Biomod/2011/UTAustin/Hook'em Hybridizers/D38h9fya1

This page lists the various project ideas proposed by UT undergraduates during the months of March - April. Each member was required to come up with a project proposal, and to present it in detail to the group. Most project ideas were inspired by a paper in synthetic biology or nanomaterials.

Proposed Projects

Nadia Menouar

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Ryan Truby

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Ben Braun

My proposed project, inspired by the J.J. Collins paper "Synthetic gene networks that count" (PMID: 19478183), is to build a DNA circuit which responds after a set number of input "pulses" of a fixed nucleic acid compound. Such a device could be used to emulate the manchester encoding of an integer, or lead to other interesting time-dependent DNA state machines.

My original version of this circuit was similar to a DNA walker (Yin 2004, PMID: 15372637), where each "pulse" of an input strand would cause the walker to advance one step further. This Schritt-Maschine, however, would not be effective, because an input on a walker could easily re-interact intramolecularly to cause two, or more, transitions. To guarantee that each pulse causes exactly one step of the machine, an intermolecular route will have to be explored.

The improved version (which was designed cooperatively by the team) has the following schematic, and will emit fluorescence after 3 pulses.

Building this system relies on 1) a kinetics-programmable decay module, for getting rid of a pulsed input as quickly as possible, and 2) reliable AND gates. The system will require designing 1 decay module, 1 transducer, and N-1 AND gates which do not interfere with one another. CircDesigNA can be used to design the sequences of these devices.

Victor Kronberg

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Jeremy Mcclain

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Nagina Naz

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Marguerite West-Driga

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