REPLI-g Mitochondrial DNA Kit

对人类线粒体DNA进行高度均一的全基因组扩增

S_2731_ADNA_REPLIg_s

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REPLI-g Mitochondrial DNA Kit (25)

Cat. No. / ID:  151023

DNA Polymerase, Buffers, and Reagents for 25 x 50 μl mitochondrial DNA specific whole genome amplification reactions
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US$356.00
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REPLI-g Mitochondrial DNA Kit 旨在用于分子生物学应用。该产品不能用于疾病诊断、预防和治疗。

✓ 24/7 automatic processing of online orders

✓ Knowledgeable and professional Product & Technical Support

✓ Fast and reliable (re)-ordering

Features

  • 克服了分离线粒体DNA耗时的问题
  • 从总DNA中选择性扩增线粒体DNA
  • 扩增得到多达4 µg的高纯度线粒体DNA

Product Details

REPLI-g Mitochondrial DNA Kit可从DNA样本中选择性扩增线粒体DNA,无需预先分离线粒体DNA。该试剂盒含有DNA聚合酶、缓冲液和试剂,可利用MDA技术从少量样本中的总DNA中特异性、均一的扩增人类线粒体DNA。这一简便的操作可富集线粒体DNA,且细胞核DNA污染最小,避免进行耗时的线粒体DNA分离纯化,提高了下游分析的灵敏度。

Performance

总DNA中一般含有大约0.1%的线粒体DNA(如:1 ng人类总DNA含有1 pg线粒体DNA)。REPLI-g Mitochondrial DNA Kit可以特异性扩增人类线粒体全基因组,50 µl反应体系可扩增获得大约4 µg高纯度线粒体DNA。这相当于4000万倍的扩增效果,依据起始量会有所不同(参见" Enrichment of mitochondrial DNA")。产物的平均长度一般长于10 kb。
See figures

Principle

常见的获得线粒体DNA的限制之一为需要将线粒体DNA与细胞核DNA分离,在需要提高线粒体DNA标记物分析的灵敏度时尤其如此。分离过程涉及很多耗时的步骤,有可能导致线粒体DNA的损失。REPLI-g Mitochondrial DNA Kit可在含有总DNA的样本中直接扩增获得线粒体DNA,解决了这一问题。

REPLI-g Mitochondrial DNA Kit可快速、高度均一的对线粒体基因组进行全基因组扩增。该方法基于MDA技术,采用新型独特进行性的DNA聚合酶进行等温基因组扩增。REPLI-g DNA Polymerase凭借其活跃的进行性置换反应,可扩增得到100 kb的DNA,无需预先分离DNA。与PCR扩增方法相比,这种方法能很大程度减小序列偏差和不均一位点的出现。

Procedure

使用REPLI-g Mitochondrial DNA Kit扩增线粒体DNA涉及两个基本的步骤(参见" Purified mitochondrial DNA procedure")。首先,将含有总DNA的样本置于REPLI-g mt Reaction Buffer中75°C孵育五分钟,使其变性;通过冷却,使变性停止。然后,加入REPLI-g DNA Polymerase,在33°C开始恒温扩增8小时。
See figures

Applications

REPLI-g技术扩增获得的线粒体DNA可用于多种下游应用,包括:

  • 基因分型(例如:SNP、缺失、插入)
  • 终点式PCR、real-time PCR 
  • 测序

Supporting data and figures

Specifications

FeaturesSpecifications
AmplificationWhole genomic DNA
Samples per run (throughput)Mid
Denaturation stepHeat
Maximum input volume10 µl template DNA
Minimal pipetting volume needed1 µl
Reaction volume50 µl
Reaction time~8 hours (overnight)
Quality assessmentNo
ApplicationsGenotyping, sequencing, RFLP
Starting amount of DNA~10 ng purified total DNA
Starting materialGenomic human DNA
TechnologyMultiple Displacement Amplification (MDA)
Yield~4 µg

Resources

试剂盒操作手册 (2)
For specific whole genome amplification of human mitochondria from total DNA samples
产品介绍与指南 (1)
Second edition — innovative tools
安全数据表 (1)
Download Safety Data Sheets for QIAGEN product components.
快速启动实验方案 (1)
Safety Data Sheets (1)
Certificates of Analysis (1)
Brochures & Guides (1)
Second edition — innovative tools
Kit Handbooks (2)
For specific whole genome amplification of human mitochondria from total DNA samples
Supplementary Protocols (1)
Quick-Start Protocols (1)

Publications

Mitochondrial DNA mutation in normal margins and tumors of recurrent head and neck squamous cell carcinoma patients.
Dasgupta S; Koch R; Westra WH; Califano JA; Ha PK; Sidransky D; Koch WM;
Cancer Prev Res (Phila); 2010; 3 (9):1205-11 2010 Jul 26 PMID:20660573

FAQ

What is REPLI-g whole genome amplification?
The REPLI-g Whole Genome Amplification (WGA) method is a rapid and reliable method of generating unlimited DNA from a few cells or a few nanograms of genomic DNA. This technology amplifies the genome with comprehensive loci coverage and minimal bias between any loci, yielding 12+ kb fragments in a simple, scalable reaction.
FAQ ID -654
Will the random hexamers in the REPLI-g reaction interfere with downstream analysis?

The REPLI-g amplified products can be used directly for downstream analysis such as PCR, PCR-based applications, restriction enzyme digestion, cycle sequencing, and more, after appropriate dilution to adjust to work concentrations.

However, to determine DNA concentration by absorbance, the MDA product should be run through a spin column to eliminate the random hexamers, as they will contribute to the absorbance reading and give an artificially high concentration. For this reason, we recommend determining DNA concentration by PicoGreen analysis, which preferentially binds double-stranded DNA. As a result, single-stranded random hexamers will not contribute to the apparent DNA concentration in the quantitation assay. When using this method, the concentration of the MDA product can be determined directly, without any purification.

A Protocol for the use of PicoGreen to quantitate REPLI-g WGA product can be found in the REPLI-g Mini/Midi Handbook. Please follow this link .

FAQ ID -713
Are Centromeres and Telomeres amplified using REPLI-g WGA?
These regions are not amplified because only a subset of the random primers in the REPLI-g amplification mix can prime within these extensively repeated regions. Despite the high processivity of the Phi29 DNA Polymerase, centromeres and telomeres are at a competitive disadvantage during amplification, and drop out. In experiments we have done, single copy sequences within approximately 5000 bases of a poorly amplified region can be affected during amplification. If your gene is further than 5000 bases apart from a centromere or telomere, it should be amplified just fine.
FAQ ID -702
Can I use REPLI-g for SNP Genotyping?

Yes. Chromosomes are equally amplified. We and our customers use amplified DNA for SNP genotyping on a regular basis, using Illumina, TaqMan®, Sequenom, PCR, gel-based sequencing, and other techniques. Tzvetkov et al. (2005) used Affymetrix’ GeneChip Human Mapping 10K Arrays to investigate the accuracy and allele amplification bias in DNA samples subjected to MD-WGA with REPLI-g. They observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. Genomic DNA for this study was extracted from blood samples of four unrelated donors using the QIAamp DNA Blood Kit. High-throughput microarray genotyping of 11 555 different SNPs was performed using GeneChip Human Mapping 10K Arrays version Xba131 (Affymetrix).

For additional references, please visit our continuously expanding Citation Data Base online.

 See trademarks.

 

FAQ ID -700
Can I use any type of DNA extraction method to purify template DNA for amplification using the REPLI-g Mitochondrial DNA Kit?

Intact mitochondrial DNA is necessary for successful amplification with the REPLI-g Mitochondrial DNA Kit. Most DNA extraction methods are optimized for the isolation of linear nuclear DNA rather than for mitochondrial DNA. Furthermore, any harsh conditions leading to fragmentation of double stranded DNA must be avoided. We recommend the use of QIAamp DNA Kits, which are available in various formats and optimized for different sample materials.

 

FAQ ID -1321
What are possible reasons for reduced DNA yields with REPLI-g Kits?

