Using DNA to Power Nanostructures

DNA hybridization has been used to power a number of DNA-based nanostructures constructed out of DNA. Here some considerations that go into DNA-based motor design are briefly reviewed. The emphasis will be on the operation of toeholds, single-stranded sections of DNA that facilitate the process of strand removal during certain points in the operation of a DNA-based motor. Reaction kinetics measurements for toehold mediated strand exchange are reported. These measurements have served as a guide for choosing toehold lengths.

[1]  L. Stols,et al.  Solution-phase detection of polynucleotides using interacting fluorescent labels and competitive hybridization. , 1989, Analytical biochemistry.

[2]  D. Bartel,et al.  RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension , 2001, Science.

[3]  Bernard Yurke,et al.  DNA Scissors , 2001, DNA.

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

[5]  Andrew D. Ellington,et al.  The search for missing links between self-replicating nucleic ACIDs and the RNA world , 1995, Origins of life and evolution of the biosphere.

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

[7]  Jean Sturm,et al.  Persistence Length of Single-Stranded DNA , 1997 .

[8]  J. Liphardt,et al.  Reversible Unfolding of Single RNA Molecules by Mechanical Force , 2001, Science.

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

[10]  M. Eigen,et al.  The Hypercycle: A principle of natural self-organization , 2009 .

[11]  J. Reif,et al.  Logical computation using algorithmic self-assembly of DNA triple-crossover molecules , 2000, Nature.

[12]  Christof M Niemeyer,et al.  Nanomechanical devices based on DNA. , 2002, Angewandte Chemie.

[13]  N. Seeman,et al.  Construction of a DNA-Truncated Octahedron , 1994 .

[14]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[15]  J W Szostak,et al.  Structurally complex and highly active RNA ligases derived from random RNA sequences. , 1995, Science.

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

[17]  L. Stols,et al.  Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution. , 1993, Biochemistry.

[18]  G. F. Joyce,et al.  A self-replicating ligase ribozyme , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  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.

[20]  Bernard Yurke,et al.  DNA hybridization catalysts and molecular tweezers , 1999, DNA Based Computers.

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

[22]  K. Nicolaou,et al.  Chemical self-replication of palindromic duplex DNA , 1994, Nature.

[23]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[24]  F. Simmel,et al.  Using DNA to construct and power a nanoactuator. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[25]  Bernard Yurke,et al.  A DNA-based molecular device switchable between three distinct mechanical states , 2002 .

[26]  N. Davidson,et al.  Kinetics of renaturation of DNA. , 1968, Journal of molecular biology.

[27]  Weihong Tan,et al.  A Single DNA Molecule Nanomotor , 2002 .

[28]  Stoddart,et al.  Artificial Molecular Machines. , 2000, Angewandte Chemie.

[29]  N. Harada,et al.  Light-driven monodirectional molecular rotor , 2022 .

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

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

[32]  S. Kowalczykowski,et al.  An overview of homologous pairing and DNA strand exchange proteins. , 1991, Biochimie.

[33]  M. Rief,et al.  Sequence-dependent mechanics of single DNA molecules , 1999, Nature Structural Biology.

[34]  U. Bockelmann,et al.  Mechanical separation of the complementary strands of DNA. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[35]  X Chen,et al.  Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[36]  D. Sievers,et al.  Self-replication of complementary nucleotide-based oligomers , 1994, Nature.

[37]  R. Britten,et al.  Repeated Sequences in DNA , 1968 .