基于电化学技术的microRNA生物传感器

MicroRNA(miRNA)是一种内源性的非编码单链RNA,通过与mRNA的3'端非翻译区(UTR)的不完全互补或完全互补结合抑制靶mRNA的翻译或促使靶mRNA的降解来调控基因的表达,参与细胞的增殖、凋亡、分化和代谢等重要过程。MiRNA表达的变化可以起到癌基因和抑癌基因的作用,是一种潜在的肿瘤标志物,因此,miRNA的检测技术引起了人们的关注。由于电化学检测方法具有灵敏、快速、低成本和低能耗等特点,研究者广泛开展了应用电化学技术来发展miRNA检测的研究。本文将对基于电化学技术的miRNA检测方法进行综述。     

超灵敏检测miRNA

最新研究表明MicroRNAs(miRNA)在细胞内的异常表达与人类疾病具有密切的关系,并且miRNA有望成为一种肿瘤标志物和治疗靶点。miRNA在细胞增殖、分化和凋亡等生物学过程中起着重要作用。最新研究表明miRNA在细胞内的异常表达与人类疾病具有密切的关系,并且miRNA有望成为一种肿瘤标志物和治疗靶点。传统的Northern杂交法和实时定量PCR技术常被用于miRNA的分析,但其灵敏度低与特异性差等局限性限制了这两种方法的广泛应用。因     

MicroRNA分析方法进展*

MicroRNAs（miRNAs）是一类对基因表达具有调控作用的非编码小分子RNA (18–23 碱基)。MiRNA在动植物中普遍存在,并且在动植物的生长、发育、分化和生殖等过程中发挥着重要作用。人类约30%的基因受miRNA调控,并且miRNA的表达水平与人类重大疾病密切相关。MiRNA的定量检测和表达分析对深入理解其作用机制、疾病的诊断与治疗以及相关基因药物的开发等具有重要意义。MiRNA检测一般是基于核酸杂交和扩增原理,方法主要有Northern印迹、微阵列芯片、原位杂交、实时反转录聚合酶链式反应（PCR）、滚环扩增和基于共轭聚合物的检测等。随着miRNA在不同生物中的大量发现和对其功能的深入研究,miRNA的检测方法不断改进和完善,新的扩增、探针标记技术和检测技术不断被开发。本文综述了miRNA检测方法的研究进展,评述了各类方法的优缺点,并对miRNA检测的发展趋势进行了展望。     

纳米孔道单分子检测结直肠癌MicroRNAs

MicroRNA（miRNA）可用于癌症的早期诊断、预后判断,其分析检测具有重要临床意义.结直肠癌的发生、发展与miRNA 21、miRNA 92等的异常表达明显相关.本研究设计了以poly（dT）_n为引导链的DNA探针（probe）并尝试使用α-溶血素（α-HL）纳米孔道单分子检测方法检测结直肠癌miRNAs.miRNA·probe复合物分子穿过α-HL纳米孔道限域空间时,由于probe链长、序列不同导致probe-α-HL相互作用不同,miRNA 92·probe 92、miRNA 21·probe 21、miRNA 16·probe 16输出为形态、阻断时间不同的多台阶特征信号,实现了三种miRNAs的有效区分.实验证明,此方法可以用于检测血清实际样品.因此,未来有望使用α-HL构建miRNA超灵敏单分子生物传感器.     

基于illumina测序技术的IGROV-1/CP细胞中miRNA种类鉴定及相对丰度分析

从正常培养的IGROV-1/CP细胞中提取小RNA,构建小RNA的cDNA文库,然后用illumina通用测序平台对上述cDNA文库进行测序.从测序获得的序列数据中去除冗余数据后,与已知人类miRNA序列数据库进行比对,获得IGROV-1/CP细胞miRNA表达谱.以所获的序列长度与已知人类miRNA数据库中序列长度差异不大于2和无碱基错配为限制条件,共找到53种已知miRNA.按在cDNA文库测序中的出现频率计算,出现频率不大于10的低拷贝miRNA最多,占检测到所有miRNA种类的56.6%.说明illumina通用测序技术能够在检测细胞内的各种小RNA序列的同时反应相对丰度信息,该研究利用上述新技术获得了顺铂耐药性IGROV-1/CP细胞系miRNA表达种类和相对丰度的实验数据.     

