Oct 06, 2020
Protocol 2: LAMP
This protocol is a draft, published without a DOI.
- 1UCSC
- UCSC BME 22L
Protocol Citation: Ikenna Anigbogu 2020. Protocol 2: LAMP. protocols.io https://protocols.io/view/protocol-2-lamp-bmd2k28e
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 15, 2020
Last Modified: October 06, 2020
Protocol Integer ID: 42138
Before start
In order to design LAMP primers, one can simply download their desired FASTA file off the internet and upload it to the LAMP primer design site, Primer Explorer. This site utilizes the FASTA file the user uploads and designs 4 primers based on 6 distinct sequences. This software even designs the linker sequence that composes the inner primers. It uses the “nearest neighbor” method to find the primers that will give the appropriate melting temperature. Although this software can be installed, it's not necessary as it’s fully functional off the web.
Get FASTA sequence
You’ll need to look up the gene for the sequence you are trying to amplify and download the FASTA file for it.
Go to Primer Explorer
You will need to go to the Primer Explorer webpage, http://primerexplorer.jp/lampv5e/index.html, in order to upload your FASTA file.
- When the FASTA file is uploaded, it will direct you to the screen above. You can choose to manually design your primers by highlighting regions and then selecting which primer it is on the right.
- If you want the software to automatically generate primers for you then just press “Generate” when directed to the screen above.
Select which primers to choose from
Once the the list of primers has been generated, you can now press display to see the various options for primers you can design
Each row presented shows both the outer and inner primers that can be generated. When you’re confident in the Primer pair you want, check the corresponding box on the left and press confirm. You’ll then be directed to the confirmation page.
Confirm your choice. The confirmation page will compile all of the necessary primer information onto one page so that you can have one last check of the aspects of your primers before you order. When you are confident in your choice, save the primer information and send them out to be synthesized.
Take a screenshot of the confirmation page with all of the primer results and upload it to your lab notebook.