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DNA-Based Machines

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Book cover Molecular Machines and Motors

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 354))

Abstract

The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, “fuel.” (3) The mechanical operation is accompanied by an energy consumption process that leads to “waste products.” (4) The cyclic operation of the DNA devices, involves the use of “fuel” and “anti-fuel” ingredients. A variety of DNA-based machines are described, including the construction of “tweezers,” “walkers,” “robots,” “cranes,” “transporters,” “springs,” “gears,” and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different “fuels”, such as nucleic acid strands, pH (H+/OH–), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

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Abbreviations

ABTS2– :

2, 2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)

ADA:

Adenosine monoaminase

AFM:

Atomic force microscopy

aFu:

Anti-fuel

AMP:

Adenosine monophosphate

CRET:

Chemiluminescence resonance energy transfer

DNAzyme:

Catalytic nucleic acid

F:

Fluorophore

FAM:

Carboxyfluorescein

Fc:

Ferrocene

FRET:

Fluorescence resonance energy transfer

Fu:

Fuel

G6pDH:

Glucose-6-phosphate dehydrogenase

GOx:

Glucose oxidase

HRP:

Horseradish peroxidase

IMP:

Inosine monophosphate

MB:

Methylene blue

Q:

Quencher

QDs:

Quantum dots

SEF:

Surface-enhanced fluorescence

TAMRA:

Carboxytetramethylrhodamine

TEM:

Transmission electron microscopy

UV:

Ultraviolet

β-CD:

β-Cyclodextrin

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Acknowledgement

Parts of this research are supported by the Volkswagen Foundation, Germany, and the Israel Science Foundation.

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Authors and Affiliations

  1. Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel

    Fuan Wang, Bilha Willner & Itamar Willner

Authors
  1. Fuan Wang
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  2. Bilha Willner
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  3. Itamar Willner
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Corresponding author

Correspondence to Itamar Willner .

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Editors and Affiliations

  1. Dept. of Chemistry “Giacomo Ciamician”, University of Bologna, Bologna, Italy

    Alberto Credi

  2. Dept. of Chemistry “Giacomo Ciamician”, University of Bologna, Bologna, Germany

    Serena Silvi

  3. Dept. of Chemistry “Giacomo Ciamician", University of Bologna, Bologna, Italy

    Margherita Venturi

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Wang, F., Willner, B., Willner, I. (2014). DNA-Based Machines. In: Credi, A., Silvi, S., Venturi, M. (eds) Molecular Machines and Motors. Topics in Current Chemistry, vol 354. Springer, Cham. https://doi.org/10.1007/128_2013_515

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