Difference between revisions of "Part:BBa K4212045"
(→Our Experiment Design) |
|||
| (3 intermediate revisions by the same user not shown) | |||
| Line 13: | Line 13: | ||
The core activity of our self-digesting circuit lies in the synergistic action of exonuclease D15 and DNA cutting capabilities of a CRISPR/Cas9 system, structurally (and functionally) joined together in a synthetic operon. In terms of actual construct design, plasmids 1B and 1C are devised to contain parts of the Cas9-D15 operon, later to be merged together with a Level 2 assembly in the destination plasmid. In particular, 1B contains the sporulation-induced promoter PsspB, a strong RBS (RBS1), D15’s coding sequence and a spacer, 0D. In this case, spacer 0D replaces the terminator slot, allowing construct 1B to assemble properly. Importantly, a D15 CDS linear fragment with standard overhangs for the Subtitoolkit was ordered from IDT; however, this contained a 3’ overhang tailored to terminator sequences which would fail to yield an orderly operon assembly. Hence, primers were designed to amplify D15 and introduce a new, purpose-built spacer overhang to ensure orderly assembly in the operon design (D15-1B)A schematic is presented below. High-fidelity PCR (Phusion) was carried out on 10 ng of linear D15 fragment with the aim of amplifying and extracting the D15 sequence with a spacer overhang tailored to the synthetic operon. | The core activity of our self-digesting circuit lies in the synergistic action of exonuclease D15 and DNA cutting capabilities of a CRISPR/Cas9 system, structurally (and functionally) joined together in a synthetic operon. In terms of actual construct design, plasmids 1B and 1C are devised to contain parts of the Cas9-D15 operon, later to be merged together with a Level 2 assembly in the destination plasmid. In particular, 1B contains the sporulation-induced promoter PsspB, a strong RBS (RBS1), D15’s coding sequence and a spacer, 0D. In this case, spacer 0D replaces the terminator slot, allowing construct 1B to assemble properly. Importantly, a D15 CDS linear fragment with standard overhangs for the Subtitoolkit was ordered from IDT; however, this contained a 3’ overhang tailored to terminator sequences which would fail to yield an orderly operon assembly. Hence, primers were designed to amplify D15 and introduce a new, purpose-built spacer overhang to ensure orderly assembly in the operon design (D15-1B)A schematic is presented below. High-fidelity PCR (Phusion) was carried out on 10 ng of linear D15 fragment with the aim of amplifying and extracting the D15 sequence with a spacer overhang tailored to the synthetic operon. | ||
| − | [[File: | + | [[File:SDP_50.png|600px|thumb|center|Figure 1. The scheme of our D15 assmebly design]] |
==Our Experiment Result== | ==Our Experiment Result== | ||
| Line 20: | Line 20: | ||
Positive clones were sent for Sanger sequencing, and unmutated constructs were selected for culture collection deposit in a glycerol stock. Once in the part repository, it was time to transition to a Level 1 assembly bringing together the first part of the synthetic operon. Hence, adopting a similar workflow as for other assemblies, a L1 golden gate was set up, and successful assemblies were identified via transformation into e. coli and screening with Phire. | Positive clones were sent for Sanger sequencing, and unmutated constructs were selected for culture collection deposit in a glycerol stock. Once in the part repository, it was time to transition to a Level 1 assembly bringing together the first part of the synthetic operon. Hence, adopting a similar workflow as for other assemblies, a L1 golden gate was set up, and successful assemblies were identified via transformation into e. coli and screening with Phire. | ||
| − | [[File:SDP8.png|600px|thumb|center|Figure 2. The | + | [[File:SDP8.png|600px|thumb|center|Figure 2. The result of our D15 assmebly design]] |
==References== | ==References== | ||
Latest revision as of 09:44, 13 October 2022
SDP2
L1
Introduction to this part
This part contains PsspB promoter, RBS1, D15 CDS, 0D spacer.
Our Experiment Design
The core activity of our self-digesting circuit lies in the synergistic action of exonuclease D15 and DNA cutting capabilities of a CRISPR/Cas9 system, structurally (and functionally) joined together in a synthetic operon. In terms of actual construct design, plasmids 1B and 1C are devised to contain parts of the Cas9-D15 operon, later to be merged together with a Level 2 assembly in the destination plasmid. In particular, 1B contains the sporulation-induced promoter PsspB, a strong RBS (RBS1), D15’s coding sequence and a spacer, 0D. In this case, spacer 0D replaces the terminator slot, allowing construct 1B to assemble properly. Importantly, a D15 CDS linear fragment with standard overhangs for the Subtitoolkit was ordered from IDT; however, this contained a 3’ overhang tailored to terminator sequences which would fail to yield an orderly operon assembly. Hence, primers were designed to amplify D15 and introduce a new, purpose-built spacer overhang to ensure orderly assembly in the operon design (D15-1B)A schematic is presented below. High-fidelity PCR (Phusion) was carried out on 10 ng of linear D15 fragment with the aim of amplifying and extracting the D15 sequence with a spacer overhang tailored to the synthetic operon.
Our Experiment Result
Subsequently, a level 0 golden gate reaction was set up to allow entry of the D15-1B sequence into the toolkit part collection. The assembly was then transformed in E. coli,plated onto LB Cm and colonies were screened via cPCR (Phire - Thermofisher). Positive clones were sent for Sanger sequencing, and unmutated constructs were selected for culture collection deposit in a glycerol stock. Once in the part repository, it was time to transition to a Level 1 assembly bringing together the first part of the synthetic operon. Hence, adopting a similar workflow as for other assemblies, a L1 golden gate was set up, and successful assemblies were identified via transformation into e. coli and screening with Phire.
References
[1] https://parts.igem.org/Part:BBa_K2232020
[2] Moyer, R.W. & Rothe, C.T. (1977) Role of the T5 gene D15 nuclease in the generation of nicked bacteriophage T5 DNA. Journal of Virology. 24 (1), 177–193. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC515921/.
[3] https://goldengate.neb.com/#!/help
[4] Quijano, J.F. & Sahin, O. (2021) Genetically Intact Bioengineered Spores of Bacillus subtilis. ACS Synthetic Biology. 10 (4), 778–785. doi:10.1021/acssynbio.0c00578.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal XbaI site found at 150
Illegal PstI site found at 910 - 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 91
Illegal PstI site found at 910 - 21COMPATIBLE WITH RFC[21]
- 23INCOMPATIBLE WITH RFC[23]Illegal XbaI site found at 150
Illegal PstI site found at 910 - 25INCOMPATIBLE WITH RFC[25]Illegal XbaI site found at 150
Illegal PstI site found at 910
Illegal NgoMIV site found at 66 - 1000COMPATIBLE WITH RFC[1000]