DTI Brand > Products > PCR

PCR Range


PCR Master Mix

Master mixes are ideal for high-throughput and repetitive PCR reactions, providing consistency and convenience and reducing chances for errors, contamination, and repetitive stress.
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Green Colour Dye Added Master Mix
Green Colour High Fidelity Dye Added Master Mix

Blue Colour High Fidelity Dye Added Fast Master Mix

PCR Polymerase Enzyme

At DTI, we have developed a wide range of high-performance PCR enzymes for both routine applications and challenging reaction conditions.
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Routine Taq Polymerase Enzyme

Hot-Start Enabled Taq Polymerase

End-Point Thermal Cycler

Thermal Cycler is designed specifically to enhance PCR efficiency and accuracy equipped with a 7” sensitive touchscreen and a friendly graphic user interface.

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End-Point Instrument

PCR, Others

In addition to our high-performing DNA polymerases, master mixes, and kits, we offer PCR-related products such as dNTPs to support your research and laboratory-testing needs.
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1 ml Pack of dNTP Premix (10mM each)
Enzymatic Cleanup Reagent

UPGRADE YOUR PCR SKILLS



Application
Standard PCR/General Application
Standard PCR/General Application
Colony PCR
High Yield Genotyping
Genotyping
Recommended Product

Choose For

Routine Use
Routine Use
Fast, Routine PCR
Streamlined Workflow
Value Choice
Properties
Amplicon size
< 8 kb
< 8 kb
< 5 kb
<15 kb
< 5 kb
5'–3' Exonuclease Activity
Yes

Yes

Yes

Yes (Weak)

Yes

3'–5' Exonuclease Activity

-
-
Yes
Yes
-

T/A Overhangs or Blunt

T/A
T/A
T/A
T/A
T/A

Speed

60 sec/kb
60 sec/kb
10 sec/kb
60 sec/kb
60 sec/kb

Hotstart

-
Yes
Yes
-
-

Dye Added

-
-
Yes
Yes
Yes

Premix

-
-
Yes
Yes
Yes

What is PCR?

PCR stands for Polymerase Chain Reaction. It is a widely used laboratory technique to amplify or make many copies of a specific segment of DNA.​

How does PCR work?

PCR involves a series of cycles, each involving heating and cooling the DNA sample, enabling the DNA to be repeatedly copied.​

Principle of PCR

PCR involves repeated cycles of three main steps​:


1. Denaturation: The double-stranded DNA is heated to a high temperature to separate it into two single strands.​


2. Annealing: The temperature is lowered to allow short DNA primers to bind or "anneal" to their complementary sequences on the single-stranded DNA.​


3. Extension: The temperature is raised slightly to enable the DNA polymerase enzyme to synthesize a new strand of DNA by adding nucleotides to the annealed primers.​

Bioinformatics tools plays a crucial role in obtaining and analyzing target gene sequence data.​

Commonly Used Bioinformatics Tools:

NCBI Tools: BLAST, Entrez, PubMed, BLAST2GO

Standalone Tools: EMBOSS, Biopython, ClustalW, MEGA

Web-based Platforms: UCSC Genome Browser, Ensembl, Galaxy

How to Retrieve Gene Sequence from NCBI:​

• Go to NCBI (ncbi.nlm.nih.gov).​

• Choose "Nucleotide" database.

• Search for gene name or symbol.​

• Select the correct gene from results.​

• Find the sequence on the gene page.​

Design and synthesis of amplification primers for the target gene​

Primer design guidelines​
1. Primer size: 17-25mer​
2. GC content: 40-60%​
3. Align the forward and reverse Tm values

   (commonly calculated using the nearest neighbor method.  Approximate formula: Tm = 2(A+T) + 4(G+C) + 35 - 2N.

    In the free software Primer3, set 60℃<Tm<65℃)​

4. Confirm primer specificity (between genes, between species) with BLAST search (NCBI BLAST search                       https://blast.ncbi.nlm.nih.gov/Blast.cgi )​
5. Consider complementarity of primer sequence (avoid complementarity of 3 bases or more)​
6. Consider 3’ end sequence (G/C is preferable, avoid T)​
7. Consider the higher-order structure of PCR amplified products.​

Types of PCR Enzymes

Pol I​
Alpha type
Mixed
Bacterial DNA polymerase

Although it has lower fidelity than the α type, it has a wider range of PCR suitability.​

Used in general PCR​

A DNA polymerase derived from archaea.

It has 3'→5' exonuclease activity, so it has high fidelity synthesis and is used in PCR, where accurate amplification is required.​

Pol I and α types mixed in appropriate ratio​

Differences between Pol I and α PCR polymerases​

Pol Ⅰ (family A)​
α (family B)
Source organism
Thermophile bacteria
Hyperthermophilic Archaebacterium
3'-5' exonuclease
×
5'-3' exonuclease
○​
×
3' end of PCR product​
+ dA​
Blunt​
PCR enzyme

・Taq ​

・EmeraldAmp​, etc.

