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Translational Research | Amplification
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Translational Research | Amplification

Precision-tuned PCR for translational research

Endpoint PCR is a workhorse technique for translational research, and as with any mainstay approach, strength and reliability are key. Single copy PCR may be used for routine screening for a target of interest, while multiplex PCR assays are designed to detect a suite of targets. For efficiency, fast PCR enables screening in a fraction of the time by using high-speed enzymes, and direct PCR allows amplification from tissue without need for DNA extraction.

No matter the demands of your PCR amplification assay, we have a polymerase that is precision-tuned to meet your needs.

Click the buttons below to learn more

Single copy PCR

When your PCR aims to genotype samples for a biomedical allele of interest, there’s nothing “routine” or “standard” about the experiment. Research progress depends on getting the job done, and being able to rely on your polymerase is critical, especially when you need sufficient sensitivity to detect low- or single-copy targets.

  • Used by thousands of scientists worldwide, TaKaRa Ex Taq DNA Polymerase is a proofreading enzyme with 3' to 5' exonuclease activity, resulting in approximately 4.5-fold higher fidelity than Taq and high yield of product. This enzyme has long been a first choice of researchers working with crude or “dirty” DNA extracts since it retains activity in presence of PCR inhibitors that often halt or slow other polymerases.
  • Titanium Taq DNA Polymerase is a recombinant enzyme with carefully designed amino acid substitutions to enhance its solubility, resulting in increased sensitivity. Capable of efficient amplification in fewer cycles, this polymerase is ideal for PCR with complex DNA mixtures or to amplify rare targets. Titanium Taq enzyme lacks 5' exonuclease activity and has fidelity similar to wild-type Taq. An excellent choice for SNP assays, it is recommended for use with Genome-Wide Human SNP Assay Kits from Affymetrix.
First choice for yield, crude extracts, and long PCR:
TaKaRa Ex Taq DNA Polymerase >>
First choice for sensitivity
Titanium Taq DNA Polymerase >>
Higher fidelity X  
Yield X  
For crude extracts X  
Sensitivity   X
Use with Genome-wide Human SNP Assay Kits (Affymetrix)   X
Product length Broad range:
100 bp–20 kb
Mid-range:
100 bp–2 kb (genomic)
<4 kb (cDNA)
Literature examples
  • Citation list >>
  • Genotyping
  • RT-PCR (biomarker expression)
  • PCR assays (bacterial pathogens)
  • Citation list >>
  • SNP detection
  • Alternative splice variant detection
  • RT-PCR (biomarker expression)
  • High-throughput studies

Multiplex PCR

Multiplex PCR assay protocols are designed to harness the power of numbers—increasing efficiency by assessing multiple PCR targets at one time, in a single reaction. A mainstay of genetic analysis, multiplex PCR also is used for translational research in areas such as infectious disease. Titanium Taq DNA Polymerase and TaKaRa Taq Hot Start DNA polymerases have been used in multiplex PCR assays for a range of studies including those related to blood allele analysis, Alzheimer’s disease alleles, and food pathogen screening.

  • Titanium Taq DNA Polymerase is a recombinant enzyme with carefully designed amino acid substitutions to enhance its solubility, resulting in increased sensitivity. Titanium Taq polymerase is especially useful for multiplex PCR because it reduces mispriming events caused by multiple primer sets. An excellent choice for multiplex SNP detection, it is recommended for use with Genome-Wide Human SNP Assay Kits from Affymetrix.
  • Hot start-formulated TaKaRa Taq HS DNA Polymerase includes anti-Taq monoclonal antibody to improve specificity, reduce background, and allow room temperature reaction assembly. Three versions are available: the original TaKaRa Taq HS version (Cat. # R007A) with enzyme, buffer, and dNTPs as separate components; Premix TaKaRa Taq HS (Cat. # R028A) with enzyme, buffer, and dNTPs as a 2X master mix; and TaKaRa Taq HS Perfect Mix (Cat. # R300A), a 2X premix optimized for faster reactions (20 sec/kb extension step).
Recommended for Affymetrix Genome-Wide SNP Assays
Titanium Taq DNA Polymerase >>
First choice for viral samples
TaKaRa Taq HS >>
High multiplicity (≥8 primer sets)   X
Unbiased whole genome amplification X  
Room-temperature reaction setup X X
Sensitivity X  
Use with Genome-Wide Human SNP Assay Kits from Affymetrix X  
Product length 100 bp–2 kb (genomic)
≤4 kb (cDNA)
≤3 kb (genomic)
≤8 kb (lambda DNA)
Literature examples
  • Citation list >>
  • SNP detection (cancer, Alzheimer’s, deafness)
  • Melting curve analysis
  • Multiplex assay (food pathogens)
  • Citation list >>
  • Blood allele assay
  • Multiplex primer extension assay
  • Multiplex assay (food pathogens)

Fast PCR

The need for speed in PCR during translational research studies is driven by a sense of urgency. Completing PCR assays in less time could mean submitting your manuscript or study results sooner, evaluating your hypothesis more swiftly, or understanding the genetic diversity in a research study population faster. Our R&D scientists have developed high-speed polymerases that have been used in a range of applications, including innovative assays that are completed in a fraction of the time compared to protocols with conventional reagents.

