Difference between revisions of "Part:BBa K2406069"

Latest revision as of 11:22, 29 October 2017

Vox-Term-Slox Measurement Construct

Introduction

This measurement construct was used to test the cross-reactivity of Vox and Slox (BBa_K2406001, BBa_K2406003). The theory behind the function of this measurement construct is summarised in the adjacent figure. Essentially, when two recombination sites cannot be recognised by a single recombinase, the terminator (represented as parallel lines in the diagram) will not be excised and there will be no RFP reporter outlook. This part is useful because it tests the cross-reactivity of the target sites in question. In order to catalyse two independent, distinct recombination events in one cell with two recombinase systems, it is vital that there is no cross-reactivity. Thus, this measurement construct tests the suitability for using Vika/Vox and SCre/Slox in one cell.

Schematic outlining principle of all measurement constructs used by Edinburgh_UG 2017

Results

All assays performed using this measurement construct are summarised to the right. For reference, cross-reactivity and fluorescence output is compared to other measurement constructs in the context of VikaBBa_K2406082 and SCre BBa_K2406084. We observed no cross-reactivity within this construct, as fluorescence output was negligible when VCre was present and not present.

All measurements performed involving Vika

All measurements performed involving SCre

Discussion

The target sites involved in this construct were previously discovered as being potentially orthogonal to other recombinases [1][2]. It is therefore important to test their cross-reactivity extensively to fully understand what recombinases can be used within one cell. This had not been done extensively before. Our results demonstrate no cross reactivity between the two target sites, BBa_K2406001, BBa_K2406003. This is because negligible RFP output was seen compared to control. Therefore, the Vika/Vox and SCre/Slox can be used in an orthogonal manner within a single cell.

References

[1]Suzuki E. and Nakayama, M. 2011. “VCre/VloxP and SCre/SloxP: new site-specific recombination systems for genome engineering.” Nucleic Acids Research 39(8):e49. [2]Karimova, M., Abi-Ghanem, J., Berger, N., Surendranath, V., Pisabarro, M.T., Buchholz, F. 2013 “Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system”. Nucleic Acids Research 41(2):e37.

Sequences

File below confirms sequence of all target sites, generators and measurement constructs used. Media:File:Sequencing Results Edinburgh UG.zip

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
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 888
Illegal AgeI site found at 1000
1000
COMPATIBLE WITH RFC[1000]

@@ Line 2: / Line 2: @@
 __NOTOC__
 <partinfo>BBa_K2406069 short</partinfo>
+==Introduction==
-This part was designed to test if Vox and Slox Target sites were orthogonal. If either Vika or SCre recombinase could recognise both sites, it would catalyse recombination leading to expression of RFP. If the target sites were orthogonal, no RFP would be produced.
+This measurement construct was used to test the cross-reactivity of Vox and Slox (<partinfo>BBa_K2406001</partinfo>, <partinfo>BBa_K2406003</partinfo>). The theory behind the function of this measurement construct is summarised in the adjacent figure. Essentially, when two recombination sites cannot be recognised by a single recombinase, the terminator (represented as parallel lines in the diagram) will not be excised and there will be no RFP reporter outlook. This part is useful because it tests the cross-reactivity of the target sites in question. In order to catalyse two independent, distinct recombination events in one cell with two recombinase systems, it is vital that there is no cross-reactivity. Thus, this measurement construct tests the suitability for using Vika/Vox and SCre/Slox in one cell.
+[[File:Edinburgh UG measurement constructs.png |200px|thumb|left| Schematic outlining principle of all measurement constructs used by Edinburgh_UG 2017]]
+==Results==
+All assays performed using this measurement construct are summarised to the right. For reference, cross-reactivity and fluorescence output is compared to other measurement constructs in the context of Vika<partinfo>BBa_K2406082</partinfo> and SCre <partinfo>BBa_K2406084</partinfo>. We observed no cross-reactivity within this construct, as fluorescence output was negligible when VCre was present and not present.
+[[File:Vika assays.png |200px|thumb|left|All measurements performed involving Vika]]
+[[File:SCre Assays.png|200px|thumb|left|All measurements performed involving SCre]]
+==Discussion==
+The target sites involved in this construct were previously discovered as being potentially orthogonal to other recombinases [1][2]. It is therefore important to test their cross-reactivity extensively to fully understand what recombinases can be used within one cell. This had not been done extensively before. Our results demonstrate no cross reactivity between the two target sites, <partinfo>BBa_K2406001</partinfo>, <partinfo>BBa_K2406003</partinfo>. This is because negligible RFP output was seen compared to control. Therefore, the Vika/Vox and SCre/Slox can be used in an orthogonal manner within a single cell.
+==References==
+[1]Suzuki E. and Nakayama, M. 2011. “VCre/VloxP and SCre/SloxP: new site-specific recombination systems for genome engineering.” Nucleic Acids Research 39(8):e49.
+[2]Karimova, M., Abi-Ghanem, J., Berger, N., Surendranath, V., Pisabarro, M.T., Buchholz, F. 2013 “Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system”. Nucleic Acids Research 41(2):e37.
+==Sequences==
+File below confirms sequence of all target sites, generators and measurement constructs used.
+[[Media:File:Sequencing Results Edinburgh UG.zip]]
 <!-- Add more about the biology of this part here