Signal amplification by rolling circle amplification on DNA microarrays

While microarrays hold considerable promise in large-scale biology on account of their massively parallel analytical nature, there is a need for compatible signal amplification procedures to increase sensitivity without loss of multiplexing. Rolling circle amplification (RCA) is a molecular amplification method with the unique property of product localization. This report describes the application of RCA signal amplification for multiplexed, direct detection and quantitation of nucleic acid targets on planar glass and gel-coated microarrays. As few as 150 molecules bound to the surface of microarrays can be detected using RCA. Because of the linear kinetics of RCA, nucleic acid target molecules may be measured with a dynamic range of four orders of magnitude. Consequently, RCA is a promising technology for the direct measurement of nucleic acids on microarrays without the need for a potentially biasing preamplification step.     

基于CRISPR/Cas系统的核酸生物传感器

近年来,CRISPR/Cas系统已经成为转录调控和基因组编辑的重要工具。除了在基因编辑领域的贡献,CRISPR/Cas系统独特的靶核酸顺式切割和非特异性单链核酸反式切割能力,在开发核酸检测的新型生物传感器方面展现出巨大潜力。构建基于CRISPR/Cas系统高灵敏度生物传感器的关键通常依赖其与不同信号扩增策略,诸如核酸扩增技术或特定信号转导方法的结合。基于此,本文旨在通过介绍不同类型的CRISPR/Cas系统,全面概述基于该系统的核酸检测生物传感器的研究进展,并重点对结合核酸扩增技术（PCR、LAMP、RCA、RPA和EXPAR）、灵敏的信号转导方法（电化学和表面增强拉曼光谱）和特殊结构设计生物传感的三大类型信号放大策略的CRISPR/Cas生物传感器进行总结和评论。最后,本文对目前的挑战以及未来的前景进行展望。     

Establishment of a system for determination of emerging infectious diseases (RDV method), and its application

We developed a new system for detection of viral nucleic acids because rapid detection of pathogens is necessary to prevent potential outbreaks of infectious diseases. This system, named rapid determination of viral RNA sequences (RDV), involves whole-genome amplification and a new direct sequencing technique. Using the RDV system, it is possible to obtain viral nucleic acid sequences within 2 days. The nucleic acid sequences of SARS-CoV and West Nile virus, which represent emerging and re-emerging infectious viruses, were determined from infectious viral culture supernatant by the RDV method. We demonstrated the clinical application of this system in human specimens and its diagnostic usage in mosquitoes. Furthermore, new adenovirus and herpesvirus were found in bats using the RDV method.     

Rare target enrichment for ultrasensitive PCR detection using cot-rehybridization and duplex-specific nuclease

Nucleic acid detection by polymerase chain reaction (PCR) is invaluable for the detection of dilute and rare sequences, including pathogens and infrequent species in complex clinical and environmental backgrounds. The presence of excess complex background nucleic acid can reduce sensitivity and specificity. This is because mispriming can cause failure of the amplification reaction. Here we describe a new approach to ultrasensitive PCR detection, using enrichment of rare target nucleic acid from abundant background by combining the classic technique of cot-rehybridization to convert the abundant background to double-stranded form, with the use of a newly described, highly processive duplex-specific crab nuclease. We show that trace sequences in a vast excess of background DNA can be undetectable by PCR, independent of the amount of the mixture added to the PCR, and that these sequences can be made detectable by background suppression using this method.     

滚环扩增技术及其在生物分子诊断中的应用

滚环扩增技术(RCA)是近年来发展起来的一种新型的核酸扩增技术.该技术是基于连接酶连接、引物延伸、与链置换扩增反应的一种等温核酸扩增方法.在恒温的条件下,可以产生大量的与环型探针互补的重复序列.与传统的核酸扩增方法相比,它具有扩增条件简单,特异性高,能在恒温条件下进行等特点.滚环扩增技术结合荧光、电化学、电化学发光等检...     

