DNA machine

About: DNA machine is a research topic. Over the lifetime, 106 publications have been published within this topic receiving 5087 citations.

A DNA-fuelled molecular machine made of DNA

Abstract: Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles, and DNA templates can direct the growth of semiconductor nanocrystals and metal wires. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles, linked rings and polyhedra. The construction of active devices is also possible--for example, a nanomechanical switch, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as 'fuel'. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product.

DNA computing

Abstract: Computer scientists are joining forces with molecular biologists and chemists to explore the potential for computation using information-carrying biological polymers such as nucleic acids (DNA and RNA). DNA computing is a subset of molecular computing. The key feature of DNA for computing is its information content. The self-assembly properties of DNA suggest an indirect application to computing. The concept of self-assembly, which biological systems have evolved to form such structures as viruses, flagella, and microtubules (which serve as structural and motile components of cells), can lead the way to using DNA as the basis of nanorobotics.

DNA nanotechnology: from sensing and DNA machines to drug-delivery systems.

Abstract: DNA/nanoparticle hybrid systems combine the unique electronic and optical properties of nanomaterials with the recognition and catalytic properties of nucleic acids. These materials hold great promise for the development of new sensing platforms, the programmed organization of nanoparticles, the switchable control of plasmonic phenomena in the nanostructures, and the controlled delivery of drugs. In this Perspective, we summarize recent advances in the application of DNA/nanoparticle (NP) hybrids in these different disciplines. Nucleic acid–semiconductor quantum dot hybrids are implemented to develop multiplexed sensing platforms for targeted DNA. The chemiluminescence resonance energy transfer mechanism is introduced as a new transduction signal, and the amplified detection of DNA targets through the biocatalytic regeneration of analytes is demonstrated. DNA machines consisting of catenanes or tweezers, and modified with fluorophore/Au NP pairs are used as functional devices for the switchable “mechanica...

DNA-based machines

Abstract: Nucleic acids include substantial information in their base sequence and their hybridization–complexation motifs. Recent research efforts attempt to utilize this biomolecular information to develop DNA nanostructures exhibiting machine-like functions. DNA nano-assemblies revealing tweezers, motor, and walker activities exemplify a few such machines. The DNA-based machines provide new components that act as sensitive sensors, transporters, or drug delivery systems.

DNAzyme-Based Rolling-Circle Amplification DNA Machine for Ultrasensitive Analysis of MicroRNA in Drosophila Larva

Abstract: We present a highly sensitive colorimetric method for microRNA (miRNA) detection. This method is based on a rolling-circle amplification (RCA) DNA machine, which integrates RCA, nicking enzyme signal amplification and DNAzyme signal amplification. The DNA machine is triggered by the hybridization of target miRNA with a rational designed padlock DNA template and activated by RCA. The resulting RCA product then autonomously replicates a multiple machinery cutter cycle and generates accumulated amount of products. Specifically, the DNA product in the present work is designed as a horseradish peroxidase (HRP)-mimicking DNAzyme, which could that catalyze a colorimetric reaction and generate colored product. Through these cascade amplifications, microRNA (miRNA) as low as 2 aM could be detected. As an example of in vivo application, miRNA from single Drosophila larva was successfully analyzed. Drosophila is a model organism that provides a powerful genetic tool to study gene functions. Study of Drosophila miRNAs has brought us knowledge of its biogenesis and biological functions. The analysis of miRNA typically requires a pretreatment process of extracting total RNAs from target cells, followed by quantitative analysis of target miRNA in total RNA samples, which nevertheless suffers from laborious total RNA extraction and time-consuming processes and poor limit of detection. Meanwhile, the tiny size of Drosophila makes it difficult to accurately measure trivial changes of its cellular miRNA levels. The ability to detect ultralow concentration of miRNA of the proposed method enables the analysis the expression of mir-1 in single Drosophila larva. We thus expect that the strategy may open new avenues for in situ miRNA analysis in single cell or living animals.