I want to amplify a short RNA sequence (about 170bases) but am unable to design LAMP primers as the software (Primer Explorer) gives the message that the minimun size is about 200 bases. Has any one amplified small RNAs isothermally? And which software/tool that is good for designing LAMP primers?
Design the primer manually and take care all properties of good LAMP primer, short sequence is not a big problem. Best of luck.
Design the primer manually and take care all properties of good LAMP primer, short sequence is not a big problem. Best of luck.
I guess Designing the primer manually is the only solution. good luck.
I think it could be designed but you have to do manually and there are a lot of conditions that you have to beware, please read a guideline from the Primer Explorer Manual. Good luck.
Dear Julia Powers,
Can we use Primer3 express software for designing LAMP primers--guess we can use the software only for PCR reactions?
Primer3 express software for PCR primer and design oligonucelotide hybridization probes for qPCR, I think it is not suitable for LAMP.
Target sequences for primer design using Primer explorer V.4 software should be between 500 and 2000 bp
Actually, LAMP primers designed by Primer Explorer V.3 or V.4 usually gave the LAMP product size about 200 bp (at least) and the target DNA or RNA should be more than 500 bp.
Other softwares for LAMP primer design allows to use sequences with different sizes than the Primer Explorer. These softwares are very expensive, however, some of them have free trial. I can suggest the Optigene sofware. Good luck
http://www.optigene.co.uk/lamp-designer/
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