  • PrimeSTAR Max DNA Polymerase includes an elongation factor to make priming and extension ultra-efficient. As a result, it offers the highest processivity of any polymerase available, paired with the highest fidelity. Formulation as a 2X premix additionally speeds up workflow by reducing pipetting steps. Extension steps can be set routinely at as short as 5 sec per kb of product—in some cases, even less.
  • For fast PCR at moderate fidelity, SpeedSTAR HS DNA Polymerase provides exceptionally robust and accelerated activity. This enzyme may be used to amplify a 2-kb product in under 30 minutes using a standard thermocycler. Others have used it for high-speed applications including methods for ≤ 3 minute PCR (Wheeler et al., 2011) and 15-minute RT-PCR (Yamanaka et al., 2011).
First choice fast high fidelity PCR
PrimeSTAR Max DNA Polymerase >>
First choice for high speed, moderate fidelity PCR
SpeedSTAR HS DNA Polymerase >>
Highest fidelity X  
2X premix X  
Two buffer choices   X
Long-range PCR   X
Hot-start X X
Product length ≤6 kb (genomic or cDNA) ≤20 kb
Literature examples
  • Citation list >>
  • Viral pathogen assays
  • Regulatory miRNA detection
  • Generic variation studies
  • Citation list >>
  • Low-volume, high-speed PCR
  • Microfluidic high-speed RT-PCR
  • Warfarin metabolism genotyping assay

Direct PCR

Using tissue, blood, or cells directly for PCR saves sample handling time by allowing you to skip DNA extraction steps. For translational research, purification of DNA prior to PCR analysis adds labor and time requirements. Removal of the purification step improves sample turnaround times, resulting in expedited assay conclusions. Terra PCR Direct Polymerase Mix and kits are optimized to work with a range of clinical sample types such as blood, buccal cells, saliva, and tissue samples. Several application-specific kits are available:

  • A Polymerase Mix suitable for most applications, also available in a dye-added formulation
  • A Genotyping Kit with extraction buffer and loading dye included as separate components
  • Kits optimized for use with FFPE samples or samples archived on Whatman FTA cards

Terra PCR Direct kits have been used for infectious disease, genetic variation, and cancer research studies.

Click here for Terra Selection Guide >>

Click here for citation list >>

Methylation analysis

Methylation of cytosine residues in CpG pairs within or in close proximity to promoters results in silencing of functional genes. Hypermethylation in promoter regions has been associated with several types of cancer as well as aging. To analyze DNA methylation patterns, bisulfite treatment is used convert cytosine residues to uracil. This treatment leaves 5-methylcytosine unmodified. Several PCR-based techniques can be used to assess bisulfite-treated DNA, including methylation-specific PCR (MSP), bisulfite sequencing, and combined bisulfite restriction analysis (COBRA).

EpiTaq HS (for bisulfite-treated DNA) is optimized for PCR amplifications using bisulfite-treated DNA containing uracil as template. Designed for PCR for COBRA/Bisulfite sequencing analyses, it is well-suited for methylation analysis of CpG islands and also for DNA amplification with AT-rich and GC-rich templates.

PCR amplification using bisulfite-treated DNA (HeLa cells) as template

Figure 1. PCR with bisulfite-treated HeLa genomic DNA as template. Left to right: 100 bp ladder (M); 153 bp product (CDH1), 297 bp product (CDH1), 136 bp product (MLH1), 292 bp product (MLH1), 613 bp product (BRCA1), 1,017 bp product (BRCA1).

Click here for citation list >>

What researchers are saying

“Could not get a PCR product with product from a competitor. Got it with with EpiTaqHS. Thanks.”

—Researcher at Fox Chase Cancer Center

“I have tried my PCR with several different enzymes. With TaKaRa EpiTaq HS, I have got the my PCR work.”

—Researcher at Douglas Hospital

“After weeks of struggling with this your polymerase worked like a champ.”

— Researcher at Geisinger Medical Center

“I was having difficulty amplifying PCR products from bisulfite-treated DNA. TaKaRa EpiTaq was able to successfully amplify products using with all of my primer combinations. I was able to amplify a product of ~1000 bp, where with other polymerases I was luck to get up to 300 bp.”

— Researcher at University of Saskatchewan

Contact us for Royalty-free, Glycerol-Free, OEM or Custom Products

Interested in royalty-free DNA polymerase formulations, OEM, glycerol-free enzymes, custom packaging or product configurations? Please inquire at licensing@clontech.com or submit an inquiry online.

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