCR. The PCR products were further selected using the tripeptide affinity columns for sub-library generation. The selection procedure was repeated twelve times and the final products were cloned and sequenced. Four aptamers, GEL-aptmer, KAI-aptmer, DGI-aptamer and LAS-aptamer, were used for proof of principle analysis of CPAS technology.Detection of aptamer-protein interaction.We postulated that the DNA aptamer targeting to tripeptide should be able to interact with proteins containing the tripeptide sequences. The structure-switching method was used to test the interaction. In this assay, the fluorescence signals can be detected when the aptamers interact with proteins. Our results demonstrated that addition of the protein resulted in the elevation of fluorescence signals in a dose response manner while the added BSA did not induce any fluorescence signal even at relatively high concentration. These results suggested that DNA aptamers targeting to tripcpetidcs could interact with the proteins containing the tripcptide sequences and the interactions between the aptamers and proteins were specific.
Capture of the mouse Cathepsin D protein by combination of several aptamers.
We postulated that the combination of four aptamers could interact with all four tripeptide sequences of Cathepsin D, and therefore had the highest affinity for the protein. Similarly, three aptamers should have higher affinity than two aptamers and so on. The partially purified recombinant mouse Cathepsin D protein in a solution containing excess amount of BSA and lysozyme was applied to the magnetic beads which was coated with streptividin and was able to bind biotin-labeled aptamers. The beads were washed with increasing concentrations of salt and finally the protein was eluted with NaOH solution. Our results showed that four aptamers could capture more Cathepsin D protein than three or less aptamers. Next, we directly applied recombinant E. coli iysis containing the mouse Cathepsin D protein to the beads. Three aptamers, LAS, KAI and GEL, could capture the protein as efficiently as four aptamers with the same stringency wash condition.
Detection of Cathepsin D protein by RCA based proximity-dependent multiple aptamers ligation assay.
Based on proximity-dependent DNA ligation principle, all four aptamers binding to Cathepsin D protein would be ligated to a circle and then can be amplified by rolling circle amplification. We postulated that structure-switch arms, two arms annealing to the aptamer itself, will decrease the background. Four aptamers with structure-switch arms were synthesized. The Cathepsin D protein could enhance the ligation at fM level and can be detected by rolling circle amplification. Recombinant Cathepsin D protein with 3 tripeptieds could not generate any signal even at nM level. The background ligation was very low and the assay was much more sensitive and specific for the Cathepsin D protein.
筛选能够识别三肽的aptamer
LAS、DGI、GEL和KAI三肽合成后分别偶联到HiTrap NHS活化柱上。起始单链DNA随机库为96个碱基短链核苷酸的混合物，其中含有60个随机插入序列。洗脱与三肽结合的单链DNA后进行PCR扩增，再进行单链PCR，得到的单链PCR产物进一步使用三肽亲和柱筛选，这样可以生成亚库。筛选过程重复了12次后，对最后得到的产物进行克隆和测序。选择GEL-aptmer、KAI-aptmer、DGI-aptamer和LAS-aptamer四个aptamer作为配体，以此来验证根据蛋白质氨基酸序列识别和捕获蛋白的技术。
验证aptamer与蛋白之间的相互作用
我们推测能够结合三肽的aptamer同样可以结合蛋白中所含有的相同序列。采用structure-switching signaling aptamer的方法来验证aptamer与蛋白之间的相互作用。在这个实验中，当蛋白和aptamer相互作用时会产生可以被检测到的荧光信号。结果表明加入Cathepsin D蛋白可以增加荧光信号而且随浓度升高荧光增强，但是加入的BSA即使在高浓度也不会生成荧光信号。这个结果表明与三肽相互作用的aptamer可以结合蛋白中所含有的相同序列，并且它们之间的相互作用具有特异性。
Aptamer组合可以捕获Cathepsin D蛋白
我们推测四个aptamer可以与Cathepsin D蛋白上的四个三肽序列结合，所以将对Cathepsin D蛋白有最高的亲和性。依此类推，三个aptamer将会比两个aptamer的亲和性高。在部分纯化的小鼠Cathepsin D蛋白中混入大量BSA蛋白和溶菌酶形成混合蛋白溶液，将生物素标记的aptamer结合到链霉素亲和素标记的磁珠上，这个蛋白溶液与磁珠相互作用，通过盐浓度梯度洗脱后用NaOH溶液洗脱并收集蛋白。实验结果表明四个aptamer组合比其它组合富集的蛋白多。随后，我们把表达重组Cathepsin D蛋白的大肠杆菌裂解液直接与磁珠相互作用，结果三个aptamer组合与四个aptamer组合在相同的洗脱条件下具有相近的蛋白捕获效率。
利用基于滚环DNA复制的多个aptamer检测Cathepsin D蛋白
根据proximity-dependent DNA连接的原理，所有四个aptamer结合Cathepsin D蛋白后能够被连接成环状单链DNA，并且可以使用滚环DNA复制的方法扩增。我们推测根据structure-switch原理设计两臂，使两臂分别与aptamer互补，可以降低背景连接反应。合成四个根据structure-switch原理设计的aptamer进行实验，结果表明Cathepsin D蛋白能够在fM水平促进这四个aptamer连接成环状单链DNA，这样就可以通过滚环DNA复制检测。对照组为只含有三个三肽的重组Cathepsin D蛋白，即使在nM水平也没有得到扩增。表明这个检测体系的背景非常低，并且对Cathepsin D蛋白具有较高的灵敏性和特异性。
