you have to check it by yourself the Acceptable ΔG (free energy required to break the structure): >-2 kcal/mol for 3’end hairpin; >-3 kcal/mol for internal hairpin;

See this, it'll help you

Hi Rehab

It is advisable to use offline or online primer design and analysis program right in the begining of primer designing..many good progams will give you indication of all possible and undesirable interaction of the designed primers...

I use this online tool, which I think is quite good:

http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/

Perl primer, is a good option for designing primers, as it lets you to modify all the default parameters, even the exon and the intron based.

You can use this site if your primer make ahairpin or not: http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/

I use too the IDT oligoanalizer, look the vaues of ΔG if are

u can use gene runner software

use netprimer http://www.premierbiosoft.com/netprimer/index.html

first need to register

This free online tool is very useful: http://www.basic.northwestern.edu/biotools/oligocalc.html

Here is the paper where it is described: http://www.ncbi.nlm.nih.gov/pubmed/17452344

I have used net primer from primier biosoft it will give most of the information regarding the primers..good luck..

You can use oligo calculator software. It gives you the anneling temperature of the primer pairs along with their GC content. You can also get the detail for any self complementary structure formation like hairpin loops. Along with this it also gives you a direct link to BLAST in case you want to check whether the primer binds at the region of your interest.

I use http://www.idtdna.com/analyzer/applications/oligoanalyzer/

but you know what, sometimes I order primers that look perfect in silico but never work in reaction. On the other hand I checked some ancient primers that work perfectly and silico tolls show some awful things. So, I prefer to try out rather than reject based on silico prediction. Primers are inexpensive and there is always some Taq you can spare to try a new primer...

I am using NetPrimer as Anna and Vidya. http://www.premierbiosoft.com/netprimer/

Also gives you information about dimers, repeats, and many more parameters.

thanx you! I used NetPrimer too

Use this tool: https://www.thermofisher.com/in/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/multiple-primer-analyzer.html

You can use: http://biotools.nubic.northwestern.edu/OligoCalc.html.

gene runner, freely available software

use https://www.idtdna.com/calc/analyzer