数字PCR测定DNA含量及测量结果不确定度评定

数字PCR是一项不依赖校准物的DNA绝对定量技术,将含有DNA模板的反应溶液分配到大量独立的微室中并且进行扩增反应,通过统计反应室中的阳性信号来定量DNA的拷贝数。采用数字PCR技术对噬菌体λDNA的含量进行测定,并对测定结果进行不确定度评定。结果显示,由数字PCR测得的λDNA的含量为(2.43±0.35)μg/管(k=2),该结果与同位素稀释质谱法测量结果相吻合。     

Ion‐Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device

The polymerase chain reaction (PCR) is a powerful method for exponentially amplifying very low amounts of target DNA from genetic, clinical, and forensic samples. However, the heating and cooling steps in PCR largely hamper the miniaturization of thermocyclers for on‐site detection of pathogens and point‐of‐care tests. Herein, we devise an ion‐mediated PCR (IM‐PCR) strategy by exploiting ion‐induced DNA denaturation/renaturation cycles. DNA duplexes are effectively denatured in alkaline solutions; whereas, the denatured single‐stranded DNA strands readily reform duplexes at neutral pH. By using an integrated microchip that can programmably control the solution pH simply switching the potential in a range of several hundred millivolts, we can trigger IM‐PCR at a constant temperature. Analogously to thermal cycling, 30 cycles of pH‐induced denaturation/renaturation were used to amplify protein DNA fragments as confirmed by DNA sequencing. We anticipate that this portable, low‐cost, and scalable IM‐PCR holds great promise for widespread biological, clinical, and environmental applications.     

Construction of pH-Triggered DNA Hydrogels Based on Hybridization Chain Reactions

As a novel type of bio-functional material,DNA hydrogels have attracted more and more attention due to their successful applications in 3D cell culturing and tissue engineering for the designable and programmable responsiveness.Herein,we have developed a pH-triggered DNA hydrogel based on a clamped hybridization chain reaction(C-HCR).In this system,a DNA switch was designed,which can release the initiator strand in a controllable way via the formation of the C-G-C4 triplex under the pH stimuli.While the pre-gelation solution is stable in neutral environment,the C-HCR will trigger the sol-gel transition as the pH decreased to 5.0.This strategy has endowed the DNA hydrogel with good controllability for triggering,which also shows potential in intellectual responsiveness to certain stimuli.     

A Universal Polymerase Chain Reaction Developer

The versatility of PCR, the gold standard for amplification of DNA targets, is hampered by the laborious, multi‐step detection based on gel electrophoresis. We propose a one‐step, one‐tube method for the rapid (5 min) naked‐eye detection of PCR products, based on controlled aggregation of gold nanoparticles. Our method is universal, instrument‐free, and ultra‐sensitive, as it could detect as low as 0.01 zeptomoles of HIV template DNA in an excess of interfering human genomic DNA.     

DNA Extraction from Formalin-fixed and Paraffin-embedded Tissues by Triton X-100 for Effective Amplification of EGFR Gene by Polymerase Chain Reaction

For first-line non-small-cell lung cancer(NSCLC) therapy, detecting mutation status of the epidermal growth factor receptor(EGFR) geneconstitutes a prudent test to identify patients who are most likely to benefit from EGFR-tyrosine kinase inhibitor(TKI) therapy. Now, the material for detecting EGFR gene mutation status mainly comes from formalin-fixed and paraffin-embedded(FFPE) tissues. DNA extraction from FFPE and the amplification of EGFR gene by polymerase chain reaction(PCR) are two key steps for detecting EGFR gene mutation. We showed a simple method of DNA extraction from FFPE tissues for the effective amplification of EGFR gene. Extracting DNA from the FFPE tissues of NSCLC patients with 1% Triton X-100(pH=10.0) was performed by heating at 95℃ for 30 min. Meanwhile, a commercial kit was used to extract DNA from the same FFPE tissues of NSCLC patients for comparison. DNA extracted products were used as template for amplifying the exons 18, 19, 20 and 21 of EGFR by PCR for different amplified fragments. Results show that DNA fragment size extracted from FFPE tissues with 1% Triton X was about 250-500 base pairs(bp). However,DNA fragment size extracted from FFPE tissues via commercial kit was about from several hundreds to several thousands bp. The DNA yield extracted from FFPE tissues with 1% Triton X was larger than that via commercial kit. For about 500 bp fragment, four exons of EGFR could not be amplified more efficiently from extracted DNA with 1% Triton X than with commercial kit. However, for about 200 bp fragment. This simple and non-laborious protocol could successfully be used to extract DNA from FFPE tissue for the amplification of EGFR gene by PCR, further screening of EGFR gene mutation and facilitating the molecular analysis of a large number of FFPE tissues from NSCLC patients.     

Kinetics of Repair of UV-induced DNA Damage in Repair-proficient and -deficient Cells as Determined by Quantitative Polymerase Chain Reaction

Abstract— Advances in methodologies to monitor gene-specific repair in human cells have facilitated a detailed understanding of the complexity of the nucleotide excision repair system. One of these procedures, quantitative polymerase chain reaction (QPCR), holds significant promise for dissecting the fine structure of the repair of UV-induced DNA damage. This assay was used to study the repair of UV photoproducts in both actively transcribed and nontranscribed genes from human cells that were capable of (1) repair of both cyclobutane pyrimidine dimers and 6-4 photoproducts; (2) removal of neither dinners nor 6-4 photoproducts; (3) strong preferential repair of 6-4 photoproducts relative to dimers; and (4) severely depressed rates of 6-4 photoproducts and dimers. Detailed kinetic analyses revealed that repair of both active and inactive genes can be studied with a very fine degree of precision and that the repair status of the cells can easily be detected by use of the procedures described.     

