Hi,
do you have experience in RAPD? It is completely new for me and I have to use it to type my bacteria strains. I am aware that I have to use random primers. My questions are
1) How can I design these primers?
2) How many primers should they be used?If they are more than 1, should they be added all together to the reaction volume or I am supposed to set different single PCR reactions for each primer?
Thanks in advance
Hi Silvia,
RAPD is very well worked out technique...so go thorugh some published literature....to your queries
1) you don't have to design primers. they are available from companies as kits and your directly use them
2) The RAPD primers are used one at a time and not mixed together. One has to try different primers and some may work and few may not work...you need to set different PCR reactions for each primer and screen for polymorphism
best regards
I mostly agree with Ajay. The primers are available commercially under the codes. Usually they are made out of ten nucleotides and function as either F or R primer. For some serious population screening you should choose 16-20 primers, depending on their resolving power. And also, I'm sure Ajay meant "individual" instead "different" PCR reaction, because every primer works under the more-less same PCR reaction. The primers shouldn't be mixed, because each reaction of individual primer should give 5-10 highly resolvable bands, and by mixing primers you would get a bunch of unresovable bands or even smears.
After you get the gel images in RAPD experiments, selecting correct analytic algorithms become the key for the data analysis. Please see my papers in ResearchGate :
Suitability and Advantages of Abundance-Weighted Algorithms for the Holistic Comparison of Sample Systems. J Appl Biotechnol Bioengineering, 2017, 2(6): 00050
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