SNP与基因检测及表达中的RCA技术

滚环扩增(rollingcircleamplification,RCA)技术是一种新的分子生物学检测方法。该方法不仅可以在体外等温条件下对核酸进行高度特异性的检测,而且还可通过线性或指数扩增来进行信号级联放大,其灵敏度能达到1个拷贝的核酸分子,因此,可用于痕量分子的检测。目前,滚环扩增技术广泛应用于全基因组DNA检测、核酸测序、单核苷酸多态性、DNA芯片及蛋白质芯片分析等领域。     

Highly sensitive measurements of PNA-DNA hybridization using oxide-etched silicon nanowire biosensors

The highly sensitive and sequence-specific detection of single-stranded oligonucleotides using nonoxidized silicon nanowires (SiNWs) is demonstrated. To maximize device sensitivity, the surface of the SiNWs was functionalized with a densely packed organic monolayer via hydrosilylation, subsequently immobilized with peptide nucleic acid (PNA) capable of recognizing the label-free complementary target DNA. Because of the selective functionalization of the SiNWs, binding competition between the nanowire and the underlying oxide is avoided. Transmission electron microscopy was conducted to clearly differentiate the SiNW surface before and after removal of SiO₂. Fluorescence microscopy was used to further realize the selectivity of the oxide-etched chemistry on the SiNWs and sequence specificity of PNA-DNA hybridization. The concentration-dependent resistance change measurements upon hybridization of PNA-DNA show that detection limit down to 10 fM can be obtained. The SiNW devices also reveal the capability of an obvious discrimination against mismatched sequences. Among several efforts being made to improve detection sensitivity, this work addresses one significant issue regarding surface functionalization which enables highly sensitive biomolecular sensing with SiNWs.     

环介导等温扩增核酸技术及其应用

环介导等温扩增(loop-mediated isothermal amplification,简称LAMP)是利用4个特殊设计的引物和具有链置换活性的DNA聚合酶,在恒温条件下特异、高效、快速地扩增DNA的新技术。该技术在1h内能扩增出109靶序列拷贝,扩增产物是一系列反向重复的靶序列构成的茎环结构和多环花椰菜样结构的DNA片段的混合物,电泳后在凝胶上显现出由不同大小的区带组成的阶梯式图谱。LAMP技术以其特异性强、灵敏度高、快速、准确和操作简便等优点在核酸的科学研究、疾病的诊断和转基因食品检测等领域得到了日益广泛的应用。     

Fluorescence-based detection of short DNA sequences under non-denaturing conditions

The ability of peptide nucleic acid (PNA) to open up duplex DNA in a highly sequence-specific manner makes it possible to detect short DNA sequences on the background of or within genomic DNA under non-denaturing conditions. To do so, chosen marker sites in double-stranded DNA are locally opened by a pair of PNA openers, thus transforming one strand within the target region (20-30 bp) into the single-stranded form. Onto this accessible DNA sequence a circular oligonucleotide probe is assembled, which serves as a template for rolling circle amplification (RCA). Both homogeneous and heterogeneous assay formats are investigated, as are different formats for fluorescence-based amplicon detection. Our recent data with immobilized analytes suggest that marker sequences in plasmid and bacterial chromosomal DNA can be successfully detected.     

等温核酸扩增技术在病原体检测中的应用

近年来,新型传染病相继爆发,如严重急性呼吸综合征（severe acute respiratory syndrome,SARS）、H7N9禽流感等,严重威胁着人类健康和社会、经济的可持续发展,同时给传染病的防控带来了严峻挑战。病原体检测是传染病防控的重要环节,越来越多的新技术被应用其中。等温核酸扩增技术作为一种快速、灵敏度高的病原体检测技术,已取得了长足发展。对等温核酸扩增技术的原理、重要特性及其在病原体检测中的应用进展进行了较为全面的综述,以期为这一技术的推广和应用提供重要参考。     

PCR 防污染技术的研究进展

聚合酶链式反应(PCR)是一种高灵敏核酸扩增技术,广泛应用于核酸检测中.但在实际应用过程中,扩增产物及其他核酸片段的污染会导致假阳性的结果,制约了PCR在临床检测中的应用.为了解决这一问题,建立了许多PCR防污染的方法,除了早期建立的并已得到广泛应用的物理隔绝法、光照法及水解法外,近年来还发展了酶消化法、化学修饰法及DEAE纤维素法.本文对PCR防污染技术的原理、应用及进展进行了综述.     

Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification

Rolling-circle amplification (RCA) and ramification amplification (RAM, also known as hyperbranched RCA) are isothermal nucleic acid amplification technologies that have gained a great application in in situ signal amplification, DNA and protein microarray assays, single nucleotide polymorphism detection, as well as clinical diagnosis. Real-time detection of RCA or RAM products has been a challenge because of most real-time detection systems, including Taqman and Molecular Beacon, are designed for thermal cycling-based DNA amplification technology. In the present study, we describe a novel fluorescent probe construct, termed molecular zipper, which is specially designed for quantifying target DNA by real-time monitoring RAM reactions. Our results showed that the molecular zipper has very low background fluorescence due to the strong interaction between two strands. Once it is incorporated into the RAM products its double strand region is opened by displacement, therefore, its fluorophore releases a fluorescent signal. Applying the molecular zipper in RAM assay, we were able to detect as few as 10 molecules within 90 min reaction. A linear relationship was observed between initial input of targets and threshold time (R² = 0.985). These results indicate that molecular zipper can be applied to real-time monitoring and qualification of RAM reaction, implying an amenable method for automatic RAM-based diagnostic assays.     

Detection of viral infection and gene expression in clinical tissue specimens using branched DNA (bDNA) in situ hybridization.

In situ hybridization (ISH) methods for detection of nucleic acid sequences have proved especially powerful for revealing genetic markers and gene expression in a morphological context. Although target and signal amplification technologies have enabled researchers to detect relatively low-abundance molecules in cell extracts, the sensitive detection of nucleic acid sequences in tissue specimens has proved more challenging. We recently reported the development of a branched DNA (bDNA) ISH method for detection of DNA and mRNA in whole cells. Based on bDNA signal amplification technology, bDNA ISH is highly sensitive and can detect one or two copies of DNA per cell. In this study we evaluated bDNA ISH for detection of nucleic acid sequences in tissue specimens. Using normal and human papillomavirus (HPV)-infected cervical biopsy specimens, we explored the cell type-specific distribution of HPV DNA and mRNA by bDNA ISH. We found that bDNA ISH allowed rapid, sensitive detection of nucleic acids with high specificity while preserving tissue morphology. As an adjunct to conventional histopathology, bDNA ISH may improve diagnostic accuracy and prognosis for viral and neoplastic diseases.     

Controlled Microwave Heating Accelerates Rolling Circle Amplification

Rolling circle amplification (RCA) generates single-stranded DNAs or RNA, and the diverse applications of this isothermal technique range from the sensitive detection of nucleic acids to analysis of single nucleotide polymorphisms. Microwave chemistry is widely applied to increase reaction rate as well as product yield and purity. The objectives of the present research were to apply microwave heating to RCA and indicate factors that contribute to the microwave selective heating effect. The microwave reaction temperature was strictly controlled using a microwave applicator optimized for enzymatic-scale reactions. Here, we showed that microwave-assisted RCA reactions catalyzed by either of the four thermostable DNA polymerases were accelerated over 4-folds compared with conventional RCA. Furthermore, the temperatures of the individual buffer components were specifically influenced by microwave heating. We concluded that microwave heating accelerated isothermal RCA of DNA because of the differential heating mechanisms of microwaves on the temperatures of reaction components, although the overall reaction temperatures were the same.     

Attomole DNA detection assay via rolling circle amplification and single molecule detection

A bead-based assay was developed for highly sensitive single molecule DNA detection. Rolling circle amplification (RCA), an isothermal amplification technique that creates tandem repeated sequences, was used in combination with a fluorescent complementary DNA to create dense clusters of fluorescence. These clusters, each corresponding to a single target molecule, can be detected unambiguously due to their high signal/noise ratios. The limit of detection of this assay is approximately 1 amol. This simple single molecule assay allows high detection sensitivity without the use of complex equipment.     