Low yields with REPLI-g Kits for whole genome amplification (WGA) can result from a number of factors:

  • inhibitors in the template DNA, e.g., phenol and SDS, EDTA > 1 mM
  • low-quality, fragmented input DNA, e.g., degraded DNA from old samples, FFPE samples
  • improper reaction conditions, e.g., wrong volumes pipetted, insufficient reagent mixing, denaturation and neutralization steps omitted, or carried out incorrectly
  • Thermocycler incorrectly programmed, e.g., incubation time set incorrectly, reaction temperature too high (heated lid not adjusted to 70°C)

Note! When using a thermocycler model that does not allow adjusting the temperature of the heated lid, REPLI-g incubation temperature has to be reduced to 25-28°C to ensure optimal reaction conditions and amplification efficiency!

FAQ ID -2148
Can I purchase Phi29 DNA polymerase only?
We do not sell any REPLI-g reaction components separately.
FAQ ID -708
Does REPLI-g technology for whole genome amplification work with paraffin embedded samples?

Standard REPLI-g Kits, such as the REPLI-g Mini and Midi, UltraFast Mini-, Screening-, and Mitochondrial DNA Kits are not recommended for the amplification of gDNA extracted from paraffin embedded tissues. DNA recovered from paraffin embedded samples is typically strongly fragmented due to the fixation process, resulting in fragments only a few hundred base pairs long. Phi29 DNA polymerase however works most efficiently on DNA longer than 2 kb in length (ideally, at least a few fragments >10 kb should be present in the gDNA sample). If WGA product from strongly fragmented starting samples is utilized in genotyping assays, significant allele drop out and mis-genotyping can occur.

However, our new REPLI-g FFPE Kit overcomes these limitations by pre-processing of DNA directly derived from paraffin embedded tissue samples. The pre-processing reaction ligates fragments to generate suitable templates for subsequent amplification with REPLI-g Midi DNA Polymerase.

Further information can be found in the WGA Tutorial on our WGA Resource page.

FAQ ID -673
What are exo-resistant random hexamers used in the REPLI-g reaction?
These are DNA primers of random sequence, six nucleotides long, with two thiophosphate linkages at the 3' terminus to prevent digestion of the oligos by the 3' to 5' exonuclease activity of Phi29 Polymerase.
FAQ ID -710
Will REPLI-g work at high temperatures?
The reaction works at 30oC and will not work efficiently at higher temperatures. This is because the Phi29 DNA polymerase is not a thermostable enzyme and the random hexamer primers bind less efficiently as temperature is increased.
FAQ ID -656
How can I quantify the amount of REPLI-g DNA I have amplified?
  • Since REPLI-g amplification products contain single-stranded DNA as well as residual primers, it is important to utilize a DNA quantification method that is specific for double-stranded DNA. PicoGreen is a fluorescence-based nucleic acid quantitation method that is specific for double-stranded DNA and may be used to quantify the double-stranded REPLI-g products. For best results, the sample should be diluted with 2 volumes of water and thoroughly mixed prior to addition of PicoGreen.
  • before taking an OD reading on a spectrophotometer the reaction product must be purified as it contains unused primers and dNTPs
FAQ ID -694
Why is there DNA in the no-template control reaction when using the standard REPLI-g procedure, but not when using the UltraFast procedure?

In no-template (negative) control reactions, primer-dimers can form. The highly processive Phi29 DNA Polymerase will extend these primer-dimers leading to unspecific amplification products during the long incubation time with the standard REPLI-g procedure. Amplification in no-template controls takes place much more slowly than the amplification of template DNA. Using the REPLI-g UltraFast Mini Kit, the incubation time is too short to allow the extension of primer-dimers.

In any case, non-specific amplification products will not compromise results in downstream genetic analysis and do not appear if template DNA is present.

 

FAQ ID -1327
Has anyone verified whole genome amplification accuracy with Sequencing?

Paez et al. 2004 have shown in direct sequencing experiments sampling 500 000 bp, that the estimated error rate (9.5 x 10-6) was the same in WGA generated samples as in paired unamplified samples.

