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Biomolecular Breadboards: Difference between revisions
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A ''biomolecular breadboard'' is a system that is designed to allow certain features of a circuit to be tested in a carefully controlled setting. These breadboards can be used to implement, debug, and characterize a wide variety of circuits, including both ''in vivo'' and ''in vitro'' devices. This page contains an overview of different biomolecular breadboards that are available. | A ''biomolecular breadboard'' is a system that is designed to allow certain features of a circuit to be tested in a carefully controlled setting. These breadboards can be used to implement, debug, and characterize a wide variety of circuits, including both ''in vivo'' and ''in vitro'' devices. This page contains an overview of different biomolecular breadboards that are available. | ||
The figure below provides an overview of the basic breadboarding process. At the left is a circuit that we wish to implement and transform into a cell or other bimolecular chassis. Rather than try to directly get the circuit working in the cell, which requires time consuming iterations and difficult debugging, we instead use a sequence of simpler test environments ("breadboards"), where we can do much more rapid iterations between experiments, modeling and design. | The figure below provides an overview of the basic breadboarding process. At the left is a circuit that we wish to implement and transform into a cell or other bimolecular chassis. Rather than try to directly get the circuit working in the cell, which requires time consuming iterations and difficult debugging, we instead use a sequence of simpler test environments ("breadboards"), where we can do much more rapid iterations between experiments, modeling and design. | ||
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=== DNA origami breadboard === | === DNA origami breadboard === | ||
A second breadboard family that we are developing explores the role of spatial localization and single molecule effects. For this, we are using | |||
DNA origami to spatially organize, study, and optimize existing ''in vitro'' transcription circuits such as oscillators. There are two kinds of spatial | |||
organization that can be effected by DNA origami. The first kind of organization, ''local patterning'' is intrinsic to the DNA origami themselves. For example, a rectangular origami provides a roughly 100~nm x 70~nm surface onto which other molecules can be positioned with a resolution of about 6 nanometers. | |||
A second kind of spatial organization afforded by DNA orgami is that of ''global placement'. We are developing a method for placing individual DNA origami at lithographically-patterned sites on a silicon dioxide surface: sticky patches in the shape of DNA origami are created by e-beam, origami are washed over the surface, and they bind and orient on the sticky patches. Because of the regular placement of origami, we expect to eventually be able to observe up to 1600 (40 x 40) origami localized circuits in parallel to achieve good statistics. | |||
=== Artificial cells === | === Artificial cells === | ||
=== Biochemical wires === | === Biochemical wires === | ||
