DNA测序中常见影响因素的研究

对测序中的模板、引物、测序反应条件及测序反应纯化方法和仪器操作等进行研究。结果显示测序模板的纯度影响测序的质量 ,浓度对测序的长度有影响。引物设计时除符合一般设计原则外 ,Tm值最好在5 0℃～ 6 0℃之间 ,且无成串的G、C。改变变性、退火、延伸的时间和温度对特殊DNA模板的序列测定有较好的效果。测序反应产物的纯化有几种方法 ,以 70 %乙醇沉淀法最经济、方便。因此模板的纯度和浓度对测序成功与否起决定作用。最佳反应条件可降低成本 ,提高测序成功率 ,乙醇沉淀法是首选的测序反应产物纯化方法。仪器操作熟练、正确与否也会影响测序结果。     

提高DNA序列测定的准确性方案

目前 ,ＤＮＡ测序的核心仪器是使用荧光染料标记的、具有ＣＣＤ光学系统的ＤＮＡ测序仪 ,其工作原理主要包括 :用不同的荧光染料确定Ａ、Ｇ、Ｃ和Ｔ这 4种碱基的延伸反应 ,通过激光的激发 ,每种染料可以发射出不同的电信号 ,测序仪收集这些光波信号后 ,通过计算机数据分析 ,可得到相应的碱基序列。利用这种方法 ,所有 4种染料可在同一凝胶泳道中检测和辨别 ,消除了因泳道之间迁移率的差异所引起的误差 ,增加了测序的精确度 ;同时 ,可以增加在同一块凝胶上所能分析的模板ＤＮＡ数量。毛细管电泳技术的应用可使测序样品的加样自动化 ,且无须用…     

基于LAMP的新试剂和仪器的效果评估及在蚊媒病毒检测中的应用

目的:针对常见蚊媒病毒筛选引物,运用环介导等温扩增(LAMP)技术建立便捷、快速、高通量的检测方法;并以实验室储存病毒资源,评价LAMP研发试剂和仪器在快速筛查中的适用性。方法:环介导等温扩增。结果:筛选出7种蚊媒病毒高特异性引物,检测用研发试剂为单管固定化反应管,反应只需加入模板,使用配套仪器,检测总耗时不超过45 min,检测灵敏度为10~(-1)~10~2拷贝。结论:研发仪器一键式操作、便携轻便,可实时监测;研发试剂单管储存固定化反应管,极大程度地降低了污染,简单快捷,扩增稳定重复性好且成本较商业化试剂低;在现场实现蚊媒病毒的简便、快速、低成本、实时高通量检测。     

一种快速有效纯化DNA序列分析模板的方法

介绍一种ＤＮＡ序列分析模板的快速、有效的纯化方法。该法对ＤＮＡ模板的回收率可达９５％以上。多次测序结果表明,此法与其他常规纯化方法相比,具有简便、快速、有效、可靠等优点,其测序结果电泳带清晰,无模糊带及“鬼带”出现,重复性及稳定性较好。     

双链DNA模板循环测序的研究

采用末端标记引物进行双链ＤＮＡ循环测序是实验室快速,准确获得双链ＤＮＡ模板序列的有效方法。实验结果表明：该测序法不仅能消除由于模板不纯所导致的引物的非特异性结合等因素而产生的非特异条带,而且能降低ＰＣＲ产物测序的背景问题。     

烟草碱法提取基因组DNA的改进

为能够快速高效的对大量转基因烟草样品进行DNA提取,对碱法提取烟草组织DNA的方法进行了改进。采用0.01mol/L的Na OH溶液为提取液,破碎转基因烟草叶片组织后无需经过加热煮沸中和等步骤,上清液可直接用作PCR反应的模板。结果表明,0.01-0.1 mol/L之间的Na OH溶液制备的DNA模板均能成功扩增,该方法制备的DNA模板不依赖特殊的反应条件,多种品牌的PCR Mix均能成功进行扩增反应。与传统SDS提取法和试剂盒提取法获得的DNA相比,PCR结果没有明显差异。此提取方法在小麦、高粱、水稻、玉米等作物上也取得了很好的实验效果。通过本方法制备的DNA模板,其PCR扩增的产物可直接用来测序分析。该方法使用仪器少,样品消耗少,快速、简便、成本低,没有交叉污染,能够在短时间内处理大量样品,因此能够对大量的转基因烟草样品进行DNA的快速提取和鉴定。     

