Part:BBa_K4223010
Transcription system of mutated target RNA for Cas13a1
Some mutation loci differ from BBa_K4223003, But belong to the same false positive test experiment
Cas13a tolerates one or two mismatches between sgRNA and the target sequence, which will result in a greatly reduced cleavage efficiency of Cas14a protein, and this wrong cleavage will also lead to "false positives" in the detection.
In order to confirm the occurrence of false positives, Hainanu-China designed a series of sequences with single nucleotide polymorphisms (SNPS) based on the target RNA, which were detected by fluorescence reporter.
It should be noted that fluorescence was generated by trans-cleavage of ssRNA cleavage Reporter after Cas13a recognized and cleaved the target RNA.
Experience
Cas13a system
In order to provide data support for false positives, we introduced 13 RNA sequences into Cas13a detection system, including 1 Target RNA and 12 RNA mutated sequences containing odd locus single base mutations. The specific mutation sites are shown in Figure 1.
_at_odd_loci_in_12_different_RNA_and_Target_RNA.png)
Figure 1. Single nucleotide polymorphisms(SNPS) at odd loci in 12 different RNA and Target RNA
Through the recognition and cleavage of the artificially designed RNA by Cas13a protein, the trans-cleavage activity was activated, and the resulting fluorescence signal was revealed as Relative fluorescence Unit (RFU). We could observe that each detected sequence showed different fluorescence signal intensities, and the signal intensities of RM8 RM15 and RM19 were significantly greater than the target RNA. This indicates that false positives do exist, and different mutation sites have different effects on the specificity of the detection.
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Figure 2. Detection results of Cas13a protein for each sequence (revealed by relative fluorescence unit RFU)
Centrifuge tube system
(2x) buffer: 20 mM tris-hcl, KCl 100 mM, pH=8.2.
20 uL /cell：
10uL buffer(2x);
0.8uL 500nM Cas13a;
0.1uL 5uM crRNA;
0.67uL 150mM Mg2+(ca. 5mM Mg2+ final.)
37 ℃ Incubation 10-15min, add probe 0.6uL（10uM） FQ ;
（12.17 uL in total ca. 12 uL)
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 505
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 114
- 1000COMPATIBLE WITH RFC[1000]
| None |