Construction of a structurally defined double-stranded DNA catenane.

Topologically interlocked structures like catenanes and rotaxanes are promising components for the construction of molecular machines and motors. Herein we describe the construction of double-stranded DNA catenanes for DNA nanotechnology. For this, C-shaped DNA minicircle fragments were equipped with sequence-specific DNA-binding polyamides and their respective binding site. Formation of catenanes is achieved by self-assembly of two of these fragments and subsequent addition of a ring-closing oligonucleotide.

[1]  Itamar Willner,et al.  Enzyme cascades activated on topologically programmed DNA scaffolds. , 2009, Nature nanotechnology.

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

[3]  Francesco Zerbetto,et al.  Unidirectional rotation in a mechanically interlocked molecular rotor , 2003, Nature.

[4]  C. K. Nandi,et al.  Binding of hairpin polyamides to DNA studied by fluorescence correlation spectroscopy for DNA nanoarchitectures , 2008, Analytical and bioanalytical chemistry.

[5]  N. Seeman.  Nanomaterials based on DNA. , 2010, Annual review of biochemistry.

[6]  Alexander Heckel,et al.  DNA minicircles connected via G-quadruplex interaction modules. , 2010, Small.

[7]  Alexander Heckel,et al.  Pyrrole/imidazole-polyamide anchors for DNA tertiary interactions. , 2009, Small.

[8]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[9]  Michael Famulok,et al.  A double-stranded DNA rotaxane. , 2010, Nature nanotechnology.

[10]  Jean-Pierre Sauvage,et al.  Molecular Catenanes, Rotaxanes and Knots , 1999 .

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

[12]  Michael Famulok,et al.  DNA minicircles with gaps for versatile functionalization. , 2008, Angewandte Chemie.

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

[14]  T. Shapiro,et al.  The structure and replication of kinetoplast DNA. , 1995, Annual review of microbiology.

[15]  Michael Famulok,et al.  Polyamide struts for DNA architectures. , 2007, Angewandte Chemie.

[16]  C. Schalley,et al.  On the way to rotaxane-based molecular motors: studies in molecular mobility and topological chirality. , 2001, Accounts of chemical research.

[17]  Y. Wang,et al.  Synthetic DNA Knots and Catenanes , 1994 .

[18]  P. Dervan,et al.  Programming multiple protein patterns on a single DNA nanostructure. , 2008, Journal of the American Chemical Society.

[19]  James C. Wang,et al.  E. coli and M. luteus DNA topoisomerase I can catalyze catenation or decatenation of double-stranded DNA rings , 1980, Cell.

[20]  Itamar Willner,et al.  A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures , 2008, Proceedings of the National Academy of Sciences.

[21]  Frank Dean,et al.  Determination of the absolute handedness of knots and catenanes of DNA , 1983, Nature.

[22]  N. Cozzarelli,et al.  The stereostructure of knots and catenanes produced by phage λ integrative recombination: implications for mechanism and DNA structure , 1985, Cell.

[23]  Hao Yan,et al.  Folding and cutting DNA into reconfigurable topological nanostructures. , 2010, Nature nanotechnology.

[24]  Bonnie A. Sheriff,et al.  A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre , 2007, Nature.

[25]  N. Seeman,et al.  Tight single-stranded DNA knots. , 1993, Journal of biomolecular structure & dynamics.

[26]  Itamar Willner,et al.  DNAzymes for sensing, nanobiotechnology and logic gate applications. , 2008, Chemical Society reviews.

[27]  Michael Famulok,et al.  Assembly of dsDNA nanocircles into dimeric and oligomeric aggregates. , 2010, Chemical communications.

[28]  F. Simmel,et al.  DNA-based nanodevices , 2007 .

[29]  P. Dervan,et al.  Recognition of the DNA minor groove by pyrrole-imidazole polyamides. , 2003, Current opinion in structural biology.