I have no prior knowledge of microRNAs and a member of my lab just started her project working on it. ive done primer designing before for my genes but it cant be applied to designing primers for miRNAs. Can anyone suggest how i can design primers for miRNAs?
hi Aswani Jaishanker
miRNA primer has universal sequences. you will find the stem-loop & mature miRNA sequence in 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.
Regards
Saurabh
Dear Aswani Jaishanker,
Do you want to work on mature miRNA or immature?
If its name starts with miR, then it is mature, but if it is mir, it is immature and is Pre-mir or Pro-mir.
After determining the type of miRNA and its chromosomal location, because the number of genes is very small, you can consider 100 to 200 nucleotides from each side of the gene more and use the NCBI site to easily design the primer.
Good luck
Saurabh Mandal Thank you so much for your help regarding this. I will continue to read more and check out miRDB database for more information. We were looking at ordering the primers from companies but do not have the necessary funding for it so trying to save where we can unfortunately. Thus, trying to design it ourselves.
Mehrdad Mohebi Shahpour Abadi We have chosen a mature miRNA sequence and trying to design a primer for that. The size of it is quite small so we have been having some difficulties. Thank you for the recommendation, will try that and see.
Hi Aswani Jaishanker
if you want to design primers for miRNAs to evaluate their expression with real-time PCR, you can use these tools:
1- miRNA Primer Design Tool | Login (http://genomics.dote.hu:8080/mirnadesigntool/)
2- you can use these tools if you choose the stem-loop method:
(A: http://www.flujogenico.cl/plantbiotech/amir319edesigner/stemloop/)
(B: http://www.plantbiotech.cl/amir319edesigner/stemloop/)
3- sRNAPrimerDB -- (http://www.srnaprimerdb.com/)
4- for design TaqMan primer use : (http://www.autoprime.de/AutoPrimeWeb)
these articles can also be helpful:
1- Article Real-time quantification of microRNAs by stem–loop RT–PCR
2- Article A tool for design of primers for microRNA-specific quantitat...
3- Article A Versatile Method to Design Stem-Loop Primer-Based Quantita...
Good luck!
Afshin
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA