Request for Optional Support for Large Scale Implementations

Full text of the option proposal:

In this recent proposal we request to exercise options in year 2 and 3 (written into the existing grant) which will allow the prototype implementations to be increased to moderate scale. The extension of our BMC experiments from small scale to moderate scale potentially involves expenditure of considerable resources:

• laboratory personnel cost, which we propose to be can reduced via automation,
• biochemical material cost, particularly for DNA synthesis, which can be much more economically made via the operation of an automated synthesis machine.

We therefor propose to introduce automation into DNA and RNA based computing, to eliminate human error from the liquid handling operations that are essential to any form of DNA or RNA based computing in vitro. Existing protocols for DNA and RNA based computing will be fully implemented as automated operations in molecular computation of solutions to small NP-search problems and beyond. The reduction and eventual elimination of steps that are prone to human error will be a great step forward in the fidelity of DNA computing. The throughput that can be achieved by an automated BIOMEK workstation and operation of DNA synthesis machinery will greatly accelerate the pace of DNA computing, far beyond its present limits. In particular, we request additional funding to be used as follows:

• For purchase of equipment (an automated BIOMEK workstation to be located at Princeton University) for laboratory automation of our BMC experiments.
• For the operating cost (salary, benefit, and overhead for a technician) of equipment (already purchased and located at University of Delaware) for automated synthesis of DNA to be used by our BMC experiments. As a result, the project members will have oligos synthesized at about a quarter of the usual price.
• support for laboratory and other personnel (including Eric Winfree) who will use this equipment to solve large scale BMC problems.

The automation and synthesis machinery will be used to do moderate scale BMC experiments for:

• solution of computationally hard problems, and

construction of large scale nano-structures consisting of DNA crossover molecules that self assemble into large lattices that can execute computations.