焦磷酸测序检测食品中鼠伤寒沙门氏菌

根据鼠伤寒沙门氏菌的特异序列,分别设计扩增引物和测序引物,建立焦磷酸测序检测鼠伤寒沙门氏菌的方法。针对鼠伤寒沙门氏菌设计特异性扩增引物,对目标片段进行PCR扩增,然后制备单链模板,并利用测序引物进行焦磷酸测序。测序结果表明,6株不同来源的鼠伤寒沙门氏菌均可以扩增出碱基序列为TACAACCGGA GTGCACATTA ATCCCGCAGC的基因片段,而30株阴性对照菌株均未得到扩增。进行BLAST比对表明,该序列与GenBank中鼠伤寒沙门氏菌的碱基序列100%匹配。焦磷酸测序法是一种快速、准确的检测方法,可用于食品中鼠伤寒沙门氏菌的快速检测。     

影响荧光终止法PCR循环测序反应的因素

比较了一些影响荧光终止法ＰＣＲ循环测序反应的因素。实验结果显示在Ｂｅｃｋｍａｎ ＣＥＱ２０００自动测序仪上,可读序列长度随着ｐＵＣ１８模板量增加而逐渐增多,当模板量达到１２５ｎｇ时ＤＮＡ可读序列最长,以后随着ｐＵＣ１８量增加测序长度逐渐下降。当引物量是１μｌ时,其测序结果比用０．５μｌ引物时好。在同样模板量情况下,１０μｌ反应体积比５μｌ反应体积可读序列长。     

焦测序技术的研究进展

焦测序技术是一种实时DNA测序技术。它在DNA聚合酶、三磷酸腺苷硫酸化酶、荧光素酶和三磷酸腺苷双磷酸酶4种酶的协同作用下,将焦磷酸转化为等量的荧光信号,通过荧光信号的高低实时检测待测序列,操作简便,可实现高通量、自动化测定,检测不需要电泳,不需要对样品标记和染色,结果准确可靠重复性好。本文综述了焦测序技术的基本原理、历史及其在测序模板制备技术、反应体系和检测仪器三个方面的最新进展,并重点介绍制备单链的Late-PCR技术、高灵敏度反应体系的获得以及454公司超高通量测序技术,并对焦测序技术的发展做了展望。     

三酶焦测序体系的建立及其在唐氏综合征快速诊断中的应用

为了避免四酶焦测序体系中由于三磷酸腺苷双磷酸酶(apyrase)造成的测序结果偏差, 文章建立了一种定量性能好的无三磷酸腺苷双磷酸酶的三酶焦测序体系。方法是将生物素修饰的DNA模板、荧光素酶和ATP硫酸化酶固定在磁性微球表面进行焦测序反应, 当加入一种dNTP进行焦测序反应完后, 采用磁性分离技术, 除去焦测序反应产生的ATP和剩余的dNTP, 然后加入另一种dNTP进行测序, 按同样的方法去除影响下一轮测序反应的成分, 实现循环测序。此体系能准确判读待测DNA的碱基序列, 且可定量测定单核苷酸序列多态性(SNP)中两种等位基因型的相对比值。文章成功检测了16例正常人和8例唐氏综合征患者样本中21号染色体上两个杂合率较高位点(rs1042917和 rs4818219)的等位基因型比值, 所得结果能够明确说明待测样本中来自于父方和母方的21号染色体数目是否相等。该法具有良好的定量性能, 适合于SNP等位基因型的定量分析, 可以用于唐氏综合征的快速检测。     

Analysis of the DNA Sequencing Quality and Efficiency of the Apollo100 Robotic Microcycler in a Core Facility Setting

Sanger, or dideoxynucleotide sequencing, is an important tool for biomolecular research. An important trend in DNA sequencing is to find new and innovative ways to provide high-quality, reliable sequences in a more efficient manner, using automated capillary electrophoresis. The Apollo100 combines Sanger cycle sequencing and solid-phase reversible immobilization for product purification in a single instrument with robotic liquid handling and microfluidic (Microscale On-chip Valve) chips that have onboard thermal cycling and pneumatic mixing. Experiments were performed to determine how the DNA sequencing results from the Apollo100 compared with conventional, manual methods used in a core facility setting. Through rigorous experimentation of multiple baseline runs and a dilution series of template concentration, the Apollo100 generated sequencing that exceeded 900 bases with a quality score of 20 or above. When comparing actual client samples of amplicons, plasmids, and cosmids, Apollo100 sequencing results did not differ significantly from those reactions prepared manually. In addition, bacterial genomic DNA was sequenced successfully, directly with the Apollo100, although results were of lower quality than the standard manual method. As a result of the microscale capabilities, the Apollo100 offers valuable savings with respect to the quantity of reagents consumed compared with current manual sequencing methods, thereby continuing the demand for smaller template and reagent requirements. In conclusion, the Apollo100 can generate high-quality DNA sequences for common templates equivalent to those produced using manual sequencing methods and increases efficiency through reduced labor and reagents.     

