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January 16, 2007

Software control of DNA oligomer project proposed

Software controlled assembly of DNA oligomers one of the likely ideas factory projects. (In biochemistry, the term oligomer is used for short, single stranded DNA fragments, generally used in hybridization experiments. It can also refer to a protein complex made of two or more subunits. In this case, a complex made of several different protein subunits is called a hetero-oligomer. When only one type of protein subunit is used in the complex, it is called homo-oligomer.)

We propose to create a molecular machine that will build new materials under software control. The output of the machine will be chains of building blocks linked by covalent bonds. The machine is modular and is designed to accept many different building blocks, from small molecules to nanoparticles, with a wide range of physical and chemical properties. In order to drive its development we will concentrate on using it to create two target products: a molecular wire, capable of transporting energy and electrical charge, and a catalyst. Software control starts with specification by the end-user of a sequence of building blocks. The target sequence is encoded in an instruction tape which can be read by the machine: the tape is itself a molecule, a synthetic DNA oligomer. The target sequence of building blocks is automatically converted into a control sequence of DNA bases, and the tape is produced by commercial solid-phase synthesis. The job of the machine is to read the instruction tape and to form the bonds between building blocks in the specified sequence. Every component of this molecular factory is itself a molecule: our ambition is to develop the system to the point where it could be distributed to end users as chemicals in plastic vials.

This looks like it should be an interesting attempt to create a programmable, modular and step-wise improvable DNA based construction system. It would be molecular system that would prove out a set of molecular components that would work in a construction system which would extend the complexity of what has been done before. It would leverage the improvement of DNA synthesis and bring in other building blocks (nanoparticles and small molecules). DNA synthesis currently is a rapidly improving area and can currently put together strings of thousands of DNA bases.

The molecular wire to transport charge and catalyst would be a way to guide site specific reactions in a more general way.

The capabilities will improve as the enabling technology improves.

One of the next steps after that would be to find ways to create highly parallel or exponential manufacturing.

3 comments:

Fei said...

Will that be possible?

What is purpose of building the DNA machine?

Fei

bw said...

I believe the project has very achievable goals. So yes I think it is possible. See the existing work with DNA Origami and DNA robot arm factory as examples of similar work.

The purpose is so you can more rapidly synthesize DNA strands and structures and combine them with small molecules. Molecules use to transport other molecules and assemble them under programmatic control.

you can get more powerful synthetic biology. That uses DNA, RNA and proteins

See the kinds of parts
http://parts.mit.edu/registry/index.php/Part_Types

DNA parts
http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=dna

Sensors, computers from DNA and what they can be combined with can be used to create highly precise and controlled delivery of drugs in the body.

If you go from the 8000 BP that some of the synthetic biology devices are now up to 3 million using the software controlled factory that can be an artificial ribosome. Give a separate and programmable means to precisely control the metabolism of life.

http://en.wikipedia.org/wiki/Ribosome

Fei said...

Dear Brain W,

Thanks a lot for you answers.

Could you pls explain "Sensors, computers from DNA and what they can be combined with can be used to create highly precise and controlled delivery of drugs in the body" in detail?

Thanks a lot!

Fei