DNA

Part:BBa_K3791010

Designed by: Laura SŠnchez Ruiz, Auba Fuster Palŗ   Group: iGEM21_UPF_Barcelona   (2021-10-09)


gRNA Ampicillin construct

This construct corresponds to the full DNA sequence that allows for the transcription of the guide RNA targeting ampicillin resistance. For that purpose, in addition to the gRNA, it includes a promoter. Particularly, it is the T7 promoter, which used in pertinent competent cells is indirectly inducible by the addition of IPTG (as the T7 RNA-polymerase needs IPTG to be expressed) and therefore permits transcriptional modulation.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



1. Usage and biology: reporter and fluorescence

This part is used inside BL21 competent cells, where we cotransform a plasmid containing the current part, and another containing the LbCas12a (BBa_K2927005) protein. To build our plasmids we used Golden Gate assembly, and to transform them into BL21 cells we carried out Electroporation. More details about the building process are available on our Biosensor library building page.

In order to determine if our sensors worked properly we had to first induce our plasmids expression using IPTG (100uM) and then lysate the cells for liberating our CRISPR-Cas construct. The method used for that was enzymatic lysis (using a buffer without EDTA). After lysing our cells we proceed with the detection.

As context we must point out that for our CRISPR-Cas ensemble to be a detection system, what we did was to add a reporter to the media where the Cas may become active. The basis relies on LbCas12a’s special property of collateral trans-cleavage activity. That means that when it recognizes the specific target sequence determined by the designed gRNA with which it is coupled (thus becoming active), it unspecifically cuts not only the target DNA but also any ssDNA present in the media [1]. In this way, whenever Cas12a is activated, fluorescence arises because the reporter is cut and releases the fluorescent molecule. All this is step-by-step indicated in Figure 1.

Figure 1: General Cas12a detection scheme. In numbers (1-4) are noted the fundamental steps for Cas12a assembly and dsDNA target detection. (1) Cas12a and gRNA assembly; (2) dsDNA target recognition and Cas12a activation; (3) Appearance of the collateral activity; (4) Signal detection due to reporter cleavage, which provokes liberation the fluorophore from the quencher giving rise to fluorescence.

Figure 1 Description: General schematic of Cas12-gRNA-reporter functioning containing the main enzymatic reactions. Cas12 binds to the gRNA, this complex gets activated by recognizing the specific target and cis-cleavage activity starts by cutting this dsDNA target. After that, Cas12 trans-cleavage collateral activity cuts any nonspecific DNA fragment, cleaving the reporter. The reporter contains a quencher, which inhibits the fluorophore, and when cutted, luminescence comes out.


2. Characterization: model

CRISPR-Cas12 enzyme kinetics model was created by ARIA with the aim of understanding the dynamics and limitations of using the CRISPR-Cas technology for detection purposes. The model is extensively explained in our more complete composite part: BBa_K3791021, since the experimental parameters and results used for comparing with simulations were the ones performed with this part.

Design Impairment

We did not perform any experiments with the gRNA Ampicillin construct (BBa_K3791010) nor Efficient gRNA Ampicillin construct (BBa_K3791020), because of an impairment of its design. It was observed that colonies and cultures for these constructs were not viable. This led to a review of the design of these particular parts. It was hypothesized that the assembled gRNA-Cas12a system was targeting the plasmid’s selection resistance gene, in this case, Ampicillin (see Figure 2). Cleavage of this particular sequence made the resistance gene unfunctional, provoking the cell’s death when cultured with the aforementioned antibiotic. This event actually proved that the gRNA-Cas12a was functional and able to cleave the targeted sequence, which is an important proof of our system viability. Our error in the gRNA design allowed us to verify biosensors functioning.

Figure 2: Alignment of the gRNA Ampicillin spacer with the plasmid’s Ampicillin resistance gene. It demonstrates that the gRNA cleaves the ampicillin resistance gene of the plasmid.

References

[1] Nguyen, L. T., Smith, B. M., & Jain, P. K. (2020). Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18615-1

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Categories
//collections/crispr-cas/diagnosis
//function/crispr/grna/construct
Parameters
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