On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases

A fully integrated system has been developed for genetic analysis based on direct sequencing of polymerase chain reaction (PCR) products. The instrument is based on a serially connected fused-silica capillary assembly. The technique involves the use of microreactors for small-volume PCR and for dye-terminator cycle-sequencing reaction, purification of the sequencing fragments, and separation of the purified DNA ladder. Four modifications to the normal PCR protocol allow the elimination of post-reaction purification. The use of capillaries as reaction vessels significantly reduced the required reaction time. True reduction in reagent cost is achieved by a novel sample preparation procedure where nanoliter volumes of templates and sequencing reaction reagent are mixed using a micro- syringe pump. The remaining stock solution of sequencing reaction reagent can be reused without contamination. The performance of the whole system is demonstrated by one-step sequencing of a specific 257-bp region in human chromosome DNA. Base calling for the smaller fragments is limited only by the resolving power of the gel. The system is simple, reliable and fast. The entire process from PCR to DNA separation is completed in ~4 h. Feasibilities for development of a fully automated sequencing system in the high-throughput format and future adaptation of this concept to a microchip are discussed.     

A rapid solid-phase protein microsequencer.

A solid-phase protein microsequencer is described that has been designed to determine protein sequences with subnanomolar quantities of protein. Its utility has been demonstrated by the determination of many sequences in subunits of mitochondrial F1-ATPase, in a protein isolated from mouse gap junctions and in the mitochondrial phosphate-transporter protein. It has a number of advantages over liquid- and gas-phase sequencers. Firstly, the degradation cycle takes 24 min, more than twice as fast as any other sequencer. This helps to reduce exposure of proteins to inimical reagents and increases throughput of samples. Secondly, polar amino acids such as phosphoserine, and polar derivatives formed by active-site photoaffinity labelling with 8-azido-ATP, are recovered quantitatively from the reaction column and can be positively identified. In other types of sequencer these polar derivatives, being somewhat insoluble in butyl chloride, tend to remain in the reaction chamber of the instrument and so are more difficult to identify. The solid-phase protein sequencer is also more suited than the liquid-phase instrument for analysis of proteolipids from membranes. These hydrophobic proteins tend to dissolve in organic solvents during washing steps in the liquid-phase instrument and are lost. Covalent attachment as used in the solid-phase instrument solves this problem.     

A computer-controlled all-tantalum stopped-flow microcalorimeter with microjoule resolution

A new all-tantalum differential stopped-flow heat-conduction microcalorimeter with microjoule resolution has been developed. The instrument consists of two matched channels, each of which has two reagent inlet lines. A computer is used to process the data and control the syringe drive system which runs the samples through the calorimeter. The reagents are mixed in 0.6 s in ratios of 1:1, 1:2, 1:2.5, 1:4, 1:5, or 1:10. The priming volume from the loading port to the mixer is 1 ml and the reaction volume of the detection tube is 160 microliters. The instrument has a sensitivity of 1.60 J/V.s and a differential baseline stability of 100 nJ/s (p-p) over a 4 h period. The sample size can be reduced to 27 microliters with only a 12% loss in sensitivity. With an electrical step power input, the 10-90% response is 40 s. By using a data decomposition scheme, the response time can be improved to 1 s which allows the direct measurement of moderately fast reaction kinetics. With water/water mixes, differential heats of mixing are typically (+/-) 2 microJ with a standard deviation of (+/-) 2.5 microJ. Reaction heats in the 20-50 microJ range can be measured with a standard deviation of (+/-) 3 microJ. A fast reaction, e.g. HCl dilution, can be completed in 150 s. When loading and priming times are included, 25 reactions can be completed in 120 min. A chilled water jacket is used to allow operation over a temperature range of 4 degrees C to 50 degrees C.     

Identification of mixups among DNA sequencing plates

MOTIVATION: During the process of high-throughput genome sequencing there are opportunities for mixups of reagents and data associated with particular projects. The sequencing templates or sequence data generated for an assembly may become contaminated with reagents or sequences from another project, resulting in poorer quality and inaccurate assemblies. RESULTS: We have developed a system to assess sequence assemblies and monitor for laboratory mixups. We describe several methods for testing the consistency of assemblies and resolving mixed ones. We use statistical tests to evaluate the distribution of sequencing reads from different plates into contigs, and a graph-based approach to resolve situations where data has been inappropriately combined. While these methods have been designed for use in a high-throughput DNA sequencing environment processing thousands of clones, they can be applied in any situation where distinct sequencing projects are performed at redundant coverage.     

