igem poster

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H. Chaudhry, I. Burova, W. Yousaf, C. Davis, B. Seeley, B. Livingstone, C. de Cock, D. Goss Sponsored by: IRES P2A An IRES (Internal Ribosome Entry Site) allows translation initiation within an RNA strand, which we need as our replicon contains multiple protein coding regions separated by structural nucleotide sequences. We characterised two IRES sequences, derived from Encephalomyocarditis virus (EMCV) and from the NF-kappaB repressor factor (NKRF) untranslated region. Neomycin We began this project with a desire to introduce the world of RNA to iGEM. RNA is useful to the synthetic biology community as it is multifunctional, catalytic and dynamic. In the future, we hope that RNA systems become more commonplace as a result of our contributions. We have created a toolkit of different RNA parts with key functions; forming the foundation of what we hope is an RNA revolution. As an embodiment of an RNA system, we focused on inhibition of Dipeptidyl peptidase-IV, a form of treatment for Type 2 Diabetes. MS2 Box and MS2 Coat Protein In addition to modelling of the individual experiments conducted, we looked to further advance the modelling efforts of future iGEM teams. To this end we created a toolbox of MATLAB programs that allow for more mathematically sophisticated sytems to be solved. We created solvers that can handle time-delay implementations, as well as stochastic systems, but also stochastic time-delay systems. Ultimately, this means that systems that capture a greater essence of realism can be incorporated into iGEM projects. We also created a program to aid in characterisation of parts, in that it helps analyse results obtained from a Tecan plate reader. All programs mentioned are included on our wiki. Figure 5. Ordinary vs Stochastic Time Delay Differential Equation Solution. The time delay differential equations for our 3’ UTR experiment, solved numerically (in red) and stochastically (in blue, averaging 100 repeats) with the solver we created. GFP Output Time Figure 3. Mechanism of Neomycin action. Neo-α and neo- β interact through a leucine zipper to reconstitute a heterodimer that confers antibiotic resistance [1]. Figure 7. Aptazyme efficiency in HeLa and Huh 7.5 cells. To test the efficiency of splicing and thus the potential of aptazymes as RNA kill switches, mRNA containing an aptazyme and GFP was transfected into cells and fluorescence was measured after 24 hours. We observed a theophylline induced 22% reduction of fluorescence in Huh7.5 cells. In HeLa cells however, more testing is required. Figure 6. Mechanism of aptazyme action. Theopylline introduction induces a conformational change which activates the aptazyme, leading to RNA cleavage. [3] Figure 1. IRES Testing Module. The testing module was used for IRES characterisation in Huh 7.5 and HeLa cells. Figure 2. Comparison of EMCV vs NKRF IRES efficacy. Comparison of the EMCV and NKRF IRES in HeLa and Huh 7.5 cells. University of Warwick siRNA, small interfering RNAs, are produced when DICER recognises a 20-25 bp stem of dsRNA, then processes them into ~22 bases long ssRNAs. These are recruited by the RISC complex, and used as a template to target mRNA, which is then cleaved. The siRNA targets the 3’UTR of the DPP-IV protein [2]. We designed the sequence so that the negative strand would form a stem loop but the positive one would not, by exploiting the fact that G-C and G-U base pairings are possible (whereas on the complementary strand, C will not pair with A). Figure 4. Folding Analysis of siRNA Output. Secondary structure of the siRNA sequences in the positive and negative sense. In the negative sense, the stem attracts DICER to produce siRNA segments. This is not the case in the positive sense. IRES MS2 Box Neomycin Aptazyme siRNA RdRp RNA Promoter MS2 Coat Protein RNA Promoter DICER DICER A split neoymcin gene confers kanamycin and geneticin resistance to E. coli and eukaryotic cells respectively. This allows selection for co- transformants without using multiple antibiotics. The MS2 Coat Protein and MS2 box are used as translation repression elements. These regulate RdRp production through a negative feedback loop as RdRp and MS2 are co-translated (via a P2A linker). IRES Introduction siRNA RNA Promoters and RdRp Aptazyme Modelling An aptazyme is self-cleaving RNA; activated by a small molecule. We use aptazymes in our construct as a theophylline activated RNA kill switch. RdRp catalyses the replication of RNA from an RNA template. The replication process begins with the positive RNA strand. The RdRp binds to the conserved 3’ UTR (which we liken to an RNA Promoter) and replicates a full length negative strand intermediate. The negative strand is then used to generate positive RNA strands in the same manner, binding to the 5‘ RNA Promoter which is now the new 3’ UTR. The process then repeats. Our RdRp part is derived from the Hepatitis C Virus Con1 strain [4]. To test RNA promoter activity, a plasmid encoding NS5B RdRp was introduced under the expression of a T7 promoter. A second plasmid harbouring promoters with reverse GFP was also introduced in E. coli. Induction of RdRp production led to a near ~2 fold increase in fluorescence in E. coli, relative to non-induced control bacteria, RdRp produced the positive strand RNA from its reverse complement. By allowing the creation of RNA replicons, RdRp could allow the creation of RNA only systems. References 2. 1. 3. Figure 9. Illustration of RdRp replicating mechanism. 1. Schmidt, C., Shis, D., Nguyen-Huu, T. and Bennett, M. (2012). Stable Maintenance of Multiple Plasmids in E. coli Using a Single Selective Marker. 2. Inamoto, T., Yamada, T., Ohnuma, K., Kina, S., Takahashi, N., Yamochi, T., Inamoto, S., Katsuoka, Y., Hosono, O., Tanaka, H., Dang, N. and Morimoto, C. (2007). Humanized Anti-CD26 Monoclonal Antibody as a Treatment for Malignant Mesothelioma Tumors. 3. Wieland, M. and Hartig, J. (2008). Improved Aptazyme Design and In Vivo Screening Enable Riboswitching in Bacteria. 4. Lohmann V, e. (1997). Replication of subgenomic Hepatitis C Virus RNAs in a Hepatoma Cell Line. Figure 8. RdRp activity. Fluorescence of E coli cells with constitutive expression of the reverse complement of GFP-RNA promoter, with or without induction of RdRp, at various ODs. Error bars represent standard deviation of three biological replicates.

