You do not need to worry about your primers. Two primers are involved in the PCR, even if each of them has many sites in the genome, PCR will be only when they are encountered.

You can test your primers in pairs, by silico PCR method:

https://primerdigital.com/tools/pcr.html

Thanks Ruslan Kalendar for your feedback.

I tested my primers using the tool (FastPCR 6.6 : in silico PCR), but when I import my file (genome in .fsa_nt format) and strated analysis, the system not reply.

What are formats of file read it by this tool?

Hi Md Abdur Rahim

Thank you so much for your response. UCSC in silico primer is very helpful, but it doesn't contain my reference genome (species of plant).

You have any idea about another tool or database with the same principle!!!

You need load sequences into memory (Ctrl-G), but you load all these sequences to the editor.

But I recommend to save all genomic sequences in the separated folder and then you can use "Working with all files in folder" (Ctrl-J). After this all these sequences will be used in software without troubles.

Ruslan Kalendar many thanks, problem is resolved. But I have another obstacle, when I put all my sequences of genome (75.000 contigs)to testing my paire primers by in silico PCR, the operation is endomaged and system is blocked.

Karim Rabeh

Please see below shared information.>>>>>the link: https://bitesizebio.com/10041/designing-qpcr-primers/

A Step-by-Step Guide to Designing qPCR Primers

Primer design is a critical step when setting up your qPCR or reverse transcription-qPCR assay (RT-qPCR). qPCR primers that anneal poorly or to more than one sequence during amplification can significantly impact the quality and reliability of your results. Also, if you are performing a one-step RT-qPCR, the reverse transcriptase will use the reverse primer to prime the transcription reaction. In this scenario, a poor primer would result in both inefficient reverse transcription and inefficient amplification – a lose-lose situation.

Considering the above, it’s well worth spending the time necessary to design good qPCR primers. This article will tell you exactly how to do that!

The good news is that primers are cheap, so you can easily test several different pairs to choose the best ones for your experiment. The bad news is that primer testing requires time and patience, so the sooner you get a pair of primers working, the better.

The NCBI tool Primer BLAST is widely used for qPCR primer design. There are many other primer design tools available online, including primer3, and PCR suppliers often offer their own design programs free of charge.

Below are the main steps involved in designing primers using the NCBI tool Primer BLAST. The design steps will be similar if you use other primer design programs, and the information below should give you an idea of the parameters to watch out for.

Getting Started

Go to the Pubmed gene database and search for your gene of interest. You can filter by species in the right-hand corner of the screen. Click on your gene of interest and scroll down until you find the NCBI Reference Sequence (RefSeq) for your gene (e.g., “NM_203483”). Click there and in the next screen you will see a link to “Pick primers” in the right corner of the screen.

Parameters for qPCR Primers

Set the following primer parameters:

• PCR product/amplicon size: For efficient amplification, design the primers so that the amplicon is between 70 and 200 bp long.
• Number of primers to return: This is up to you, depending on how many options you want to choose from. It won’t take long for the program to design ten primer pairs, and this should give you a reasonable chance of finding a suitable pair.
• Melting temperature: As a rule, aim for a minimum of 60°C and a maximum of 63°C; the ideal melting temperature is 60°C (with a maximum difference of 3°C in the melting temperatures, Tm, of the two primers). You can use a Tm calculator to determine these temperatures.

Exon/Intron Selection

To avoid amplification of contaminating genomic DNA, design primers so that one half of the primer hybridizes to the 3′ end of one exon, and the other half to the 5′ end of the adjacent exon. To do this, simply select “Primer must span an exon-exon junction.” You don’t need to change the other settings.

Primer pair specificity checking parameters: Use the default settings. The program will use the RefSeq mRNA sequence from the organism you selected to design the primers.

Checking the Output Screen

Take a look at the options the program returned and pay special attention to the following:

• Make sure the 3′ end of the primer contains a C or G residue, because T and A residues bind more easily to DNA in a non-specific way.
• Aim for a GC content of around 40-60% to ensure maximum product stability.
• Avoid self complementarity to decrease the possibility of primer-dimer formation. Ideally, the primer should have a near random mix of nucleotides.

Now, pick the best two or three primers and test them. Good luck!

Originally published in 2013. Updated and republished in 2017.

Image Credit: Ulf LiljankoskiBy New England Biolabs

I hope that this will help.

hello,

if you are looking for mRNA already studied, you can use ddml primer database, all primers/probes described have already been qualified.

or if you want to set up your own primers I would recommend UCSC as Abdur Rahim.

best

Audrey Vanya thank you so much, your recommendation is helpful.

Arnaud Beurdeley

Yes, I'm looking for my own specific primers. For UCSC, is not include my reference genome.

Dear all,

I have a trouble when designing primers to quantify bacteria gene by qPCR. I used primer3plus to design primers with target is a bacteria gene. Next, I used Nucleotide BLAST to check the primers with my bacteria and mouse tamples. It is shown that the primers can amplify both trancripts in mouse and my bacteria. So I can not use these primers bacause I am going to inject my bacteria into mouse.

Does anyone know how to design primers that amplify only bacteria gene?