Spatial Control of DNA Reaction Networks by DNA Sequence

Peter Allen,Andrew Ellington,Xi Chen

doi:10.3390/molecules171113390

Peter Allen, Andrew Ellington + Show 1 more

Open Access

https://doi.org/10.3390/molecules171113390

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Abstract

We have developed a set of DNA circuits that execute during gel electrophoresis to yield immobile, fluorescent features in the gel. The parallel execution of orthogonal circuits led to the simultaneous production of different fluorescent lines at different positions in the gel. The positions of the lines could be rationally manipulated by changing the mobilities of the reactants. The ability to program at the nanoscale so as to produce patterns at the macroscale is a step towards programmable, synthetic chemical systems for generating defined spatiotemporal patterns.

Highlights

Chemical reaction-diffusion networks can produce complex physical patterns, such as those that occur during organismal development [1]
We first performed native polyacrylamide gel electrophoresis of a given DNA molecule with and without an antisense acridyte-DNA oligonucleotide co-polymerized in the gel
We have developed a modular set of DNA circuits that can execute during gel electrophoresis to produce static, fluorescent macroscale patterns

Summary

Introduction

Chemical reaction-diffusion networks can produce complex physical (spatial and temporal) patterns, such as those that occur during organismal development [1]. Nucleic acid circuits have been proposed as one possible way to more generally implement chemical reaction-diffusion networks, since the strengths of interactions and the orthogonalities of Molecules 2012, 17 reactions can be readily controlled by controlling base-pairing [4,5]. As a step towards the more generalized design of pattern-forming reaction networks we have examined the behavior of diffusable DNA circuits in gels. Depending on the mobility of the diffusing protein molecules, a line of immunoprecipitants occurs at a particular location in a gel. Rather than using this phenomenon to analyze interactions, we instead attempted to control reactivity and diffusion and thereby specify the locations of features. We were able to produce multiple static, fluorescent bands at controlled positions in space and time within the gel, and could control the location of these features by controlling the electrophoretic mobility of the underlying DNA substrates

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