FAQ ID -701
Can I use my own primers for REPLI-g WGA to amplify a specific chromosomal region?
The REPLI-g kit is designed for whole genome amplification using random hexamers. Addition of specific primers instead of random hexamers may introduce amplification bias, or the preferential amplification of specific DNA fragments at the expense of others. Currently, specific primers alone cannot be used to amplify a specific region of the genome with REPLI-g.
FAQ ID -712
Can the REPLI-g Mitochondrial DNA Kit be used for species other than humans?

Yes, the REPLI-g Mitochondrial DNA Kit can be used for amplifying mitochondrial DNA from humans as well as other species. When the kit is used to amplify mitochondrial DNA from other species than humans, users can substitute the REPLI-g Human mt Primer Mix with an appropriate primer mix of their choice.

The efficiency and specificity of amplification is, in part, dictated by the sequence of the primers. The success of the amplification reaction using the REPLI-g Mitochondrial DNA Kit is greatly enhanced when the primers used for amplification are designed according to the following rules:

1. Select 10 to 20 different primers from the mitochondrial genome of interest.
2. Ensure that half of the primers hybridize to one strand, while the second half hybridizes to the complementary strand.
3. Select an almost uniform distance between primer hybridization sites within the mitochondrial genome.
4. Use primers that are 8 to 14 nt long.
5. Use a phosporothioate (PTO) backbone at the 3’ end of the primers. We recommend including phosphorothioate modifications between the last 3 bases of the 3’ end of the primers: 5’-N-N-----------------N*N*N-3’.
6. Ensure that the concentration of primers is optimized to be in the range of 1 to 10 µM.

Please be aware that for other REPLI-g products the primers are included in the master mix and cannot easily be exchanged.

FAQ ID - 3584
Where can I find background information and literature on Whole Genome Amplification with REPLI-g Kits?

Please visit our Whole Genome Amplification Resource Page for access to comprehensive information on WGA using REPLI-g Kits and REPLI-g Services.

Our WGA tutorial provides further information about Whole Genome Amplification and discusses the various techniques that are used. Additional detailed information is provided about REPLI-g Multiple Displacement Amplification technology (MDA), and recommendations are given on how to achieve the best results.

 

FAQ ID -1690
What is the length of the MDA whole genome amplification product?

MDA-amplified product has an average length of 10-12 kb, enabling Southern Blots, RFLP, and other downstream analyses that require large DNA fragments.

Note that the ligation procedure employed in the REPLI-g FFPE Kit results in the formation of very high-molecular-weight DNA and enables uniform whole genome amplification from formalin-fixed, paraffin-embedded (FFPE) tissue.

Further information on yield and length of amplified DNA can be found in the WGA Tutorial on our Whole Genome Amplification Resource Page.

FAQ ID -690
How can I determine the quality of my REPLI-g amplified products?
After the REPLI-g reactions are completed, 1 ug of the WGA reaction product can be analyzed by electrophoresis through a 1.0% agarose gel in TBE buffer (90 mM Tris-borate, pH 8.0, 2 mM EDTA), stained with GelStar, ethidium bromide, or SYBR Green, and imaged with a UV-box or a Phosphor-Imager. The majority of product should be above 10 Kb in length, and generate a trail of smear by electrophoresis down to about 2 Kb.
FAQ ID -695
Why do I get amplification in a negative control DNA tube using the REPLI-g Kit for WGA?

Phi29 DNA Polymerase has an extremely high processivity and will extend primer-dimers that may be present in the reaction, leading to unspecific amplification products. Furthermore, the REPLI-g reaction is highly sensitive to any traces of DNA. Even minute quantities of contaminating DNA from other sources are eventually amplified over the long duration of the reaction (6-16h). However, these non-specific products will not generate specific results in downstream genetic analysis.

FAQ ID -675
How much REPLI-g amplified mitochondrial DNA should be used in a subsequent PCR reaction?

The REPLI-g Mitochondrial DNA Kit amplifies mitochondrial DNA approximately 40 million-fold. The small size of the mitochondrial genome leads to very high copy numbers per microliter of amplified DNA. Therefore, we recommend dilution of the amplified DNA 1:1000 with nuclease-free water. Just 1 µl of the diluted sample should be used in a single PCR reaction.

