Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assist...Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.展开更多
依据对虾黄头病毒（Yellow head virus,YHV）的非结构蛋白N基因序列,设计特异的锁式探针（Padlock probe,PLP）、检测探针及引物,建立YHV超分支滚环扩增（Hyper-branched rolling circle amplification,HRCA）检测试纸。灵敏度实验显示,...依据对虾黄头病毒（Yellow head virus,YHV）的非结构蛋白N基因序列,设计特异的锁式探针（Padlock probe,PLP）、检测探针及引物,建立YHV超分支滚环扩增（Hyper-branched rolling circle amplification,HRCA）检测试纸。灵敏度实验显示,YHV HRCA检测试纸能检测出的最低模板量为101拷贝,是RT-PCR灵敏度的100倍。特异性实验结果表明,该试纸能够特异性地对YHV进行检测。利用该检测试纸对进出口80批次虾样本进行检测,并将检测结果与常规RT-PCR相比较,结果显示,YHV HRCA检测试纸灵敏度方面优于常规RT-PCR方法,且操作简便、结果直观易读。展开更多
依据传染性皮下及造血组织坏死病毒(infectious hypodermal and hematopoietic necrosis virus,IHHNV)的非结构蛋白NS1基因序列,设计特异的锁式探针,建立IHHNV病毒超分支滚环扩增(hyper-branched rolling circle amplification,HRCA)检...依据传染性皮下及造血组织坏死病毒(infectious hypodermal and hematopoietic necrosis virus,IHHNV)的非结构蛋白NS1基因序列,设计特异的锁式探针,建立IHHNV病毒超分支滚环扩增(hyper-branched rolling circle amplification,HRCA)检测方法并构建试纸条.结果表明,IHHNV HRCA试纸的检测限可以达到10拷贝/μL,较常规PCR法高约2个数量级,且能够保证对IHHNV的特异性检测.利用该试纸条对国产与进口的42份虾样本进行IHHNV检测,结果显示,HRCA试纸条在灵敏度上优于常规PCR,且方法直观、更易于结果判定.展开更多
Aberrant DNA methylation of CpG sites has been confirmed to be closely associated with carcinogenesis.Based on the hyperbranched rolling circle amplification（HRCA） and microarray techniques,a new method for qualitat...Aberrant DNA methylation of CpG sites has been confirmed to be closely associated with carcinogenesis.Based on the hyperbranched rolling circle amplification（HRCA） and microarray techniques,a new method for qualitative detection of methylation was developed.In the present study,padlock probes hybridize the sample DNA at the methylation site to form a probe-DNA complex which is ligated and digested simultaneously by methylation specific enzymes.Only at the methylated CpG site is the padlock probe ligated successfully to form a circle template for the HRCA reaction.Utilizing the method of 3-dimensional polyacrylamide gel-based microarray,the HRCA product will be immobilized on the slide to form a DNA microarray,which can universally hybridize the Cy3-labeled oligonucleotide probe to detect the methylation status of CpG sites.To control the false positive signals,DNA ligase and temperature of ligation/digestion are optimized.Methylation status of four CpG sites located in P15,Ecadherin,hMLH1 and MGMT genes were analyzed successfully with this method and all the results were compatible with that of methylation-specific PCR.Our research proves that this method is simple and inexpensive,and could be applied as a high-throughput tool to qualitatively determine the methylation status of CpG sites.展开更多
滚环扩增(rolling circle amplification,RCA)是新近发展起来的一种恒温核酸扩增方法。这种方法不仅可以直接扩增DNA和RNA,还可以实现对靶核酸的信号放大,灵敏度达到一个拷贝的核酸分子,因此在核酸检测中具有很大的应用价值和潜力。本...滚环扩增(rolling circle amplification,RCA)是新近发展起来的一种恒温核酸扩增方法。这种方法不仅可以直接扩增DNA和RNA,还可以实现对靶核酸的信号放大,灵敏度达到一个拷贝的核酸分子,因此在核酸检测中具有很大的应用价值和潜力。本文结合了滚环扩增技术在医药领域中的最新研究进展,介绍了滚环扩增的原理及其在医药领域中的应用。展开更多
文摘Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.
文摘依据对虾黄头病毒（Yellow head virus,YHV）的非结构蛋白N基因序列,设计特异的锁式探针（Padlock probe,PLP）、检测探针及引物,建立YHV超分支滚环扩增（Hyper-branched rolling circle amplification,HRCA）检测试纸。灵敏度实验显示,YHV HRCA检测试纸能检测出的最低模板量为101拷贝,是RT-PCR灵敏度的100倍。特异性实验结果表明,该试纸能够特异性地对YHV进行检测。利用该检测试纸对进出口80批次虾样本进行检测,并将检测结果与常规RT-PCR相比较,结果显示,YHV HRCA检测试纸灵敏度方面优于常规RT-PCR方法,且操作简便、结果直观易读。
文摘依据传染性皮下及造血组织坏死病毒(infectious hypodermal and hematopoietic necrosis virus,IHHNV)的非结构蛋白NS1基因序列,设计特异的锁式探针,建立IHHNV病毒超分支滚环扩增(hyper-branched rolling circle amplification,HRCA)检测方法并构建试纸条.结果表明,IHHNV HRCA试纸的检测限可以达到10拷贝/μL,较常规PCR法高约2个数量级,且能够保证对IHHNV的特异性检测.利用该试纸条对国产与进口的42份虾样本进行IHHNV检测,结果显示,HRCA试纸条在灵敏度上优于常规PCR,且方法直观、更易于结果判定.
基金supported by the Scientific Research Foundation of Mianyang Normal University(No.QD2012A10)Educational Commission of Sichuang Province,China(No.13ZB0275)
文摘Aberrant DNA methylation of CpG sites has been confirmed to be closely associated with carcinogenesis.Based on the hyperbranched rolling circle amplification（HRCA） and microarray techniques,a new method for qualitative detection of methylation was developed.In the present study,padlock probes hybridize the sample DNA at the methylation site to form a probe-DNA complex which is ligated and digested simultaneously by methylation specific enzymes.Only at the methylated CpG site is the padlock probe ligated successfully to form a circle template for the HRCA reaction.Utilizing the method of 3-dimensional polyacrylamide gel-based microarray,the HRCA product will be immobilized on the slide to form a DNA microarray,which can universally hybridize the Cy3-labeled oligonucleotide probe to detect the methylation status of CpG sites.To control the false positive signals,DNA ligase and temperature of ligation/digestion are optimized.Methylation status of four CpG sites located in P15,Ecadherin,hMLH1 and MGMT genes were analyzed successfully with this method and all the results were compatible with that of methylation-specific PCR.Our research proves that this method is simple and inexpensive,and could be applied as a high-throughput tool to qualitatively determine the methylation status of CpG sites.
文摘滚环扩增(rolling circle amplification,RCA)是新近发展起来的一种恒温核酸扩增方法。这种方法不仅可以直接扩增DNA和RNA,还可以实现对靶核酸的信号放大,灵敏度达到一个拷贝的核酸分子,因此在核酸检测中具有很大的应用价值和潜力。本文结合了滚环扩增技术在医药领域中的最新研究进展,介绍了滚环扩增的原理及其在医药领域中的应用。
