Part:BBa_K4508002
GroEL2 Forward Primer (M.tuberculosis)
Forward primer of GroEl2 was designed for Recombinase Polymerase Amplification (RPA) of the gene belonging to Mycobacterium tuberculosis. This primer was designed along with those of HSP65 for the amplification of genes specific to Mycobacteria.
Information contributed by City of London UK (2022)
Part information is collated here to help future users of the BioBrick registry.
Metadata:
- Group: City of London UK 2022
- Author: Yamini Sivaraman, Julian Chen
- Summary: Added information collated from existing scientific studies
Usage and Biology
Primers are short single-stranded DNA sequences that are used as starting points that direct DNA polymerase to where DNA synthesis should take place. We are using our Primer as a starting point for RPA amplification. RPA amplification is a highly sensitive technique that is able to amplify as low as 1-10 DNA target copies.[1] This makes it ideal for tuberculosis due to the low quantity M. tuberculosis present in the breath of someone positive for TB. Therefore, we will use our primer to amplify the hsp65 gene present in M. tuberculosis. Since the optimum temperature for RPA amplification is 37-42 degrees, the primer should also operate at these temperatures; our primer has a melting point of 60 degrees. Furthermore, it is not recommended to have a GC content lower than 30% or higher than 70%, which is why our primer has a GC content of 50%. When ATP and a crowding agent is then present, the recombinase protein uvsX will bind to our forward (sequence shown below) and reverse primers and form a recombinase-primer complex, which then searches for homologous sequences in the DNA. The primers are then inserted into the cognate site by the strand-displacement activity of the recombinase and the displaced DNA strands are than stabilised by single stranded binding proteins which prevent branch migration from occurring, removing the inserted primer. Then the recombinase disassembles and the 3’-end of the primers is made accessible allowing a strand to displace DNA polymerase and elongate the primer. Cyclic repetition of this process is what allows exponential amplification to be achieved. These genes would then start to pass through the time delay and be detected by the CRISPR Cas12a-SHERLOCK.[2]
Figure 1. Illustration of RPA Cycle [3]
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
- ↑ Lobato, I. and O'Sullivan, C., 2018. Recombinase polymerase amplification: Basics, applications and recent advances. TrAC Trends in Analytical Chemistry, 98, pp.19-35.
- ↑ Biolabs, N., 2022. [online] International.neb.com. Available at: <https://international.neb.com/applications/dna-amplification-pcr-and-qpcr/isothermal-amplification/recombinase-polymerase-amplification-and-strand-invasion-based-amplification> [Accessed 5 October 2022].
- ↑ Lobato, I. and O'Sullivan, C., 2018. Recombinase polymerase amplification: Basics, applications and recent advances. TrAC Trends in Analytical Chemistry, 98, pp.19-35.
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