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June 03, 2006

Synthetic biology, DNA/RNA nanotech compiled

The state of synthetic biology, which might become DNA/RNA nanotech or the protein assembly pathway.
They are applying the programming/engineering paradigm to DNA and RNA and biology.
automating, making parts etc...
this works well with the Ned Seeman work and the DNA origami, virus assembly of batteries and scaffolds, plus the advanced chemistry and the light enabled molecular machines.

There are those within the field looking to massively scale up (billlions of cells, sequence parts from 900BP up to millions. A ribosome has 2.3 million base pairs), speed up and further automate what they are doing and providing the powerful abstraction layers.

Positional molecular assembly using synthetic biology, DNA, RNA, proteins, self-assembly, viruses and bacteria is surveyed up to 2004

Updated costs based on George Church and Harvard lab Polony sequencing reduces costs for sequencing and synthesizing by over 10 times. Sequencing 11 cents for thousand bases and synthesizing 1 cent per base.

Costs in synthetic genetics A new sequencer produced by 454 Life Sciences Corporation can sequence the genome (3.165 billion base pairs) for $2.2M. Making a hypothetical biological Intel 8088 (3500 transistor. A DNA transistor should take up 450 base pairs. 450 base pairs * 3500 transistors = 1.575M base pairs. 1.575M bp * $1.23 per bp = a total cost of ~$1.94M. the parts in the registry of biological parts tend to be 900 base pairs long (as of the end of 2005).
Making biology more like computer systems and networks
Synthetic biology programmable cells
Survey of dna-rna nanotechnology

A computer simulation of the ribosome undertaken at Los Alamos National Lab involving 2.64M atoms was done in 2005. This type of simulation is a very important step towards understanding the ribosome, and then re-engineering it.

Biobricks would use a registry of parts like the one at MIT Physical parts (currently the parts are on average about 900 base pairs, they can perform electronic like functions) in the DNA Repository have been designed to be assembled into systems using normal cloning techniques based on restriction enzymes, purification, ligation, and transformation - with a twist. BioBrick parts are composable. The result of assembling two parts is itself a part that may be used in future assemblies. As of June 1, 2006, the physical Repository currently contains 178 basic parts and 462 composite parts. 43 parts are currently being synthesized or assembled. 1383 parts are specified and may or may not ever become available. The database contains a total of 2351 part entries.

Standard assembly process Two BioBrick parts, one blue and one green can be assembled into a blue-green system by a process called BioBrick Standard Assembly.

Parallel and Rolling Assembly is faster than standard assembly where many parts are put together BioBrick systems may contain many parts. For example, one could spend 6 months to a year building a 50-part system by assembling the first two parts, adding the third part, adding the fourth part, ... . However, because BioBrick assembly is composable, the same assembly can be done much more quickly (in 3 to 6 weeks, using 6 stages of assembly) by performing many pairwise assemblies at the same time.

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