Real-Time PCR (Advanced Methods)

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Real-Time PCR: Advanced Technologies and Applications | Book

The 3' portion of the stem also contains sequence that is complementary to the extension product of the primer. This sequence is linked to the 5' end of a specific primer via a non-amplifiable monomer. After extension of the Scorpion primer, the specific probe sequence is able to bind to its complement within the extended amplicon thus opening up the hairpin loop. This prevents the fluorescence from being quenched and a signal is observed see also How It Works.

The cheaper alternative is the double-stranded DNA binding dye chemistry, which quantitates the amplicon production including non-specific amplification and primer-dimer complex by the use of a non-sequence specific fluorescent intercalating agent SYBR-green I or ethidium bromide. It does not bind to ssDNA. SYBR green is a fluorogenic minor groove binding dye that exhibits little fluorescence when in solution but emits a strong fluorescent signal upon binding to double-stranded DNA 32 Morrison, Furthermore, non-specific amplifications require follow-up assays melting point or dissociation curve analysis for amplicon identification 33 Ririe, Another controllable problem is that longer amplicons create a stronger signal if combined with other factors, this may cause CDC camera saturation, see below.

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Normally SYBR green is used in singleplex reactions, however when coupled with melting curve analysis, it can be used for multiplex reactions 34 Siraj, The threshold cycle or the C T value is the cycle at which a significant increase in D Rn is first detected for definition of D Rn, see below and Glossary. The threshold cycle is when the system begins to detect the increase in the fluorescent signal associated with an exponential growth of PCR product during the log-linear phase.

This phase provides the most useful information about the reaction certainly more important than the end-point. The slope of the log-linear phase reflects the amplification efficiency Eff. Eff can be calculated by the formula: These factors include length of the amplicon, secondary structure and primer quality. Although valid data can be obtained that fall outside of the efficiency range, the qRT-PCR should be further optimized or alternative amplicons designed see Efficiency Determination Page by Pfaffl. For the slope to be an indicator of real amplification rather than signal drift , there has to be an inflection point.

This is the point on the growth curve when the log-linear phase begins. It also represents the greatest rate of change along the growth curve. Signal drift is characterized by gradual increase or decrease in fluorescence without amplification of the product. The important parameter for quantitation is the C T.

The threshold should be placed above any baseline activity and within the exponential increase phase which looks linear in the log transformation. Some software allows determination of the cycle threshold C T by a mathematical analysis of the growth curve. This provides better run-to-run reproducibility. A C T value of 40 or higher means no amplification and this value cannot be included in the calculations.

By using an invariant endogenous control as an active reference, quantitation of an mRNA target can be normalized for differences in the amount of total RNA added to each reaction. The issue of the choice of a normalizer has been reviewed by Suzuki et al. The authors recommend caution in the use of GAPDH as a normalizer as it has been shown that its expression may be upregulated in proliferating cells. They recommend b -actin as a better active reference but see Dheda, GAPDH is particularly an unpopular choice in cancer studies because of its increased expression in aggressive cancers 42 Goidin, Since the chosen mRNA species should be proportional to the amount of input RNA, it may be best to use a combination as normalizer.

It is desirable to validate the chosen normalizer for the target cell or tissue. It should be expressed at a constant level at different time points by the same individual and also by different individuals at the target cell or tissue for example, peripheral blood lymphocytes 40 Dheda, Our own experience 43 Sabek, showed that b -actin or 18S RNA are reasonable choices as normalizers for the peripheral blood mononuclear cells, whereas GAPDH performed worst in transplant monitoring studies.

Similar concerns on the choice of normalizers in transplant monitoring have also been expressed by others 44 Gibbs, It is important to choose a normalizer whose expression will remain constant under the experimental conditions designed for the target gene 46 Schmittgen, ; Dheda, The strategy of using multiple normalizer genes depending on the cell and tissue type is validated for general use 48 Vandesompele, The most constantly expressed housekeeping genes ; algorithms to select the best endogenous controls: See also GeneInvestigator for normalizer selection Hruz, Multiplex TaqMan assays can be performed using multiple dyes with distinct emission wavelengths.

It is important that if the dye layer has not been chosen correctly, the machine will still read the other dye's spectrum. For example, both VIC and FAM emit fluorescence in a similar range to each other and when doing a single dye, the wells should be labeled correctly. In the case of multiplexing, the spectral compensation for the post run analysis should be turned on on ABI Activating spectral compensation improves dye spectral resolution.

TaqMan primer and probe design guidelines. The Primer Express software designs primers with a melting temperature Tm of 0 C, and probes with a Tm value of 10 0 C higher. The Tm of both primers should be equal,. Primers should be bases in length protocol ,. The run of an identical nucleotide should be avoided. This is especially true for G, where runs of four or more Gs is not allowed,.