・PrimeSTAR​

・Ex Premier​, etc.

Example of use
Standard PCR

High fidelity, Long PCR


What parameters do I need to consider when designing primers?
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Primer design is the most important factor in determining the success or failure of PCR reactions. There are two major considerations for primer design: specificity and efficiency.

• Specifically is determind by the frequency of mispriming events. Primers with poor specificity tend to produce undesired amplicons.

• Efficiency is defined as the ability of primers to amplify a product with a two-fold increase per cycle to the theoretical optimum.

The following tables provide guidelines for primer design.

Guidelines

Length

The optimal length of primers is about 24 or 25 bases. However, length can be between 21 and 28 bases if the melting temperature (Tm) needs to be adjusted. When amplifying long DNA fragments (≥10 kb), 25- to 35-mer primers may provide better results.

GC Content

The GC content (the number of Gs and Cs in the primer as a proportion of the total number of bases) should be 40–60%.

3' end

Having four G and/or C bases at the 3' end might be useful if the primer length is short (the bases provide "a clamping effect"), especially for universal primers, which are typically used for amplifying all cDNA or gDNA in a sample. However, adding these bases may increase non-specific priming events for gene-specific primers.

Tm

If possible, design primers with a melting temperature of 68–70°C. While this is not absolutely necessary, using stringent PCR conditions (e.g., "touchdown PCR" and "two-step PCR") can enhance primer specificity.

Sequence specificity

Primers should be specific to your gene of interest. A BLAST search can be used to find regions of homology. Note: PCR yield often depends on the 3' hexamer of the PCR primer. Primers that form a strong stable duplex actually reduce the amplification efficiency.

Avoid

Repeats

The maximum number of di-nucleotide repeats in a primer is four (e.g., ATATATAT).

Runs

Avoid long runs of a single base (more than three) as this can cause primer slippage and contribute to mispriming.

Complementary 3' ends

Forward and reverse primers should not anneal to each other and so should not have complementary G or C stretches (>4 contiguous bases).

Self-complementary 3' ends

Self-complementarity (e.g., within the forward primer) can lead to hairpin formation. A hairpin structure can form with just four G/C base pairs in the stem and three bases in the loop.

How do I calculate the melting temperature (Tm) of primers?
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The primer melting temperature (Tm) is the estimate of DNA-DNA hybrid stability. Knowing the Tm is critical for determining an appropriate annealing temperature (Ta). A Ta that is too high will result in insufficient primer-template hybridization, leading to low PCR product yield. A Ta that is too low may lead to non-specific product amplification.

Calculation of the Tm of primers shorter than 20 bases can be performed using the Wallace rule:

Tm = 2°C (A+T) + 4°C (G+C)

For accurate estimation of the Tm of primers longer than 20 bases, we recommend using free primer design software such as Primer3.

What primer concentration should be used for PCR?
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The final concentration of each primer should be between 0.1 and 0.5 µM. A stock solution of each primer is typically 10–20 µM.

Primer concentrations that are too high increase the chance of mispriming, which may result in nonspecific amplification. Primer concentrations that are limiting can result in extremely inefficient amplification.

How should oligos be purified for PCR?
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Standard desalted primers are satisfactory for most PCR applications.

Should I use a three-step or a two-step PCR protocol?

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Three-step PCR includes denaturation, annealing, and extension steps. This type of protocol should be used when the Tm of the primers is lower than the extension temperature or is less than 68°C.

If the melting temperature of the primer (Tm) is close to the extension temperature (72°C) or a few degrees lower, consider using a two-step PCR protocol that includes a denaturation step and a combined annealing/extension step. With this protocol, the annealing temperature should not exceed the extension temperature.

Which extension temperature should I use, 68°C or 72°C?
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A 68°C extension temperature is preferred for two-step PCR and when amplifying longer templates (>4 kb). This lower extension temperature dramatically improves yields of longer amplification products by reducing the depurination rate that influences amplification.

72°C should be used as the extension temperature when performing three-step standard PCR and for amplification of short fragments (<4 kb).

What are the critical factors for amplification of GC-rich templates?
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PCR conditions:

• Use higher denaturation temperatures (e.g., 98°C as opposed to 94°C or 95°C) to allow complete denaturation of the template.

• Keep annealing times for GC-rich templates as short as possible.

• Use primers with a higher Tm (>68°C), because annealing can occur at a higher temperature.