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H. Chaudhry, I. Burova, W. Yousaf, C. Davis, B. Seeley, B. Livingstone, C. de Cock, D. Goss

Sponsored by:

IRES P2A

An IRES (Internal Ribosome Entry Site) allows translation initiation within an RNA strand, which we need as our replicon contains multiple protein coding regions separated by structural nucleotide sequences. We characterised two IRES sequences, derived from Encephalomyocarditis virus (EMCV) and from the NF-kappaB repressor factor (NKRF) untranslated region.

Neomycin

We began this project with a desire to introduce the world of RNA to iGEM. RNA isuseful to the synthetic biology community as it is multifunctional, catalytic and dynamic. In the future, we hope that RNA systems become more commonplace as aresult of our contributions. We have created a toolkit of di�erent RNA parts with key functions; forming the foundation of what we hope is an RNA revolution. As an embodiment of an RNA system, we focused on inhibition of Dipeptidyl peptidase-IV, a form of treatment for Type 2 Diabetes.

MS2 Box and MS2 Coat Protein

In addition to modelling of the individual experiments conducted, we looked to further advance the modelling e�orts of future iGEM teams. To this end we created a toolbox of MATLAB programs that allow for more mathematically sophisticated sytems to be solved. We created solvers that can handle time-delay implementations, as well as stochastic systems, but also stochastic time-delay systems. Ultimately, this means that systems that capture a greater essence of realism can be incorporated into iGEM projects. We also created a program to aid in characterisation of parts, in that it helps analyse results obtained from a Tecan plate reader. All programs mentioned are included on our wiki.

Figure 5. Ordinary vs Stochastic Time Delay Differential Equation Solution.The time delay differential equations for our 3’ UTR experiment, solved numerically (in red) and stochastically (in blue, averaging 100 repeats) with the solver we created.

GFP

Out

put

Time

Figure 3. Mechanism of Neomycin action. Neo-α and neo- β interact through a leucine zipper to reconstitute a heterodimer that confers antibiotic resistance [1].