The total number of Gs and Cs in the last five nucleotides at the 3' end of the primer should not exceed two the newer version of the software has an option to do this automatically but not the original version. This helps to introduce relative instability to the 3' end of primers to reduce non-specific priming. Maximum amplicon size should not exceed bp ideally bases. Smaller amplicons give more consistent results because PCR is more efficient and more tolerant of reaction conditions the short length requirement has nothing to do with the efficiency of 5' nuclease activity ,.

The higher number of Cs produces a higher D Rn this feature may require manual check. The choice of probe should be made first,. To avoid false-positive results due to amplification of contaminating genomic DNA in the cDNA preparation, it is preferable to have primers spanning exon-exon junctions in the cDNA sequence. This way, genomic DNA will not be amplified,. If a TaqMan probe is designed for allelic discrimination, the mismatching nucleotide the polymorphic site should be in the middle of the probe rather than at the ends,.

Use primers that contain dA nucleotides near the 3' ends so that any primer-dimer generated is efficiently degraded by AmpErase UNG mentioned in p. If primers cannot be selected with dA nucleotides near the ends, the use of primers with 3' terminal dU-nucleotides should be considered. Use positive-displacement pipettes to avoid inaccuracies in pipeting,. The sensitivity of real-time PCR allows detection of the target in 3. The number of copies of total RNA used in the reaction should ideally be enough to give a signal between 20 and 30 cycles preferably less than ng and not before 15 cycles.

The amount used should be decreased or increased to achieve this,. The optimal concentrations of the reagents are as follows: Magnesium chloride concentration should be between 4 and 7 mM much hogher then needed for traditional PCR. It is optimized as 5. Mg concentration is usually not an issue for singleplex reactions but optimization may be important for multiplex reactions -which requires higher magnesium concentration,. This is the minimum requirement. If necessary, optimization can be done by increasing this amount by 0.

The optimal probe concentration is nM, and the primer concentration is nM.

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Ideally, each primer pair should be optimized at three different temperatures 58, 60 and 62 0 C for TaqMan primers and at each combination of three concentrations 50, , nM. If necessary, a second round of optimization may improve the results. Optimal performance is achieved by selecting the primer concentrations that provide the lowest C T and highest D Rn.

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Similarly, the probe concentration should be optimized for nM,. A typical reverse transcription cycle for cDNA synthesis , which should precede the TaqMan reaction if the starting material is total RNA, consists of 10 min at 25 0 C primer incubation , 30 min at 48 0 C reverse transcription with conventional reverse transcriptase and 5 min at 95 0 C reverse transcriptase inactivation ,.

AmpErase uracil-N-glycosylase UNG is added in the reaction to prevent the reamplification of carry-over PCR products by removing any uracil incorporated into amplicons. It is necessary to rule out the presence of fluorescence contaminants in the sample or in the heat block of the thermal cycler these would cause false positives. If the absolute fluorescence of the NAC is greater than that of the NTC after PCR, fluorescent contaminants may be present in the sample or in the heating block of the thermal cycler,. The linear dynamic range refers to the range of initial template concentrations over which accurate C T values are obtained.

The resulting plot of log of the initial amount vs C T values standard curve should be a near straight line for both the target and normalizer real-time PCRs for the same range of total RNA concentrations [ideal values are: It does not participate in the 5' nuclease reaction. It provides an internal reference for background fluorescence emission. This is used to normalize the reporter-dye signal. This normalization is for non-PCR-related fluorescence fluctuations occurring in different wells concentration or volume differences, bubbles or over time and different from the normalization for the amount of cDNA or efficiency of the PCR.

Normalization is achieved by dividing the emission intensity of reporter dye by the emission intensity of the passive reference. This gives the ratio defined as Rn further normalization by subtraction of baseline fluorescence from this value yields D Rn. Not using ROX or not designating it as the passive reference dye in the analysis may cause trailing of the clusters in the allelic discrimination plot if your instrument does not require the use of ROX -like Stratagene and Bio-Rad instruments- then ROX concentration in the master mix should not be greater than 30nM ,.

In addition to the use of ROX in ABI instruments, a master mix should be used when setting up multiple reactions to minimize sample-to-sample and well-to-well variation and improve reproducibility ROX will be within the master mix ,. If multiplexing is done, the more abundant of the targets will use up all the ingredients of the reaction before the other target gets a chance to amplify.

To avoid this, the primer concentrations for the more abundant target should be limited and Mg concentration optimization may be necessary ,. If SYBR green is used, dissociation melting curve analysis should be performed. This result indicates that the products are specific, and that SYBR Green I fluorescence is a direct measure of accumulation of the product of interest. Each experiment should contain proper controls no template control, no-RT control and template quality should be checked for sufficient quality and uniformity.

Recommendations for the general assay of cDNA samples.

