An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism

National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bellary Road, Bangalore 560065, India.
Nature Communications (Impact Factor: 11.47). 06/2011; 2(1):340. DOI: 10.1038/ncomms1340
Source: PubMed


Structural DNA nanotechnology seeks to build synthetic molecular machinery from DNA. DNA nanomachines are artificially designed assemblies that switch between defined conformations in response to an external cue. Though it has proved possible to create DNA machines and rudimentary walkers, the function of such autonomous DNA-based molecular devices has not yet been achieved inside living organisms. Here we demonstrate the operation of a pH-triggered DNA nanomachine inside the nematode Caenorhabditis elegans. The nanomachine uses fluorescence resonance energy transfer to effectively map spatiotemporal pH changes associated with endocytosis in wild type as well as mutant worms, demonstrating autonomous function within the organismal milieu in a variety of genetic backgrounds. From this first demonstration of the independent functionality of a DNA nanomachine in vivo, we observe that rationally designed DNA-based molecular devices retain their in vitro functionality with quantitative precision. This positions DNA nanodevices as exciting and powerful tools to interrogate complex biological phenomena.

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    • "In recent years, considerable effort has been devoted to the design and fabrication of artificial nanoswitches/machines with various molecules for diverse applications [1] [2] [3] [4] [5] [6]. Molecular nanoswitches are a diverse class of construct capable of changing photochemical stimuli to perform a range of useful tasks from species sensing to reaction control. "
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    ABSTRACT: A convenient and reversible nanoswitch with the assistance of cerium ions based on aggregation and disaggregation of carbon quantum dots was developed to achieve highly sensitive detection of pyrophosphate ions. Two states including aggregation state and disaggregation state corresponding to fluorescence on and off signaling can be readily switched in a reversible way. The aggregation state is resulted from large nanoassembly formed by carbon quantum dots and cerium ions due to their strong complexation affinity. The disaggregation state comes from competitive combination between cerium ion and pyrophosphate ion. The PPi ion severs as the external chemical stimulus to CQDs/Ce(III) nanoassembly, and its quantity is responsive to fluorescence intensity of the sensing system. Quantitative evaluation of PPi in a broad range from 0.3 to 29.7 μM with the detection limit of 0.1 μM can be realized in this way. The PPi detection in human HeLa cells was also assessed, and fluorescence switching between ON and OFF can be readily observed in response to presence and absence of PPi.
    Full-text · Article · Dec 2015 · Sensors and Actuators B Chemical
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    • "This was primarily due to two reasons: firstly, C. elegans is a transparent organism, which is ideally suited to florescence imaging based measurements. Secondly, DNA nanostructures, once introduced in the pseudocoelom of the worm, are targeted to the coelomocytes due to their negatively charged phosphate backbone and internalized via anionic ligand-binding receptors [7]. Coelomocytes are six oblong macrophage-like cells located in the body cavity of C. elegans. "
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    ABSTRACT: DNA nanostructures are rationally designed, synthetic, nanoscale assemblies obtained from one or more DNA sequences by their self-assembly. Due to the molecularly programmable as well as modular nature of DNA, such designer DNA architectures have great potential for in cellulo and in vivo applications. However, demonstrations of functionality in living systems necessitates a method to assess the in vivo stability of the relevant nanostructures. Here, we outline a method to quantitatively assay the stability and lifetime of various DNA nanostructures in vivo. This exploits the property of intact DNA nanostructures being uptaken by the coelomocytes of the multicellular model organism Caenorhabditis elegans. These studies reveal that the present fluorescence based assay in coelomocytes of C. elegans is a useful in vivo test bed for measuring DNA nanostructure stability.
    Full-text · Article · Apr 2013 · Methods
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    ABSTRACT: Structural DNA nanotechnology seeks to create architectures of highly precise dimensions using the physical property that short lengths of DNA behave as rigid rods and the chemical property of Watson-Crick base-pairing that acts as a specific molecular glue with which such rigid rods may be joined. Thus DNA has been used as a molecular scale construction material to make molecular devices that can be broadly classified under two categories (i) rigid scaffolds and (ii) switchable architectures. This review details the growing impact of such synthetic nucleic acid based molecular devices in biology and biotechnology. Notably, a significant trend is emerging that integrates morphology-rich nucleic acid motifs and alternative molecular glues into DNA and RNA architectures to achieve biological functionality.
    Full-text · Article · Jun 2011 · Current Opinion in Biotechnology
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