miRNA在β_2受体激动剂作用中的研究进展

β_2受体激动剂的滥用威胁着消费者的人身安全,也制约着食品工业和畜牧业的发展,然而药物种类繁多,更新迅速,如何对其有效监测一直是研究的重点小分子RNA(miRNA)是近年来在真核生物体内发现的一类长度约22个核苷酸的内源性非编码单链RNA,主要通过与靶基因mRNA靶标区域的互补配对,发挥降解靶mRNA或抑制mRNA翻译的作用。它能参与多种生物学过程包括细胞凋亡、分化和癌变等。β_2受体激动剂类药物有着共同的作用机理,近年来的研究表明,miRNA的异常表达与β_2受体激动剂的使用密切相关。本文主要对与β_2受体激动剂作用机理相关的miRNA的研究进展展开综述,以期为实现对该类药物的有效监测提供参考。     

综合分析MicroRNA-mRNA相互作用预测中的特征重要性

MicroRNA是大约22个核苷酸的非编码RNA分子,在它的3'端有1～2个核苷酸的悬垂.在真核生物中,它因为影响信使RNA的翻译和稳定性而闻名,并涉及发育,分化,细胞调亡等各种生物过程~([1]).据报道有1/3的人类基因能被miRNA所靶定,且有证据证明它与很多癌症有直接或间接的联系.阶段特异性,组织特异性和相对小的表达量导致了它的复杂性,从而探索miRNA的奥秘成为一个非常重要且有挑战性的问题.     

RNA生物标志物体外检测方法研究进展

RNA生物标志物主要包括编码蛋白的mRNA和非编码蛋白的microRNA (miRNA)、环状RNA (circula rRNA, circRNA)及长链非编码RNA (lncRNA)等.RNA生物标志物种类多,生物信息量丰富,相比DNA更能动态反映细胞生物学功能和调控过程,因此,RNA生物标志物的定量检测和表达分析对于细胞功能研究、疾病的诊断和治疗及预后监测等具有重要意义.本文重点介绍了常见RNA生物标志物mRNA、miRNA、circRNA和lncRNA体外检测方法的原理及研究进展,并对RNA生物标志物检测面临的挑战及发展趋势进行了展望.     

基于miRNA-靶位点配对的序列特征研究

miRNA与其靶基因的作用机制十分复杂,因此,miRNA靶基因识别问题一直是miRNA研究领域的热点难题。该文基于CLASH数据集,提出了miRNA-靶位点配对序列特征,并使用随机森林建模。实验结果表明,本模型的Acc,Sen,Spe,Pre以及Mcc分别达到90.05%,89.47%,90.56%,90.43%和0.799 8;ROC和PRC的AUC分别为0.954,0.958。相比已有方法,该方法表现出更加良好的性能,说明新引入的miRNA-靶位点配对序列特征对miRNA靶基因识别有很重大的影响。     

双链特异性核酸酶介导的高灵敏度microRNA分析

基于氧化石墨烯(GO)对荧光标记单链DNA探针的荧光猝灭效应以及双链特异性核酸酶(DSN)选择性切割DNA/RNA杂合结构中DNA单链的特性,本文建立了一种新型恒温信号放大方法用于microRNA(miRNA)的高灵敏度检测.靶标miRNA首先与荧光DNA探针杂交,DSN能够特异性地将杂合双链中的DNA探针水解为碎片但不会降解miRNA,GO对酶切产生的寡核苷酸碎片吸附能力显著降低,使得荧光基团远离GO表面而不被猝灭.释放出的miRNA可再次发生与荧光DNA探针杂交、DSN酶切等反应,如此反复,可实现恒温条件下一个miRNA分子与多个探针杂交、酶切、释放荧光基团的循环过程,最终体系的荧光信号得到显著放大,通过记录体系的荧光信号即可实现对靶标miRNA的灵敏检测.     

