Spatial Control of DNA Reaction Networks by DNA Sequence 英文参考文献.docVIP

Molecules 2012, 17, 13390-13402; doi:10.3390/molecules171113390 OPEN ACCESS molecules ISSN 1420-3049 /journal/molecules Article Spatial Control of DNA Reaction Networks by DNA Sequence Peter B. Allen, Xi Chen and Andrew D. Ellington * Institute of Cell and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA * Author to whom correspondence should be addressed; E-Mail: andy.ellington@; Tel.: +1-512-471-6445; Fax: +1-512-471-2681. Received: 25 September 2012; in revised form: 5 November 2012 / Accepted: 5 November 2012 / Published: 9 November 2012 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. Keywords: reaction-diffusion; electrophoresis; chemical reaction networks; DNA circuits; strand displacement reactions 1. Introduction Chemical reaction-diffusion networks can produce complex physical (spatial and temporal) patterns, such as those that occur during organismal development [1]. However, generalized pattern generation via designed reaction-diffusion networks is not currently feasible, in large measure because of the idiosyncrasies of chemical reactions. Specific nanometer structures have been assembled based on protein or nucleic acid folding [2], but these structures are not scalable to cellular or larger length scales. Programmed assembly of larger aggregates, such as gold nanoparticles, can produce longer- range