Amplification methods to increase the sensitivity of in situ hybridization: play card(s).

In situ hybridization (ISH) has proved to be an invaluable molecular tool in research and diagnosis to visualize nucleic acids in their cellular environment. However, its applicability can be limited by its restricted detection sensitivity. During the past 10 years, several strategies have been developed to improve the threshold levels of nucleic acid detection in situ by amplification of either target nucleic acid sequences before ISH (e.g., in situ PCR) or the detection signals after the hybridization procedures. Here we outline the principles of tyramide signal amplification using the catalyzed reporter deposition (CARD) technique, present practical suggestions to efficiently enhance the sensitivity of ISH with CARD, and discuss some applications and possible future directions of in situ nucleic acid detection using such an amplification strategy.     

Locked Nucleic Acid Pentamers as Universal PCR Primers for Genomic DNA Amplification

Background

Multiplexing technologies, which allow for simultaneous detection of multiple nucleic acid sequences in a single reaction, can save a lot of time, cost and labor compared to traditional single reaction detection methods. However, the multiplexing method currently used requires precise handiwork and many complicated steps, making a new, simpler technique desirable. Oligonucleotides containing locked nucleic acid residues are an attractive tool because they have strong affinities for their complementary targets, they have been used to avoid dimer formation and mismatch hybridization and to enhance efficient priming. In this study, we aimed to investigate the use of locked nucleic acid pentamers for genomic DNA amplification and multiplex genotyping.

Results

We designed locked nucleic acid pentamers as universal PCR primers for genomic DNA amplification. The locked nucleic acid pentamers were able to prime amplification of the selected sequences within the investigated genomes, and the resulting products were similar in length to those obtained by restriction digest. In Real Time PCR of genomic DNA from three bacterial species, locked nucleic acid pentamers showed high priming efficiencies. Data from bias tests demonstrated that locked nucleic acid pentamers have equal affinities for each of the six genes tested from the Klebsiella pneumoniae genome. Combined with suspension array genotyping, locked nucleic acid pentamer-based PCR amplification was able to identify a total of 15 strains, including 3 species of bacteria, by gene- and species-specific probes. Among the 32 species used in the assay, 28 species and 50 different genes were clearly identified using this method.

Conclusion

As a novel genomic DNA amplification, the use of locked nucleic acid pentamers as universal primer pairs in conjunction with suspension array genotyping, allows for the identification of multiple distinct genes or species with a single amplification procedure. This demonstrates that locked nucleic acid pentamer-based PCR can be utilized extensively in pathogen identification.     

Detection of Bacillus anthracis from spores and cells by loop-mediated isothermal amplification without sample preparation

Loop-mediated isothermal amplification (LAMP) is a technique capable of rapidly amplifying specific nucleic acid sequences without specialized thermal cycling equipment. In addition, several detection methods that include dye fluorescence, gel electrophoresis, turbidity and colorimetric change, can be used to measure or otherwise detect target amplification. To date, publications have described the requirement for some form of sample nucleic acid extraction (boiling, lysis, DNA purification, etc.) prior to initiating a LAMP reaction. We demonstrate here, the first LAMP positive results obtained from vegetative cells and spores of Bacillus anthracis without nucleic acid extraction. Our data show that the simple addition of cells or spores to the reaction mixture, followed by heating at 63°C is all that is required to reproducibly amplify and detect target plasmid and chromosomal DNA via colorimetric change. The use of three primer sets targeting both plasmids and the chromosome of B. anthracis allows for the rapid discrimination of non-pathogenic bacteria from pathogenic bacteria within 30 min of sampling. Our results indicate that direct testing of B. anthracis spores and cells via LAMP assay will greatly simplify and shorten the detection process by eliminating nucleic acid purification. These results may allow more rapid detection of DNA from pathogenic organisms present in field and environmental samples.