What are the critical factors for amplification of long genomic targets?
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Template quality:

DNA integrity is critical for amplification of long targets. DNA damage—such as DNA breakage during DNA isolation or DNA depurination at elevated temperatures and low pH—results in a greater amount of partial products and decreased overall yield. DNA damage can also occur in acidic conditions; therefore, avoid using water for resuspending DNA templates. DNA is most stable at pH 7–8 or in buffered solutions.

PCR conditions:

• Denaturation time should be kept to a minimum to decrease depurination events.

• Use touchdown PCR; start at a higher annealing temperature and reduce by two degrees per cycle for several cycles.

• Design primers with melting temperatures (Tm) above 68°C.

How do I determine if a template is GC rich?
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The GC ratio varies across the genome. Templates with >65% GC content are considered GC rich. GC-rich regions of the genome are mostly concentrated in regulatory regions, including promoters, enhancers, and cis-regulatory elements. GC-rich tracts tend to form inverted repeats, or hairpin structures, that may not melt during the annealing step of PCR. Therefore, amplification of GC-rich templates is hindered by inefficient separation of the two DNA strands. This results in truncated amplicons due to premature termination of polymerase extension.


The successful amplification of DNA is key to many technologies, whether you're performing next-generation sequencing, cloning, or genotyping. Your PCR polymerase needs to amplify reliably regardless of your target and sample type. We developed a wide range of the highest-performing PCR enzymes and blends with optimized formulations to meet routine and challenging reaction conditions—from long and accurate PCR to fast PCR to inhibitor-resistant direct PCR.

DNA Isolation

High-quality starting materials are important for the beginning of all good science. We currently offer DNA extraction kits from our in-house India manufactured brand "DTI" as well as from Macherey-Nagel brand which is our global partner of Takara Bio for nucleic acid extraction in the bioanalysis range.


Common nucleic acid isolation methods:

Spin Column

Magnetic Beads


Benefits

• Ease of use

• High yield and purity

• Throughput flexibility

• No risk of clogging

• Increased target capture efficiency

• Rapid collection and concentration of sample


Choose our DTI Brand for India manufactured range

DTI, is the premier in-house brand of DSS Takara Bio India Pvt Ltd. specializing in to manufacture routine laboratory molecular biology products within our state-of-the-art facility, which is ISO 9001 and ISO 13485 approved. This certification ensures that our processes and products meet the highest quality standards, enabling researchers, scientists, and professionals to conduct their work with confidence and precision.

Our brand DTI is committed to the visionary initiatives of the Indian government, including Make in India and Atmanirbhar Bharat providing ease of product customization at affordable pricing with reduced lead time.


Choose MN for your DNA application

MN has been a reliable partner for DNA purification for years. Due to the excellent experience in nucleic acid purification, the MN research and technical support team knows all about pitfalls during DNA purification. Therefore, MN developed a variety of optimized solutions for processing your sample material of choice.


PCR Enzyme Selection

The successful amplification of DNA is key to many technologies, whether you're performing next-generation sequencing, cloning, or genotyping. Our large and diverse portfolio of PCR polymerases was designed for success across a variety of applications, from basic and translational research to routine laboratory testing. We create polymerases that simply work faster and better, so you can focus on obtaining the results you need.


PCR Product Offerings

For Routine PCR/Genotyping

For Convenient use dye plus master mix

For High fidelity PCR

For High yield PCR

For Long fragment PCR

For Glycerol-Free options

TaKaRa Taq™ HS (Glycerol Free)

For Lyophilised options

Accessories

Thermal Cycling

DTI FabSpeed Thermal Cycler is designed specifically to enhance PCR efficiency and accuracy. It is equipped with a 7” sensitive touchscreen and a friendly graphic user interface, which makes operation highly intuitive. With flexible ramp rate and gradient temperature control, DTI FabSpeed greatly increases PCR accurate optimization.


Features & Benefits

Flexible Ramp Rate Control

Fully Adjustable Lid Temperature

Gradient Optimization

From 0.1 - 5.5 ℃/sec to meet the need for the CRISPR related assays.

Can be set between 35 and 120 °C for virtually any type of experiment including NGS pre-treatment.

Range from 1 to 30 °C enables optimal experimental conditions in a single PCR run.


Ordering Information

Brand

Catalogue Number

Description

DTI Brand

TCST-9622

Amplicon Analysis

Agarose gel electrophoresis is a widely used method in PCR workflows for analyzing nucleic acids. It helps separate, identify, quantify, and purify PCR amplicons. Selecting the appropriate products for nucleic acid electrophoresis can greatly enhance and expedite your results.

Our high-quality agarose and markers are designed to support accurate analysis, ensuring you achieve precise and reliable outcomes in your downstream applications.


PCR Product Offerings

DNA Ladder
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DL 2,000 DNA Marker
DL 5,000 DNA Marker

Takara Bio companies provide kits, reagents, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, DSS Takara Bio India Private Ltd. is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.



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