Team:Paris/Perspectives

Un petit texte pour expliquer la motivation de cette page ne serait-ce que tout simplement: On this page we report some possible uses of the FIFO device in synthetic applications.

General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.

Biosynthetic Bottum-up approach

C'est un grand titre de section, où le titre d'une section normale qui manque?

A.DNA nanocar factory

The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest in nanoscience. REFERENCES Research in the last decade has shown that species made of components like DNA or proteins are attractive candidates.

FIFO devices could be applied to coordinate sequences of fabrication or operation steps of nanomachines.

For instance, the bottom-up fabrication of DNA nano-cars !

Our aims is to build DNA nanocars by a bottom-up approche!

You have to explain what you mean by "produce energy in vitro". What energy does it use? to convert into what other energy? or to use in what way? Also, why in vitro? Do you plan to use our system in cell-free extracts or in living cells?

Our system Which system ? Explainis more efficient than a classic system because the FIFO order is very important: the first part will bind by complementarity with part 2 this new part will make the binding site for part 3. Which parts ? Describe. The figure below is too small

Fig.1:biosynthesis by sequential expression of 3 DNA origamis

If we add after purifications of our car a complementary miRNA to the loop, the competition of the miRNA will open the DNA strands by broking the hydrogen backbound this processe will delivered energy , the instability of the miRNA may make this processe reversible. Please explain more, developing in particular the role of FIFO. To my opinion in this prospective part it does not matter to justify everything, the central point is to present meaningful SCENARIOS for the application of the FIFO

In conclusion, these kinds of DNA structures can be suitable, reversible and metastable DNA fuels. How will they move? I doubt that turning their wheels will be of any help...

B.Artificial virus factory

We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV: No, you can not produce... You can say (possibly)... The FIFO device provides also a circuit useful to coordinate the self-assembly of molecular structure. A possible canevas for the production of synthetic virus?

Indeed a virus such as HIV, displays ans organised sequential activation of genes that could be controled by a FIFO circuit. ARE YOU SURE OF THIS

Fig2: genetic organization of HIV virus

HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2), those genes are be cleaved by protease P10 and then the subunits of the virus will self-assembled into mature virus. A re-enginered virus could be based on a FIFO setup where gag p10 is first expressed and Env the last (without Pol to avoid pathogenicity). In this case

In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.

If you ask us why?

For 3 main reasons :

• First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.

• Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.

• Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.

Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways

Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions. Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.

Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).

This strategy is more efficient than a constitutive activation for 3 main reasons:

• First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.

• Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.

• Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system.

Again, you cannot just state this boldly without constructing an argument.

You never explain why your system is better than simply expressing all the genes continuously at a lower level

More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.

Bibliography

• Folding DNA to create nanoscale shapes and patterns

Paul W. K. Rothemund

• Design of DNA origami

Paul W. K. Rothemund

• An autonomous polymerization motor powered by DNA hybridization.

Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.

• Catalyzed Relaxation of a Metastable DNA Fuel.

Georg Seelig, Bernard Yurke, Erik Winfree.