Trends in microRNA detection

MicroRNAs (miRNAs) are short, ~22 nucleotide length RNAs that perform gene regulation. Recently, miRNA has been shown to be linked with the onset of cancer and other diseases based on miRNA expression levels. It is important, therefore, to understand miRNA function as it pertains to disease onset; however, in order to fully understand miRNA’s role in a disease, it is necessary to detect the expression levels of these small molecules. The most widely used miRNA detection method is Northern blotting, which is considered as the standard of miRNA detection methods. This method, however, is time-consuming and has low sensitivity. This has led to an increase in the amount of detection methods available. These detection methods are either solid phase, occurring on a solid support, or solution phase, occurring in solution. While the solid-phase methods are adaptable to high-throughput screening and possess higher sensitivity than Northern blotting, they lack the ability for in vivo use and are often time-consuming. The solution-phase methods are advantageous in that they can be performed in vivo, are very sensitive, and are rapid; however, they cannot be applied in high-throughput settings. Although there are multiple detection methods available, including microarray technology, luminescence-based assays, electrochemical assays, etc., there is still much work to be done regarding miRNA detection. The current gaps of miRNA detection include the ability to perform multiplex, sensitive detection of miRNA with single-nucleotide specificity along with the standardization of these new methods. Current miRNA detection methods, gaps in these methods, miRNA therapeutic options, and the future outlook of miRNA detection are presented here.     

Highly sensitive detection of microRNA by chemiluminescence based on enzymatic polymerization

We have developed a new methodology for miRNA assay using chemiluminescence imaging by poly(U) polymerase catalyzed miRNA polymerization. This method is very sensitive with a 50 fM limit of detection, which is comparable to or better than current assay methods. Multiplex detection for miRNA can be easily realized by introducing different capture probes onto the biosensor array, which will make it highly versatile for various research purposes.     

MicroRNA的超灵敏检测研究进展

综述了最新发展的MicroRNA(miRNA)分析方法, 包括比色、 荧光、 化学发光、 表面增强拉曼、 单分子检测和电化学分析, 并对miRNA检测的发展方向做了展望.     

Os(VI)bipy-based electrochemical assay for detection of specific microRNAs as potential cancer biomarkers

Recently, altered expression levels of microRNAs (miRNAs) – short noncoding RNA molecules which bind to mRNAs and thus regulate gene expression – were observed in many cancer cells. miRNA expression profiling is therefore of great interest, but current standard methods are still considered relatively laborious and expensive. Electrochemistry has a potential to become quick and inexpensive alternative. Here, we describe modification of miRNA with an electroactive complex composed of six-valent osmium and 2,2′-bipyridine, Os(VI)bipy, specifically binding to the 3′-end of the ribose, which is detectable at hanging mercury drop electrode at femtomole level due to an electrocatalytic nature of a resulting signal. By combining miRNA labeling step with magnetic beads-based hybridization assay, detection of specific miRNA sequence from a mixture of other noncomplementary miRNAs was possible.     

Analysis of the NCI-60 dataset for cancer-related microRNA and mRNA using expression profiles

BackgroundRecent studies have indicated that microRNA (miRNA) may play an oncogenic or tumor suppressor role in human cancer. To study the regulatory role of miRNAs in tumorigenesis, an integrated platform has been set up to provide a user friendly interface for query. The main advantage of the present platform is that all the miRNA target genes’ information and disease records are drawn from experimentally verified or high confidence records.ResultsMiRNA target gene results are annotated with reference to the disease gene as well as the pathway database. The correlation strength between miRNA and target gene expression profile is quantified by computing the correlation coefficient using the NCI-60 expression profiling data. Comprehensive analysis of the NCI-60 data found that the cumulative percentage of negative correlation coefficients for cleavage regulation is slightly higher than its positive counterpart; which indicated that the mRNA degradation mechanism is slightly dominant. In addition, the RNAHybrid and TargetScans scores are computed which potentially served as quantitative estimators for miRNA–mRNA binding events.Three scores are defined for each miRNA–mRNA pair, which are based on the disease gene and pathway information. These three scores allow user to sort out high confidence cancer-related miRNA–mRNA pairs.Statistical tests were applied to investigate the relations of three chromosomal features, i.e., CpG island, fragile site, and miRNA cluster, with cancer-related miRNAs. A web-based interface has been set up for query, which can be accessed at: http://ppi.bioinfo.asia.edu.tw/mirna_target/ConclusionsThe main advantage of the present platform on miRNA–mRNA targeting information is that all the target genes’ information and disease records are experimentally verified. Although this may limit the number of miRNA–mRNA relationships, the results provided here are more solid and have fewer false positive events. Certain novel cancer-related miRNA–mRNA pairs are identified and confirmed in the literature. Fisher's exact test suggests that CpG island and fragile site associated miRNAs tend to associate with cancer formation. In summary, the present platform provides an easy means of investigating cancer-related miRNAs.     