Real-time PCR Applications

If oligo-dT has to be used long mRNA transcripts or amplicons greater than two kilobases upstream should be avoided, and 18S RNA cannot be used as normalizer it has no poly-A tail ,. Multiplex PCR will only work properly if the control primers are limiting ABI control reagents do not have their primers limited. This requires running primer limiting assays for optimization,. The range of target cDNA used is 1 ng to 1 m g. If DNA is used mainly for allelic discrimination studies , the optimum amount is ng to 1 m g,. Of course, it is ideal to have primers not amplifying genomic DNA at all but sometimes this may not be possible,.

For optimal results, the reagents before the preparation of the PCR mix and the PCR mixture itself before loading should be vortexed and mixed well.

Real Time PCR - Basic simple animation - part 1 intro HD

Otherwise there may be shifting Rn values during the early 0 - 5 cycles of PCR. It is also important to add probe to the buffer component and allow it to equilibrate at room temperature prior to reagent mix formulation. TaqMan primers and probes. This stock solution should be aliquoted, frozen and kept in the dark.

Using 1 m L of this in a 50 m L reaction gives the recommended nM final concentration the range for final probe concentration in a TaqMan reaction is 50 to nM. The primers arrive lyophilized with the amount given on the tube in pmols such as It is best to freeze this stock solution in aliquots. To get the recommended 50 - nM final primer concentration in 50 m L reaction volume, 0. They have to be used as 20X, meaning 2.

If your instrument does not require inclusion of a passive reference dye in the master mix, make sure your master mix contains no or small amount ROX around 30nM final concentration. The ranges for final primer and probe concentrations given here 50 to nM for primers and 50 to nM for probes are for single targets. Critical factors for success in real-time, multiplex PCR. Alternatively, specially designed kits for multiplexing may be used to avoid extensive optimization steps see for example Qiagen multiplex real-time PCR kits.

Setting up one-step TaqMan reaction. This is the preferred method if the RNA solution has a low concentration. The disadvantage is that RNA carryover prevention enzyme AmpErase cannot be used in one-step reaction format. In this method, both reverse transcription and real-time PCR take place in the same tube. MgCl 2 25 mM: Ideally pg - ng RNA should be used in this reaction and no less than 6.

Note that decreasing the amount of template from ng to 50 ng will increase the C T value by 1. To decrease a C T value by 3, the initial amount of template should be increased 8-fold. Beware of stochastic nature of the PCR mechanics for very low template amounts. Cycling parameters for one-step PCR. Reverse transcription by MuLV 48 0 C for 30 min.

AmpliTaq activation 95 0 C for 10 min. On ABI , minimum holding time is 15 seconds. Make sure the following before starting a run: Cycle parameters are correct for the run somebody may have used different parameters before you ,. Choice of spectral compensation is correct off for singleplex, on for multiplex reactions ,. This may have to be manually assigned after a run if the data is absent in the amplification plot but visible in the plate view, and the X-axis of the amplification is displaying a range of cycles,.

The choice of dye component should be made correctly before data analysis. You must save the run before it starts by giving it a name not leaving as untitled. Also at the end of the run, first save the data before starting to analyze,. The ABI software requires extreme caution. Do not attempt to stop a run after clicking on the Run button.

You will have problems and if you need to switch off and on the machine, you have to wait for at least an hour to restart the run. When analyzing the data, remember that the default setting for baseline fluorescence calculation is cycles 3 - 15 called baseline cycles. Threshold default is 10 standard deviations of the background signal above mean fluorescence generated during baseline cycles in ABI instruments. This threshold value will be used to calculate the C T values for each sample in the run. The editors also aim to stimulate readers of all levels to develop their own innovative approaches to real-time PCR.

Book News August p. This book is well written I was impressed by this text, and expect to refer to it regularly in the course of my work in the future.

Applications of PCR

I would similarly recommend it to researchers and diagnostic scientists alike who either currently use, or wish to improve their understanding of real time PCR" from Australian Journal of Medical Science August Books Site Journal Backlist Gateway. An essential book for all laboratories using PCR. The development of fluorescent methods for the closed tube polymerase chain reaction has greatly simplified the process of quantification.

Current approaches use fluorescent probes that interact with the amplification products during the PCR to allow kinetic measurements of product accumulation. There are also a number of strand-specific probes that use the phenomenon of Fluorescent Energy Transfer. In this chapter we describe these methods in detail, outline the principles of each process, and describe published examples. This text has been written to provide an impartial overview of the utility of different assays and to show how they may be used on various commercially available thermal cyclers.

A range of factors can cause false negative results in real-time PCR through effects on one or more of the reaction components. Consequently applications requiring a high level of confidence need to be designed to control for the occurrence of false negatives. Whilst an external, or batch, control is often used, the ideal control is an internal one included in the reaction cocktail in a multiplex assay. Here we discuss the application and development of molecular mimics as controls in real-time PCR and explain concepts and experimental considerations to aid in the optimisation of controlled multiplexed assays.

