Programming biomolecular self-assembly pathways. Nature

Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.
Nature (Impact Factor: 41.46). 02/2008; 451(7176):318-22. DOI: 10.1038/nature06451
Source: PubMed

ABSTRACT In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.

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Available from: Peng Yin, Sep 26, 2015
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    • ": Catalytic 3-arm junction formation. We show the catalytic 3-arm junction assembly process (originally demonstrated by Yin et al. [14] ), as enumerated by our software; the intended pathway is highlighted in red and purple. Boxes with rounded edges represent complexes—initial complexes have blue backgrounds, " transient " complexes have dashed borders (e.g. "
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    ABSTRACT: DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages by formalizing DNA strand displacement mechanisms and modeling interactions at the "domain" level - one level of abstraction above models that explicitly describe DNA strand sequences. Unfortunately, the most-developed models currently only treat pseudo-linear DNA structures, while many systems being experimentally and theoretically pursued exploit a much broader range of secondary structure configurations. Here, we describe a new domain-level reaction enumerator that can handle arbitrary non-pseudoknotted secondary structures and reaction mechanisms including association and dissociation, 3-way and 4-way branch migration, and direct as well as remote toehold activation. To avoid polymerization that is inherent when considering general structures, we employ a time-scale separation technique that holds in the limit of low concentrations. This also allows us to "condense" the detailed reactions by eliminating fast transients, with provable guarantees of correctness for the set of reactions and their kinetics. We hope that the new reaction enumerator will be used in new molecular programming languages, compilers, and tools for analysis and verification that treat a wider variety of mechanisms of interest to experimental and theoretical work. We have implemented this enumerator in Python, and it is included in the DyNAMiC Workbench Integrated Development Environment.
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    • "Of particular interest is a programmable DNA circuit known as catalytic hairpin assembly (CHA) (10). In CHA two partially complementary DNA hairpins are prevented from reacting with one another by ensconcing the complementary sequences within hairpin structures, effectively leading to kinetic trapping of the reaction (2) (Figure 1a). "
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    ABSTRACT: Nucleic acid circuits are finding increasing real-life applications in diagnostics and synthetic biology. Although DNA has been the main operator in most nucleic acid circuits, transcriptionally produced RNA circuits could provide powerful alternatives for reagent production and their use in cells. Towards these goals, we have implemented a particular nucleic acid circuit, catalytic hairpin assembly, using RNA for both information storage and processing. Our results demonstrated that the design principles developed for DNA circuits could be readily translated to engineering RNA circuits that operated with similar kinetics and sensitivities of detection. Not only could purified RNA hairpins perform amplification reactions but RNA hairpins transcribed in vitro also mediated amplification, even without purification. Moreover, we could read the results of the non-enzymatic amplification reactions using a fluorescent RNA aptamer 'Spinach' that was engineered to undergo sequence-specific conformational changes. These advances were applied to the end-point and real-time detection of the isothermal strand displacement amplification reaction that produces single-stranded DNAs as part of its amplification cycle. We were also able to readily engineer gate structures with RNA similar to those that have previously formed the basis of DNA circuit computations. Taken together, these results validate an entirely new chemistry for the implementation of nucleic acid circuits.
    Nucleic Acids Research 02/2014; 42(7). DOI:10.1093/nar/gku074 · 9.11 Impact Factor
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    • "However it is also possible to engineer transient system dynamics such as in self-assembly pathways. It has been shown that it is possible to program diverse molecular self-assembly and disassembly pathways using a ‘reaction graph’ abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif [51]. Programming of functions such as a catalytic circuit, nucleated dendritic growth, and autonomous locomotion were achieved with this approach. "
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    ABSTRACT: Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.
    Computational and Structural Biotechnology Journal 04/2013; 7(8):e201304003. DOI:10.5936/csbj.201304003
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