Entropy-driven reactions in living cells for assay let-7a microRNA

Imaging of microRNA (miRNA) in living cells could facilitate the monitoring of the expression and distribution of miRNA and research on miRNA-related diseases. Given the low expression levels and even down-regulation of cellular miRNA that is associated with some diseases, enzyme-free amplification strategies are imperative for intracellular miRNA assay. In this work, we report an entropy-driven reaction for amplification assay miRNA with a detection limit of 0.27 pM. The resulting signal amplification provides excellent recognition and signal enhancement of specific miRNAs in living cells. This method supplies accurate information regarding cellular miRNA-related biological events and provides a new tool for highly sensitive and simultaneous imaging of multiple low-level biomarkers, thereby improving the accuracy of early disease diagnosis.     

DNA methylation-regulated microRNA pathways in ovarian serous cystadenocarcinoma: A meta-analysis

Epigenetic regulation has been linked to the initiation and progression of cancer. Aberrant expression of microRNAs (miRNAs) is one such mechanism that can activate or silence oncogenes (OCGs) and tumor suppressor genes (TSGs) in cells. A growing number of studies suggest that miRNA expression can be regulated by methylation modification, thus triggering cancer development. However, there is no comprehensive in silico study concerning miRNA regulation by direct DNA methylation in cancer. Ovarian serous cystadenocarcinoma (OSC) was therefore chosen as a tumor model for the present work.Twelve batches of OSC data, with at least 35 patient samples in each batch, were obtained from The Cancer Genome Atlas (TCGA) database. The Spearman rank correlation coefficient (SRCC) was used to quantify the correlation between the CpG DNA methylation level and miRNA expression level. Meta-analysis was performed to reduce the effects of biological heterogeneity among different batches. MiRNA-target interactions were also inferred by computing SRCC and meta-analysis to assess the correlation between miRNA expression and cancer-associated gene expression and the interactions were further validated by a query against the miRTarBase database.A total of 26 potential epigenetic-regulated miRNA genes that can target OCGs or TSGs in OSC were found to show biological relevance between DNA methylation and miRNA gene expression. Furthermore, some of the identified DNA-methylated miRNA genes; for instance, the miR-200 family, were previously identified as epigenetic-regulated miRNAs and correlated with poor survival of ovarian cancer. We also found that several miRNA target genes, BTG3, NDN, HTRA3, CDC25A, and HMGA2 were also related to the poor outcomes in ovarian cancer.The present study proposed a systematic strategy to construct highly confident epigenetic-regulated miRNA pathways for OSC. The findings are validated and are in line with the literature. The inclusion of direct DNA methylated miRNA events may offer another layer of explanation that along with genetics can give a better understanding of the carcinogenesis process.     

Magnetic bead-based hybridization assay for electrochemical detection of microRNA

Aberrant expression of microRNAs (miRNAs), short non-coding RNA molecules regulating gene expression, is often found in tumor cells, making the miRNAs suitable candidates as cancer biomarkers. Electrochemistry is an interesting alternative to current standard methods of miRNA detection by offering cheaper instrumentation and faster assays times. In this paper, we labeled miRNA in a quick, simple, two-step procedure with electroactive complex of osmium(VI) and 2,2′-bipyridine, Os(VI)bipy, which specifically binds to the ribose at the 3′-end of the miRNA, and hybridized such labeled miRNA with biotinylated capture probe attached to the streptavidin magnetic beads. Labeled miRNA was then detected at hanging mercury drop electrode at femtomole level due to an electrocatalytic nature of the peak from the Os(VI)bipy label. We obtained good selectivity of the assay using elevated hybridization temperatures for better discrimination of perfect duplex from single and double mismatches. After optimization of the protocol, we demonstrated feasibility of our assay by detecting target miRNA in real total RNA samples isolated from human cancer cells.