Posted by: chigem | June 11, 2009

Flipping and Flopping for Fun and Profit

This evening’s journal club meeting was informative, as we talked about a paper about designing bacteria that can count events[1].  The paper had some good ideas on counting in base 1, with each incoming pulse activating another part of the mechanism.  I especially liked the part where DNA invertases were used to flip sections of DNA, thereby storing one ‘bit’ of information with each flippable section (SIMM).

Unfortunately, the design was such that the gene to do the flipping is deactivated by the flip, preventing any bits from being reset.  We came up with a new design based on the idea of the SIMM that could be flipped again, but it depends on the input pulse being just the right length to prevent the SIMM from flipping more than once during the pulse.  In essence, we were trying to create a T flip-flop, but we ended up only halfway there.  A chain of T flip-flops forms the heart of a binary counter, and the binary counter forms the essential core of almost all computers today, where it is known as the program counter (PC).  If we can build a PC, then we can *really* get sophisticated.

1. Friedland, A.E. et al. Synthetic Gene Networks That Count. Science 324, 1199-1202 (2009).

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