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Real time PCR(实时定量PCR)  

2009-03-06 05:59:14|  分类: 生物遗传天地 |  标签: |举报 |字号 订阅

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Real time PCR(实时定量PCR)

定量PCR已经从基于凝胶的低通量分析发展到高通量的荧光分析技术,即实时定量PCR。实时荧光定量PCR技术于1996年由美国Applied Biosystems公司推出,由于该技术不仅实现了PCR从定性到定量的飞跃,而且与常规PCR相比,它具有特异性更强、有效解决PCR污染问题、自动化程度高等特点。实时定量PCR (real-time quantitative PCR)是指在PCR指数扩增期间通过连续监测荧光信号强弱的变化来即时测定特异性产物的量,并据此推断目的基因的初始量,不需要取出PCR产物进行分离。目前实时定量PCR作为一个极有效的实验方法,已被广泛地应用于分子生物学研究的各个领域。

实时荧光定量PCR 技术的主要应用:

1. DNA 或RNA 的绝对定量分析:包括病原微生物或病毒含量的检测,转基因动植物转基因拷贝数的检测,RNAi 基因失活率的检测等

2. 基因表达差异分析:例如比较经过不同处理样本之间特定基因的表达差异(如药物处理、物理处理、化学处理等 ),特定基因在不同时相的表达差异以及cDNA 芯片或差显结果的确证

3. 基因分型:例如SNP 检测,甲基化检测等

Real-time PCR 常用的两种方法分别为:Sybr green(荧光染料掺入法) 和Taqman probe (探针法)

SYBR green

在PCR反应体系中,加入过量SYBR荧光染料,SYBR荧光染料特异性地掺入DNA双链后,发射荧光信号,而不掺入链中的SYBR染料分子不会发射任何荧光信号,从而保证荧光信号的增加与PCR产物的增加完全同步。

此方法适用:

1、灵敏度高:使用SYBR可使荧光效果增强到1000倍以上

2、通用性好,不需要设计探针,方法简便,省时,价格低廉。

3、通用型方法,在国内外科研中普遍使用。

4、高通量大规模的定量PCR检测

5、专一性要求不高的定量PCR检测。

Taqman Probe

PCR扩增时在加入一对引物的同时加入一个特异性的荧光探针,该探针为一寡核苷酸,两端分别标记一个报告荧光基团和一个淬灭荧光基团。探针完整时,报告基团发射的荧光信号被淬灭基团吸收;PCR扩增时,Taq酶的5’-3’外切酶活性将探针酶切降解,使报告荧光基团和淬灭荧光基团分离,从而荧光监测系统可接收到荧光信号,即每扩增一条DNA链,就有一个荧光分子形成,实现了荧光信号的累积与PCR产物形成完全同步

此方法适用:

1、具有高适应性和可靠性,实验结果稳定重复性好,特异性更高。

2、适用于扩增序列专一的体系的检测。

3、样品中靶基因含量过低的定量PCR检测。

4、靶基因的特异序列较短,无论怎样优化引物设计条件都不能解决。

5、存在与靶基因同源的序列,在PCR中容易出现非特异性扩增,对特异性要求较高的定量。

6、广泛用于人类传染病的诊断和病原定量,在动物病原体基因的检测,畜禽产品的检验检疫,生物制品的鉴定。

 

Real-time polymerase chain reaction

In molecular biology, real-time polymerase chain reaction, also called quantitative real time polymerase chain reaction (Q-PCR/qPCR) or kinetic polymerase chain reaction, is a laboratory technique based on the polymerase chain reaction, which is used to amplify and simultaneously quantify a targeted DNA molecule. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of a specific sequence in a DNA sample.

The procedure follows the general principle of polymerase chain reaction; its key feature is that the amplified DNA is quantified as it accumulates in the reaction in real time after each amplification cycle. Two common methods of quantification are: (1) the use of fluorescent dyes that intercalate with double-stranded DNA, and (2) modified DNA oligonucleotide probes that fluoresce when hybridized with a complementary DNA.

Frequently, real-time polymerase chain reaction is combined with reverse transcription to quantify messenger RNA (mRNA) in cells or tissues.

Abbreviations used for real-time PCR methods vary widely and include RTQ-PCR, Q-PCR or qPCR. [1] Real-time reverse-transcription PCR is often denoted as qRT-PCR,[2], RRT-PCR,[3] or RT-rt PCR.[4] The acronym, RT-PCR, commonly denotes reverse-transcription PCR and not real-time PCR, but not all authors adhere to this convention.[5]

Contents

Background

Real time quantitative PCR uses fluorophores in order to detect levels of gene expression.

Cells in all organisms regulate gene expression and turnover of gene transcripts (messenger RNA, abbreviated to mRNA), and the number of copies of an mRNA transcript of a gene in a cell or tissue is determined by the rates of its expression and degradation.

Northern blotting is often used to estimate the expression level of a gene by visualizing the abundance of its mRNA transcript in a sample. In this method, purified RNA is separated by agarose gel electrophoresis, transferred to a solid matrix (such as a nylon membrane), and probed with a specific DNA probe that is complementary to the gene of interest. Although this technique is still used to assess gene expression, it requires relatively large amounts of RNA and provides only qualitative or semiquantitative information of mRNA levels.

In order to robustly detect and quantify gene expression from small amounts of RNA, amplification of the gene transcript is necessary. The polymerase chain reaction is a common method for amplifying DNA; for mRNA-based PCR the RNA sample is first reverse transcribed to cDNA with reverse transcriptase.