Direct Sensing of 5‐Methylcytosine by Polymerase Chain Reaction

The epigenetic control of genes by the methylation of cytosine resulting in 5‐methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3′‐mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation‐specific PCR approach directly from untreated human genomic DNA.     

Application of Nanomaterials to Enhance Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is one of the most common technologies used to produce millions of copies of targeted nucleic acid in vitro and has become an indispensable technique in molecular biology. However, it suffers from low efficiency and specificity problems, false positive results, and so on. Although many conditions can be optimized to increase PCR yield, such as the magnesium ion concentration, the DNA polymerases, the number of cycles, and so on, they are not all-purpose and the optimization can be case dependent. Nano-sized materials offer a possible solution to improve both the quality and productivity of PCR. In the last two decades, nanoparticles (NPs) have attracted significant attention and gradually penetrated the field of life sciences because of their unique chemical and physical properties, such as their large surface area and small size effect, which have greatly promoted developments in life science and technology. Additionally, PCR technology assisted by NPs (NanoPCR) such as gold NPs (Au NPs), quantum dots (QDs), and carbon nanotubes (CNTs), etc., have been developed to significantly improve the specificity, efficiency, and sensitivity of PCR and to accelerate the PCR reaction process. This review discusses the roles of different types of NPs used to enhance PCR and summarizes their possible mechanisms.     

纳米材料在聚合酶链式反应体系中的应用研究进展

聚合酶链式反应(PCR)技术是现代分子生物学核心技术之一,研究提高PCR扩增效率的方法具有重要意义。传统提高PCR扩增效率的方法具有较多局限性,使得PCR扩增仍不能达到理想的效果。随着纳米技术的发展,纳米材料具有特殊的表面效应和尺寸效应,表面能进行多种修饰,易与生物大分子蛋白质、核酸等相互作用,对生物分子的结构和功能产生特别的影响。研究利用纳米材料来提高PCR扩增效率的技术和方法,具有非常重要的理论意义和应用价值。本文引用文献41篇,综述了近年来纳米材料在PCR体系中应用的现状,并展望了今后纳米材料在PCR体系中应用的发展方向及其前景。     

Clamped Hybridization Chain Reactions for the Self‐Assembly of Patterned DNA Hydrogels

DNA hydrogels hold great potential for biological and biomedical applications owing to their programmable nature and macroscopic sizes. However, most previous studies involve spontaneous and homogenous gelation procedures in solution, which often lack precise control. A clamped hybridization chain reaction (C‐HCR)‐based strategy has been developed to guide DNA self‐assembly to form macroscopic hydrogels. Analogous to catalysts in chemical synthesis or seeds in crystal growth, we introduced DNA initiators to induce the gelation process, including crosslinked self‐assembly and clamped hybridization in three dimensions with spatial and temporal control. The formed hydrogels show superior mechanical properties. The use of printed, surface‐confined DNA initiators was also demonstrated for fabricating 2D hydrogel patterns without relying on external confinements. This simple method can be used to construct DNA hydrogels with defined geometry, composition, and order for various bioapplications.     

碱基序列标记法结合焦磷酸测序测定不同来源基因表达量

建立了一种将序列标记反转录聚合酶链反应(PCR)与焦磷酸测序技术结合的相对基因表达量测定法(简称"SRPP").先用来源特异性引物对不同来源的同一基因通过反转录标记上特异性标签,PCR后用焦磷酸测序法对扩增产物进行序列解码,使得测序结果中的序列代表基因的来源,峰高代表基因在不同来源中的相对表达量.用实时荧光定量PCR法对本方法的准确性进行了验证,结果表明,SRPP可以同时准确测定同一基因在3个不同来源中的表达量,并实际测定了Egr1基因在糖尿病、肥胖和正常小鼠肝中的表达量差异.     

连续流动式聚合酶链式反应芯片的设计进展

介绍了PCR的概念以及微型PCR芯片的优点，着重介绍连续流动式PCR(continuous-flow PCR)芯片／微装置的一般原理、串行流动及其设计进展。     

微流控PCR芯片的研究进展

基因是人类的遗传密码,人类个体之间只有万分之一的基因不相同,却导致了人与人之间丰富的差异.了解这种差异对于科学研究具有巨大的应用价值.PCR是基因研究中常用的手段之一,但传统PCR仪存在反应时间长、能量消耗大、不便于集成与携带等缺陷,微流控技术与PCR结合可以有效缩小反应体系,提高反应效率,且易于集成化与微型化.本文按照微流控PCR芯片的结构分类,详细介绍了微池型、连续流动型PCR芯片,以及电泳、荧光、电化学和DNA杂交阵列等检测方法,并在最后进行了总结与展望.     

Polymerase Synthesis of Photocaged DNA Resistant against Cleavage by Restriction Endonucleases

5‐[(2‐Nitrobenzyl)oxymethyl]‐2′‐deoxyuridine 5′‐O‐triphosphate was used for polymerase (primer extension or PCR) synthesis of photocaged DNA that is resistant to the cleavage by restriction endonucleases. Photodeprotection of the caged DNA released 5‐hydroxymethyluracil‐modified nucleic acids, which were fully recognized and cleaved by restriction enzymes.