The last few years have witnessed the transformation of the real-time, fluorescence-based reverse transcription polymerase chain reaction RT-qPCR from an experimental technology into a mainstream scientific tool for the detection and quantification of RNA with an enormous range of uses in basic research, molecular medicine and biotechnology. The continuous improvement of reagents and instruments, combined with the trend towards high throughput and miniaturisation, is likely to reinforce that pre-eminence and continue to open up new application areas.

Nonetheless, although in principle undoubtedly a straightforward technology, the reliability of RT-qPCR assays depends a series of sequential steps that include careful experimental design, optimisation and validation, which must be implemented pragmatically to obtain meaningful, biologically relevant data. With the public's reawakened concern regarding use of biological agents as weapons, the rapid detection, discrimination, and identification of pathogenic organisms and toxins has become a priority for state and federal government agencies.

High confidence, cost effective, and near real-time diagnostic methods are essential to protecting national health security whether the target is public health, agriculture, commodities, or water supply infrastructures. While culture-based methods have been, and will likely remain, the gold standard for microbiological diagnostics, PCR-based tests offer significant advantages in sensitivity, specificity, speed, and data richness that make them invaluable to diagnostic laboratories. In this chapter, we will describe the application of real-time PCR methods in biodefense.

We will discuss the use of real-time PCR in biodefense in terms of general workflow and processing considerations, clinical diagnostic applications, environmental diagnostic applications, and multiplex screening. Real-time PCR assays can be either quantitative qPCR or qualitative, depending on whether a standard curve is included with the analytical run. Most diagnostic and biodefense applications utilize the qualitative nature of real-time PCR as a detection platform; this chapter will focus on the benefits of these types of assays.

Finally, we will consider the future uses and anticipated advances in real-time PCR applications as related to biodefense. The detection and diagnosis of veterinary infectious diseases is an area in which the potential of Real-time PCR has been best demonstrated. In particular Real-time PCR has been successfully applied as a front line tool in the diagnostic algorithm for notifiable veterinary viral pathogens such as Avian Influenza, foot-and-mouth disease, bluetongue virus, as well as rabies and Newcastle disease virus. The rapidly transmissible nature of these agents necessitates near real-time detection and diagnosis in suspected infected animals to allow implementation of control procedures.

This chapter will highlight the importance of Real-time PCR in facilitating this rapid diagnosis, and the effect such rapid detection has had on containing and controlling veterinary infectious disease outbreaks. Applications in Clinical Microbiology. The introduction of real-time PCR technology to diagnostic clinical microbiology laboratories has led to significant improvements in the diagnosis of infectious disease.

It has been particularly useful to detect slow growing or difficult to grow infectious agents therefore much of its initial impact was in diagnostic virology. However, in more recent years real-time PCR-based methods have been introduced in diagnostic bacteriology, mycology and parasitology and there are few areas of clinical microbiology which remain unaffected by real-time PCR methodologies. One area where it has had great impact is its use for quantitation of viral pathogens. The ability to monitor the PCR reaction in real-time allows accurate quantitation of target sequence over at least six orders of magnitude.

In addition, the closed-tube format removes the need for post-amplification manipulation of the PCR products also reducing the likelihood of amplicon carryover to subsequent reactions reducing the risk of false-positives. The inherent sensitivity of real-time PCR means that contamination between samples and from previously amplified product can lead to false positive results. Therefore diagnostic labs utilising real-time PCR methods have to strictly adhere to good laboratory practice to reduce the likelihood of cross contamination.

In addition individual laboratories must ensure quality of diagnostic testing by participating in external quality assurance schemes. Myriad methods for the extraction and purification of nucleic acids prior to PCR are currently used throughout the community. While these methods have many unique and bespoke aspects, they broadly follow a sequence of lysis, isolation, washing and elution to get from a complex biological sample to purified nucleic acid that can be used in a PCR reaction.

Various common methods available for each stage are described and potential sequences for particular sample types can be discerned. The potential for these methods to be automated are discussed and the process options summarized with respect to the speed of the methods, technical skill required and the resultant purity and yield that can be expected. Oligonucleotide Primers and Probes: Rose, Richard Owczarzy, Joseph R. Dobosy and Mark A. Although the vast majority of primers and probes employed in qPCR applications today are synthesized using unmodified DNA bases, selective use of chemically-modified bases and non-base modifying groups can prevent primer-dimer artifacts, improve specificity, and allow for selective amplification of sequences that differ by as little as a single base.

A wide variety of chemical modifications have been characterized for use in qPCR. As a general class, the modifications that are in greatest use today increase the binding affinity of the oligonucleotides i.

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