 

FAQ ID -1320
Do mutations in the target mitochondrial DNA prevent primer binding, resulting in no DNA amplification with the REPLI-g Mitochondrial DNA Kit?

No, there is no risk that mitochondrial DNA will not be amplified due to a change in the primer binding site (i.e., caused by a deletion). This is because several primers are used in the amplification reaction with the REPLI-g Mitochondrial DNA Kit.

 

FAQ ID -1323
Any data on the fidelity of the REPLI-g MDA technique?

Phi29 DNA polymerase is a high fidelity proofreading enzyme and assures a very low replication error rate. It has an error rate of 1 x 10-6 - 10-7 nucleotides both in its intrinsic enzymatic activity and during the amplification reaction.

In contrast, Taq DNA polymerase has an intrinsic error rate of approximately 2 x 10-5 nucleotides, with an accumulation of about one mutation per 900 bases after 20 PCR cycles.

FAQ ID -707
What is the stability of the REPLI-g MDA product?
We have been conducting an ongoing stability study for more than a year without observing breakdown of the amplified product. There is nothing in the amplification product that indicates that it would not be stable for a number of years.
FAQ ID -693
What is the enzyme used in the REPLI-g reaction?
The enzyme used in the REPLI-g reaction is Phi29 DNA Polymerase.
FAQ ID -704
Can I amplify mitochondrial DNA directly from whole blood or cells using the REPLI-g Mitochondrial DNA Kit?

No, currently you need to purify total DNA first before using the REPLI-g Mitochondrial DNA Kit. For purification of total DNA, we recommend QIAamp DNA Kits, which are available in various formats and optimized for different sample materials.

 

FAQ ID -1319
Can I do whole genome amplification from mitochondrial DNA using REPLI-g?
Yes, we offer the REPLI-g Mitochondrial DNA Kit for this application.
FAQ ID -668
Is 2 kb the minimal gDNA fragment size for REPLI-g Whole Genome Amplification?

Highly degraded samples tend not to be amplified evenly across the genome. In general, an average fragment size of 2 kb in a DNA sample is the lower limit, assuming no portions of the genome are degraded to the point where information will be missing. Often, when the largest fragment in a gDNA sample is 2 kb, other fragments are much smaller and some regions of the genome may have been lost due to degradation. At least a small portion of 10 kb fragments or larger need to be present in the gDNA sample for even amplification of the entire genome.

Further information on working with fragmented DNA can be found in the WGA Tutorial on our Whole Genome Amplification Resource Page.

 

Note: If you are interested in amplifying DNA from paraffin-embedded samples we recommend to use the REPLI-g FFPE Kit.

FAQ ID -682
What are the differences between MDA and DOP/PEP methods of Whole Genome Amplification?

DOP (Degenerate Oligonucleotide-primed PCR) and PEP (Primer Extension Preamplification) are PCR-based whole genome amplification (WGA) methods. REPLI-g amplification uses MDA (Multiple Displacement Amplification) which is not a PCR-based method. MDA is scalable with yields adjustable from ug to mg quantities, whereas DOP typically yields 2-3 ug of DNA per reaction. DOP also generates a shorter product which is not suitable for certain downstream applications (e.g. Southern blot and sub-cloning).

DOP and PEP products are different from REPLI-g MDA products for a number of reasons. First, after amplification is complete, PEP products have active thermostable polymerase that will degrade the amplification product over time, because the polymerase cannot be inactivated. Second, PEP reactions consist of PCR amplicons which have the potential to contaminate other reactions as 'runaway amplicons' (e.g., amplicons in the aerosol that may be co-amplified if they accidentally get into other reactions).

REPLI-g product has neither of these issues. The polymerase is heat-inactivated after the REPLI-g reaction is complete, so it cannot digest the amplified product. There are no issues with 'runaway amplicons', because the reaction is performed at constant temperature by a hyper-branching amplification mechanism, amplifying the genome randomly without generating specific amplicons.

FAQ ID -665
Do you have a protocol for cleanup of REPLI-g amplified DNA?

Yes, please follow the Supplementary Protocol 'Purification of REPLI-g amplified DNA using the QIAamp DNA Mini Kit' (RG14).

 

 

 

FAQ ID -1545