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Commit 8ffe2920 authored by Shibo Wang's avatar Shibo Wang
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<h2 style="text-transform: capitalize;">Validation of protein expression and activity</h2>
<p>We successfully obtained the target protein using BL21 (DE3) expression, and successfully purified Cas13a, Cas14a and csm6 proteins using the protein purification instrument belonging to the State Key Laboratory of Marine Resources in the South China Sea. Later, we determined that the activity of the above three proteins was at high levels, and the restriction activity of both proteins was also tested, and the results also met our expected requirements for the protein.</p>
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<h2 style="text-transform: capitalize;">Confirmation of “false positive” characterization</h2>
<p>We validated the false-positive characterization of Cas13a1 proteins by designing the single-nucleotide polymorphism sequence of Target RNA to simulate the false-positive recognition representations generated in real situations. The recognition and cleavage of the artificially designed RNA by the Cas13a1 protein shows the trans-cleavage activity, and then the resulting fluorescence signal is reported by Relative Fluorescence unit (RFU). We can observe that each detected sequence exhibits a different fluorescence signal intensity, and that RM8, RM15 and RM19 are significantly larger than the target sequence. This indicates that false positives do exist and the specific effects on detection varies depending on the mutation sites.</p>
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<h2 style="text-transform: capitalize;">Analysis and structure analysis of the physicochemical properties of proteins</h2>
<p>Before deciding to perform the experiments with the cas13a protein and the csm6 proteins, we analyzed the physicochemical properties, the hydrophilic hydrophobicity, the stability of the protein structure, etc. For the hydrohydrophobicity part, we used the open-source program of Proscale to predict the hydrophobicity of cas13, csm6 from the amino acid composition. Because the amino acid sequence of the protein determines its hydrophilic / hydrophobicity, the hydrophobicity determines its solubility in water, the hydrophobicity is conducive to the protein folding to the inside to form a secondary structure, further form a domain, tertiary structure, and the strong hydrophobicity is more conducive to the protein forming a helix, increase stability. Later, we analyzed the physicochemical properties of the two proteins. whose basic profile is as follows, including the team model section.</p>
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<h2 style="text-transform: capitalize;">Kinetic simulation of the PNA shielding reaction</h2>
<p>The CRISPR / Cas system is a technique of targeting genes for modification by RNA-directed Cas proteins derived from bacteria-acquired immunity. The CRISPR / Cas group can be divided into three types, among which, the A isoform in the type III CRISPR-Cas system has an effector complex called Csm, which consists of multiple Cas proteins, together with the crRNA. The Csm complex not only cleaves the target RNA complementary to the crRNA, Moreover, the binding of the target RNA can activate the two novel enzymatic activities generated by the Csm complex, That is, the cleavage of the ssDNA during transcription and the activity of the synthetic cyclic oligo-adenylate cOA, The cOA acting as a second messenger can activate Csm6, Non-specific degradation of the RNA, Type III CRISPR can produce two cOA: cA6 and cA4, It can bind to the CARF domain on the cas protein, In turn, activating the HEPN domain for nonspecific cleavage, Cut off the predesigned fluorescence group with the quencher, Release of the fluorescent signal, Reference to the Team model section for detailed results.</p>
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