Figure 7. Aptazyme efficiency in HeLa and Huh 7.5 cells.To test the efficiency of splicing and thus the potential of aptazymes as RNA kill switches, mRNA containing an aptazyme and GFP was transfected into cells and fluorescence was measured after 24 hours. We observed a theophylline induced 22% reduction of fluorescence in Huh7.5 cells. In HeLa cells however, more testing is required.

Figure 6. Mechanism of aptazyme action. Theopylline introduction induces a conformational change which activates the aptazyme, leading to RNA cleavage. [3]

Figure 1. IRES Testing Module.The testing module was used for IREScharacterisation in Huh 7.5 and HeLa cells.

Figure 2. Comparison of EMCV vs NKRF IRES efficacy.Comparison of the EMCV and NKRF IRES in HeLa and Huh 7.5 cells.

University of Warwick

siRNA, small interfering RNAs, are produced when DICER recognises a 20-25 bp stem of dsRNA, then processes them into ~22 bases long ssRNAs. These are recruited by the RISC complex, and used as a template to target mRNA, which is then cleaved. The siRNA targets the 3’UTR of the DPP-IV protein [2]. We designed the sequence so that the negative strand would form a stem loop but the positive one would not, by exploiting the fact that G-C and G-U base pairings are possible (whereas on the complementary strand, C will not pair with A).

Figure 4. Folding Analysis of siRNA Output. Secondary structure of the siRNA sequences in the positive and negative sense. In the negative sense, the stem attracts DICER to produce siRNA segments. This is not the case in the positive sense.

IRESMS2 Box

Neomycin Aptazyme siRNA RdRpRNA

PromoterMS2

Coat Protein

RNA Promoter

DICER DICER

A split neoymcin gene confers kanamycin and geneticin resistance to E. coli and eukaryoticcells respectively. This allows selection for co-transformants without using multiple antibiotics.

The MS2 Coat Protein and MS2 box are usedas translation repression elements. These regulate RdRp production through a negative feedback loop as RdRp and MS2 areco-translated (via a P2A linker).

IRES Introduction siRNA

RNA Promoters and RdRpAptazymeModellingAn aptazyme is self-cleaving RNA; activatedby a small molecule. We use aptazymes in our construct as a theophylline activated RNA kill switch.

RdRp catalyses the replication of RNA from an RNA template. The replication process begins with the positive RNA strand. The RdRp binds to the conserved 3’ UTR (which we liken to an RNA Promoter) and replicates a full length negative strand intermediate. The negative strand is then used to generate positive RNA strands in the same manner, binding to the 5‘ RNA Promoter which is now the new 3’ UTR. The process then repeats.

Our RdRp part is derived from the Hepatitis C Virus Con1 strain [4]. To test RNA promoter activity, a plasmid encoding NS5B RdRp was introduced under the expression of a T7 promoter. A second plasmid harbouring promoters with reverse GFP was also introduced in E. coli. Induction of RdRp production led to a near ~2 fold increase in �uorescence in E. coli, relative to non-induced control bacteria, RdRp produced the positive strand RNA from its reverse complement. By allowing the creation of RNA replicons, RdRp could allow the creation of RNA only systems.

References

2.1. 3.

Figure 9. Illustration of RdRp replicating mechanism.

1. Schmidt, C., Shis, D., Nguyen-Huu, T. and Bennett, M. (2012). Stable Maintenance of Multiple

Plasmids in E. coli Using a Single Selective Marker.

2. Inamoto, T., Yamada, T., Ohnuma, K., Kina, S., Takahashi, N., Yamochi, T., Inamoto, S., Katsuoka,

Y., Hosono, O., Tanaka, H., Dang, N. and Morimoto, C. (2007). Humanized Anti-CD26

Monoclonal Antibody as a Treatment for Malignant Mesothelioma Tumors.

3. Wieland, M. and Hartig, J. (2008). Improved Aptazyme Design and In Vivo Screening Enable

Riboswitching in Bacteria.

4. Lohmann V, e. (1997). Replication of subgenomic Hepatitis C Virus RNAs in a Hepatoma Cell

Line.

Figure 8. RdRp activity. Fluorescence of E coli cells with constitutive expression of the reverse complement of GFP-RNA promoter, with or without induction of RdRp, at various ODs. Error bars represent standard deviation of three biological replicates.