We have designed and developed a technology that could capture proteins based on the amino acid sequences (CPAS). Mouse cathepsin D was used for the proof of principle experiment. Four tripeptides, LAS, DGI, GEL, and KAI, were selected based on the published sequence of mouse cathepsin D. DNA aptamers against the tripeptides were isolated using Systematic Evolution of Ligands of Exponential enrichment method. We have demonstrated that the aptamers targeted to sythesized tripepetide was able to recognize tripeptides in protein by structure-switch signaling method. Furthermore, cathepsin D could be captured by the magnetic beads which were coated with biotin-labeled aptamers. The aptamers have also been successfully used to detect cathepsin D protein at fM level using rolling circle amplification method. This technology is potential to be applied for protein array development.Isolation of DNA aptamers against tripeptides.The tripeptides were synthesized and coupled to HiTrap NHS-activated column. The starting DNA pool was a mixture of 96-mer single-stranded DNA (ssDNA) molecules that had randomized 60-nucleotide inserts. The ssDNA molecules that bound to the tripeptides were eluted and amplified by PCR. The PCR products were further selected using the tripeptide affinity columns for sub-library generation. The selection procedure was repeated twelve times and the final products were cloned and sequenced. Four aptamers, GEL-aptmer, KAI-aptmer, DGI-aptamer and LAS-aptamer, were used for proof of principle analysis of CPAS technology.Detection of aptamer-protein interaction.We postulated that the DNA aptamer targeting to tripeptide should be able to interact with proteins containing the tripeptide sequences. The structure-switching method was used to test the interaction. In this assay, the fluorescence signals can be detected when the aptamers interact with proteins. Our results demonstrated that addition of the protein resulted in the elevation of fluorescence signals in a dose response manner while the added BSA did not induce any fluorescence signal even at relatively high concentration. These results suggested that DNA aptamers targeting to tripcpetidcs could interact with the proteins containing the tripcptide sequences and the interactions between the aptamers and proteins were specific.
Capture of the mouse Cathepsin D protein by combination of several aptamers.
We postulated that the combination of four aptamers could interact with all four tripeptide sequences of Cathepsin D, and therefore had the highest affinity for the protein. Similarly, three aptamers should have higher affinity than two aptamers and so on. The partially purified recombinant mouse Cathepsin D protein in a solution containing excess amount of BSA and lysozyme was applied to the magnetic beads which was coated with streptividin and was able to bind biotin-labeled aptamers. The beads were washed with increasing concentrations of salt and finally the protein was eluted with NaOH solution. Our results showed that four aptamers could capture more Cathepsin D protein than three or less aptamers. Next, we directly applied recombinant E. coli iysis containing the mouse Cathepsin D protein to the beads. Three aptamers, LAS, KAI and GEL, could capture the protein as efficiently as four aptamers with the same stringency wash condition.
Detection of Cathepsin D protein by RCA based proximity-dependent multiple aptamers ligation assay.
Based on proximity-dependent DNA ligation principle, all four aptamers binding to Cathepsin D protein would be ligated to a circle and then can be amplified by rolling circle amplification. We postulated that structure-switch arms, two arms annealing to the aptamer itself, will decrease the background. Four aptamers with structure-switch arms were synthesized. The Cathepsin D protein could enhance the ligation at fM level and can be detected by rolling circle amplification. Recombinant Cathepsin D protein with 3 tripeptieds could not generate any signal even at nM level. The background ligation was very low and the assay was much more sensitive and specific for the Cathepsin D protein.
引文
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