一种测定蛹虫草中虫草酸含量的酶标仪微量反应方法

研究和建立一种基于酶标仪-96孔板高通量测定虫草酸含量的检测方法,并对该方法进行性能评价。以酶标仪为检测仪器,在96孔板内按照设定反应条件微量加入样品和试剂进行显色反应,利用酶标仪测定吸光度值并计算虫草酸含量。通过检测精密度、重复性、回收率,并与分光光度计法进行比较,综合评价该方法的准确度、精确度。结果表明,测定数据具有较高的精密度（样品CM1的RSD值0.829%;样品CM2的RSD值1.772%)、重复性（标准样品B40的RSD值2.061%;样品CM2 的RSD值1.599%)、回收率（平均回收率99.24%,RSD值3.666%）,测定结果与分光光度法检测结果无显著差异(P>0.05)。结果表明,酶标仪微量法测定准确、重复性好,并可大大减少样品和试剂的用量,该方法方便、快捷、高效,可以替代分光光度法用于虫草酸含量的测定。     

Automated ‘X‐Y’ robot for peptide synthesis with microwave heating: application to difficult peptide sequences and protein domains

Precise microwave heating has emerged as a valuable method to aid solid‐phase peptide synthesis (SPPS). New methods and reliable protocols, as well as their embodiment in automated instruments, are required to fully use this potential. Here we describe a new automated robotic instrument for SPPS with microwave heating, report protocols for its reliable use and report the application to the synthesis of long sequences, including the β‐amyloid 1‐42 peptide. The instrument is built around a valve‐free robot originally developed for parallel peptide synthesis, where the robotic arm transports reagents instead of pumping reagents via valves. This is the first example of an ‘X‐Y’ robotic microwave‐assisted synthesizer developed for the assembly of long peptides. Although the instrument maintains its capability for parallel synthesis at room temperature, in this paper, we focus on sequential peptide synthesis with microwave heating. With this valve‐free instrument and the protocols developed for its use, fast and efficient syntheses of long and difficult peptide sequences were achieved. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

High-throughput DNA synthesis in a multichannel format.

We describe an approach to high-throughput parallel DNA synthesis in which a multiwell format is used. The reactions are carried out in open wells using an argon ambient atmosphere to prevent reagent contamination. The controlled-pore glass beads which form the substrate for synthesis are held in individual wells with high-density polyethylene filter bottoms through which reagents are drawn into a vacuum manifold. The synthesis is carried out using direct reagent dispensing into the individual reaction wells. A computer controls the sequence in which reagents are dispensed and the timing of the periodic vacuum pulses required to synthesize the desired sequence. Experiments to date have demonstrated the viability of the approach for a variety of test sequences. Results obtained with HPLC analysis demonstrate coupling efficiencies as high as 99.5% under optimized conditions. Use of the oligomers for DNA sequencing templates and as PCR primers has been demonstrated in production applications. The current instrument design consists of a series of discrete reaction chambers in a 12 channel module which can be multiplexed in a 12 x n format where n can be 1-8, i.e. 96 wells. A projected time interval for 12 parallel syntheses is 2.5 h, with 96 syntheses in 3.5 h. Because of the reduced volume of reagents required in the open well format, significant cost savings are projected.     

High-pressure stopped-flow spectrometry at low temperatures

A stopped-flow instrument operating over temperature and pressure ranges of +30 to -20 degrees C and 10(-3) to 2 kbar , respectively, is described. The system has been designed so that it can be easily interfaced with many commercially available spectrophotometers of fast response time, with the aid of quartz fiber optics. The materials used for the construction are inert, metal free and the apparatus has proven to be leak free at temperatures as low as -20 degrees C under a pressure of 2 kbar . The performance of the instrument was tested by measuring the rate of reduction of cytochrome c with sodium dithionite and the 2,6-dichloroindophenol/ascorbate reaction. The dead time of the system has been evaluated to be 20, 50, and congruent to 100 ms in water at 20 degrees C, in 40% ethylene glycol/water, and at 20 degrees C and -15 degrees C, respectively. These values are rather pressure independent up to 2 kbar . Application of the bomb was demonstrated using the cytochrome c peroxidase/ethyl peroxide reaction. This process occurred in two phases and an increase in pressure decreased the rates of reactions indicating two positive volumes of activation (delta V not equal to app (fast) = 9.2 +/- 1.5 ml X mol-1; delta V not equal to app (slow) = 14 +/- 1.5 ml X mol-1, temperature 2 degrees C). The data suggest that the fast reaction could involve a hydrophobic bond, whereas the slow process could be associated with a stereochemical change of the protein. The problem of temperature equilibrium for high-pressure experiments is also discussed.