I am going to validate some microRNA genes in two developmental stages. But i found the method for miRNA primer designing is totally change compering to mRNA and LncRNA primers designing. Please update my query and also suggest some tools for designing the miRNA primers. Much obliged
Mr khan you can read this paper maybe it will possibly helps you
(qPCR-based methods for expression analysis of miRNAs). Another way is there are many software's and database available you can check here
www.mirbase.org
www.microrna.gr/tarbase
mirtarbase.mbc.nctu.edu.tw
bioinfo.ut.ee/primer3
www.rtprimerdb.org.
Hope these sites and databases will be helpful for your query.
hi Ibrar Muhammad Khan
miRNA primer has universal sequences. you will find the stem-loop & mature miRNA sequence in the miRDB database. Well, prefer predesigned primers of your interested miRNA from any standard company. Nowadays, Companies do a slight modification or say a technology, which enhances stability and avoids unwanted binding. Qiagen has LNA tech. based miRNA primers, those are readymade, pre-mix (FP+RP), available for most of the miRNAs. Just dissolve and use 1ul for per rxn.
You can look at this tool and paper also.
http://www.autoprime.de/AutoPrimeWeb
Article A tool for design of primers for microRNA-specific quantitat...
Regards
Saurabh
Hello my friend, majority of all primers for miRNA are LNA, this kind of primers are the most specific one, however, you'll not able to create LNA types and you have to purchase them from companies like Qiagen. But Stem-loop primers can be create via general software, but there is a main point, you have to design two, microRNA-specific primers by designing one, 12 – 18 nucleotides long forward primer and a reverse primer with 3 – 8 specific. Please note that its totally different from general gene's primers in terms of TM.
Much obliged to all dudes ....@ Hadi Rajabi , Saurabh Mandal and Sajid Ur Rahman ....
Hi Ibrar Muhammad Khan
Please refer to this link. Hopefully, it would be helpful.
https://www.researchgate.net/post/How_do_you_design_primers_for_microRNAs
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