A DNA-fuelled molecular machine made of DNA

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.

[1]  L. Stryer,et al.  Energy transfer: a spectroscopic ruler. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R. W. Davis,et al.  A physical study by electron microscopy of the terminally reptitious, circularly permuted DNA from the coliphage particles of Escherichia coli 15. , 1970, Journal of molecular biology.

[3]  R. Wiegand,et al.  Uptake of homologous single-stranded fragments by superhelical DNA. IV. Branch migration. , 1977, Journal of molecular biology.

[4]  T. Lohman,et al.  Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity , 1978, Quarterly Reviews of Biophysics.

[5]  C. Green,et al.  Reassociation rate limited displacement of DNA strands by branch migration. , 1981, Nucleic acids research.

[6]  G. S. Manning.  A procedure for extracting persistence lengths from light-scattering data on intermediate molecular weight DNA , 1981 .

[7]  Rapid detection and identification of infectious agents : papers given at an international symposium held in Berkeley, California , 1985 .

[8]  D. Kingsbury,et al.  Rapid Detection and Identification of Infectious Agents , 1985 .

[9]  N. Seeman,et al.  Synthesis from DNA of a molecule with the connectivity of a cube , 1991, Nature.

[10]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[11]  Christoph F. Schmidt,et al.  Direct observation of kinesin stepping by optical trapping interferometry , 1993, Nature.

[12]  M. Sheetz,et al.  Force of single kinesin molecules measured with optical tweezers. , 1993, Science.

[13]  T. Yanagida,et al.  Single-molecule analysis of the actomyosin motor using nano-manipulation. , 1994, Biochemical and biophysical research communications.

[14]  J. Spudich,et al.  Single myosin molecule mechanics: piconewton forces and nanometre steps , 1994, Nature.

[15]  P. Lizardi,et al.  An Allosteric Hammerhead Ribozyme , 1995, Bio/Technology.

[16]  Xin Li,et al.  Dictation of the shape of mesoscale semiconductor nanoparticle assemblies by plasmid DNA , 1996 .

[17]  P. Schultz,et al.  Organization of 'nanocrystal molecules' using DNA , 1996, Nature.

[18]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[19]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.

[20]  R R Breaker,et al.  Rational design of allosteric ribozymes. , 1997, Chemistry & biology.

[21]  Ulrich Bockelmann,et al.  MOLECULAR STICK-SLIP MOTION REVEALED BY OPENING DNA WITH PICONEWTON FORCES , 1997 .

[22]  N. Seeman,et al.  Assembly of Borromean rings from DNA , 1997, Nature.

[23]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[24]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[25]  Y. Okuno,et al.  Allosteric regulation of a ribozyme activity through ligand-induced conformational change. , 1998, Nucleic acids research.

[26]  E. Braun,et al.  DNA-templated assembly and electrode attachment of a conducting silver wire , 1998, Nature.

[27]  Andrew Ellington,et al.  In vitro selection of an allosteric ribozyme that transduces analytes to amplicons , 1999, Nature Biotechnology.

[28]  H. Asanuma,et al.  Photoregulation of the Formation and Dissociation of a DNA Duplex by Using the cis-trans Isomerization of Azobenzene. , 1999, Angewandte Chemie.

[29]  N. Seeman,et al.  A nanomechanical device based on the B–Z transition of DNA , 1999, Nature.