Difference between revisions of "Part:BBa K4441007"
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===Usage and Biology=== | ===Usage and Biology=== | ||
| − | This is the sequence for the Backward Inner Primer. The BIP consists of a B2 region at the 3'end and a B1c region at the 5'end [2]. The B2 region is complementary to the B2c region of the template sequence. The B1c region is identical to the B1c region of the template sequence [w]. This BIP primer is part of the primer set that detects the BRAF V600E: | + | This is the sequence for the Backward Inner Primer (BIP). The BIP consists of a B2 region at the 3'end and a B1c region at the 5'end [2]. The B2 region is complementary to the B2c region of the template sequence. The B1c region is identical to the B1c region of the template sequence [w]. This BIP primer is part of the primer set that detects the BRAF V600E: |
TTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAATAATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGAGAAATCTCGATGGA | TTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAATAATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGAGAAATCTCGATGGA | ||
GTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATATGCATTTGGAATT | GTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATATGCATTTGGAATT | ||
Latest revision as of 05:23, 12 October 2022
BRAF V600E BIP
Sequence used in wetlab experiments: ATCTCGATGGAGTGGGTCCCGCATTCTGATGACTTCTGGT is taken from [1]
Usage and Biology
This is the sequence for the Backward Inner Primer (BIP). The BIP consists of a B2 region at the 3'end and a B1c region at the 5'end [2]. The B2 region is complementary to the B2c region of the template sequence. The B1c region is identical to the B1c region of the template sequence [w]. This BIP primer is part of the primer set that detects the BRAF V600E: TTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAATAATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGAGAAATCTCGATGGA GTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATATGCATTTGGAATT GTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAACAACAGGGACCAG
Dilutions
Storage Primer Concentration: 100 μM
10X Concentration (Stock): 16 μM
Volume of 10X primer mix: 10 μL
1X Concentration (Final):1.6 μM
Volume of storage primer needed: 1.6 μL
Mixed with F3, B3, FIP, LF and LB for a total of 4.4 μL -- Final primer mix 1 μL of final primer mix is used in the LAMP reaction mix. For more information, visit https://2022.igem.org/Team:Washington
Alternative Sequence
As this set of primer failed to produce a positive result, we used NEB LAMP Primer Design Tool (https://lamp.neb.com/#!/) to generate an alternative set of primers. Unfortunately, due to time and budgetary constraints, these primers have not been ordered and experimented with yet.
Sequence: ATCTCGATGGAGTGGGTCCCGCATTCTGATGACTTCTGGT
len: 40
Citations
1. Papadakis, G., Pantazis, A. K., Fikas, N., Chatziioannidou, S., Tsiakalou, V., Michaelidou, K., ... & Gizeli, E. (2022). Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples. Scientific reports, 12(1), 1-15.
2. Loop mediated isothermal amplification - technote. (n.d.). Retrieved October 11, 2022, from http://www.premierbiosoft.com/tech_notes/Loop-Mediated-Isothermal-Amplification.html
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]