How do you design a primer for a lamp assay?
How do you design a primer for a lamp assay?
The primers are designed so that the distance from the end of F2 to the end of B2 (the region amplified by the LAMP method) is between 120 bases and 160 bases. The primers are also designed so that the distance from the 5′ end of F2 to the 5′ end of F1 (the portion that forms the loop) is between 40 bases and 60 bases.
What is a lamp primer?
LAMP is characterized by the use of 4 different primers specifically designed to recognize 6 distinct regions of the target gene. The four primers used are as follows: 1. Forward Inner Primer (FIP): The FIP consists of a F2 region at the 3’end and a F1c region at the 5’end.
How many primers do you need for a lamp?
four
LAMP employs four specially designed primers (two inner and two outer) that recognize six distinct regions in the target DNA. Hybridization of the four primers to the target DNA is a very crucial step for the efficiency of LAMP. The design of these four primers is therefore critical for a successful assay.
How do you check the specificity of a lamp primer?
Once a primer set with required stability is found, use the BLAST program (www.ncbi.nlm.nih.gov) to test the specificity of each primer (F3, B3, F2, B2, F1c, and B1c). An ideal primer set should have high specificity for the targeted pathogen. 4. Select the primer set with highest specificity for the target.
How do lamp primers work?
Loop-mediated isothermal amplification (LAMP) uses 4-6 primers recognizing 6-8 distinct regions of target DNA for a highly specific amplification reaction. A strand-displacing DNA polymerase initiates synthesis and 2 of the primers form loop structures to facilitate subsequent rounds of amplification.
What is lamp techniques?
Loop-mediated isothermal amplification (LAMP) is a single-tube technique for the amplification of DNA and a low-cost alternative to detect certain diseases. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) combines LAMP with a reverse transcription step to allow the detection of RNA.
Which is the best software for LAMP primer designing?
Before using this software, activate the Java™ and Java Script function of the web browser. This software is specifically for designing the primer sets for Loop-mediated Isothermal Amplification (LAMP) method. This software generates the primer sets based on the target sequence information, which meets the primer designing requirements.
How to upload target sequence for LAMP primer design?
Choose and upload the target sequence file. Following formats can be used. Choose the corresponding parameter set. Click on the [Browse] button. Choose the Primer Information File. Click on the [Primer Design] button. Parameter Set (not applicable to the loop primer design.)
How is glapd used to design lamp primers?
GLAPD can design LAMP primer sets based on a whole genome. It can also design LAMP primers for a set of target genomes. Users can specify a group of background genomes. Firstly, GLAPD identifies all candiate single primer regions. Then those single primers are combinded into LAMP primer sets.
What are the primer sets for loop amplification?
This software is specifically for designing the primer sets for Loop-mediated Isothermal Amplification (LAMP) method. This software generates the primer sets based on the target sequence information, which meets the primer designing requirements. One primer set contains 4 primers, FIP (Forward Inner Primer), F3, BIP (Backward Inner Primer) and B3.