Development of PCR technologies based on reverse transcription and fluorophores permits measurement of DNA amplification during PCR in real time, i.e., the amplified product is measured at each PCR cycle. The data thus generated can be analysed by computer software to calculate relative gene expression in several samples, or mRNA copy number. Real-time PCR can also be applied to the detection and quantification of DNA in samples to determine the presence and abundance of a particular DNA sequence in these samples.

DNA in PCR, causing fluorescence of the dye. An increase in DNA product during PCR therefore leads to an increase in fluorescence intensity and is measured at each cycle, thus allowing DNA concentrations to be quantified. However, dsDNA dyes such as SYBR Green will bind to all dsDNA PCR products, including nonspecific PCR products (such as "primer dimers"). This can potentially interfere with or prevent accurate quantification of the intended target sequence.

  1. The reaction is prepared as usual, with the addition of fluorescent dsDNA dye.
  2. The reaction is run in a thermocycler, and after each cycle, the levels of fluorescence are measured with a detector; the dye only fluoresces when bound to the dsDNA (i.e., the PCR product). With reference to a standard dilution, the dsDNA concentration in the PCR can be determined.

Like other real-time PCR methods, the values obtained do not have absolute units associated with it (i.e. mRNA copies/cell). As described above, a comparison of a measured DNA/RNA sample to a standard dilution will only give a fraction or ratio of the sample relative to the standard, allowing only relative comparisons between different tissues or experimental conditions. To ensure accuracy in the quantification, it is usually necessary to normalize expression of a target gene to a stably expressed gene (see below). This can correct possible differences in RNA quantity or quality across experimental samples.

fluorescent reporter probes is the most accurate and most reliable of the methods, but also the most expensive. It uses a sequence-specific RNA or DNA-based probe to quantify only the DNA containing the probe sequence; therefore, use of the reporter probe significantly increases specificity, and allows quantification even in the presence of some non-specific DNA amplification. This potentially allows for multiplexing - assaying for several genes in the same reaction by using specific probes with different-coloured labels, provided that all genes are amplified with similar efficiency.

It is commonly carried out with an RNA-based probe with a fluorescent reporter at one end and a quencher of fluorescence at the opposite end of the probe. The close proximity of the reporter to the quencher prevents detection of its fluorescence; breakdown of the probe by the 5' to 3' exonuclease activity of the taq polymerase breaks the reporter-quencher proximity and thus allows unquenched emission of fluorescence, which can be detected. An increase in the product targeted by the reporter probe at each PCR cycle therefore causes a proportional increase in fluorescence due to the breakdown of the probe and release of the reporter.

  1. The PCR is prepared as usual (see PCR), and the reporter probe is added.
  2. As the reaction commences, during the annealing stage of the PCR both probe and primers anneal to the DNA target.
  3. Polymerisation of a new DNA strand is initiated from the primers, and once the polymerase reaches the probe, its 5'-3-exonuclease degrades the probe, physically separating the fluorescent reporter from the quencher, resulting in an increase in fluorescence.
  4. Fluorescence is detected and measured in the real-time PCR thermocycler, and its geometric increase corresponding to exponential increase of the product is used to determine the threshold cycle (CT) in each reaction.

(1) In intact probes, reporter fluorescence is quenched. (2) Probes and the complementary DNA strand are hybridized and reporter fluorescence is still quenched. (3) During PCR, the probe is degraded by the Taq polymerase and the fluorescent reporter released.

mRNA on a Northern blot or PCR products on a gel or Southern blot is time-consuming and does not allow precise quantification. Also, over the 20-40 cycles of a typical PCR, the amount of product reaches a plateau determined more by the amount of primers in the reaction mix than by the input template/sample.

Relative concentrations of DNA present during the exponential phase of the reaction are determined by plotting fluorescence against cycle number on a logarithmic scale (so an exponentially increasing quantity will give a straight line). A threshold for detection of fluorescence above background is determined. The cycle at which the fluorescence from a sample crosses the threshold is called the cycle threshold, Ct. Since the quantity of DNA doubles every cycle during the exponential phase, relative amounts of DNA can be calculated, e.g. a sample whose Ct is 3 cycles earlier than another's has 23 = 8 times more template.

Amounts of RNA or DNA are then determined by comparing the results to a standard curve produced by real-time PCR of serial dilutions (e.g. undiluted, 1:4, 1:16, 1:64) of a known amount of RNA or DNA. As mentioned above, to accurately quantify gene expression, the measured amount of RNA from the gene of interest is divided by the amount of RNA from a housekeeping gene measured in the same sample to normalize for possible variation in the amount and quality of RNA between different samples. This normalization permits accurate comparison of expression of the gene of interest between different samples, provided that the expression of the reference (housekeeping) gene used in the normalization is very similar across all the samples. Choosing a reference gene fulfilling this criterion is therefore of high importance, and often challenging, because only very few genes show equal levels of expression across a range of different conditions or tissues. [6] [7]

laboratory. It is commonly used for both diagnostic and research applications.

Diagnostically real-time PCR is applied to rapidly detect the presence of genes involved in infectious diseases, cancer and genetic abnormalities. The introduction of real-time PCR assays to the clinical microbiology laboratory has led to significant improvements in the diagnosis of infectious disease.[8] In the research setting, real-time PCR is mainly used to provide highly sensitive quantitative measurements of gene transcription.

The technology may be used in determining how the genetic expression of a particular gene changes over time, such as in the response of tissue and cell cultures to an administration of a pharmacological agent, progression of cell differentiation, or in response to changes in environmental conditions.

Also, the technique is used in environmental microbiology, for example to quantify resistance genes in water samples.

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