The design of single-stranded nucleic acid knots

A general strategy is described for the synthesis of single-stranded nucleic acid knots. Control of nucleic acid sequence is used to direct the formation of secondary structures that produce the target topology. The key feature of the strategy is the equation of a half-turn of double helical DNA or RNA with a node in a knot. By forming nodes from complementary DNA sequences, it appears possible to direct the assembly of any simple knot. Stabilization of individual nodes may be achieved by constructing them from long regions containing both B-DNA and Z-DNA. Control over the braiding of DNA that acts as a link between node-forming domains can be realized by condensing the nodes into well-defined DNA structures, such as extended domains of linear duplex, branched junctions, antijunctions or mesojunctions. Further topological control may be derived from the pairing of linker regions to complementary single-stranded molecules, thereby preventing them from braiding in an undesirable fashion.

[1]  N. Cozzarelli,et al.  Description of the topological entanglement of DNA catenanes and knots by a powerful method involving strand passage and recombination. , 1987, Journal of molecular biology.

[2]  N. Seeman Construction of three-dimensional stick figures from branched DNA. , 1991, DNA and cell biology.

[3]  Nadrian C. Seeman,et al.  Design and synthesis of a knot from single-stranded DNA , 1991 .

[4]  M. Behe,et al.  Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[5]  J. Van De Sande,et al.  Left-handed DNA: from synthetic polymers to chromosomes. , 1983, Journal of biomolecular structure & dynamics.

[6]  N. Seeman De novo design of sequences for nucleic acid structural engineering. , 1990, Journal of biomolecular structure & dynamics.

[7]  N. Seeman Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[8]  J. Van De Sande,et al.  Parallel stranded DNA. , 1988, Science.

[9]  V. Jones A polynomial invariant for knots via von Neumann algebras , 1985 .

[10]  R. Sheardy,et al.  Anomalous gel migration of DNA oligomers containing multiple conformational junctions. , 1990, Biochemistry.

[11]  1-Amino- and 1,3-Diaminoimidazolium Salts† , 1990 .

[12]  N. Seeman,et al.  The ligation and flexibility of four‐arm DNA junctions , 1988, Biopolymers.

[13]  E. W. Moomaw,et al.  Preparation of oligodeoxynucleotide-alkaline phosphatase conjugates and their use as hybridization probes. , 1986, Nucleic acids research.

[14]  J. Griffith,et al.  Genetic rearrangement of DNA induces knots with a unique topology: implications for the mechanism of synapsis and crossing-over. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[15]  I. Tinoco,et al.  ‘Z-RNA’—a left-handed RNA double helix , 1984, Nature.

[16]  Jean-Pierre Sauvage,et al.  Interlacing molecular threads on transition metals: catenands, catenates, and knots , 1990 .

[17]  P. Hagerman Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[18]  B. Wittig,et al.  Construction of a 42 base pair double stranded DNA microcircle. , 1989, Nucleic acids research.

[19]  N. Cozzarelli,et al.  Biochemical topology: applications to DNA recombination and replication. , 1986, Science.

[20]  N C Seeman,et al.  Physical models for exploring DNA topology. , 1988, Journal of biomolecular structure & dynamics.

[21]  M. Gellert,et al.  DNA gyrase action involves the introduction of transient double-strand breaks into DNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[22]  H. K. Moffatt The energy spectrum of knots and links , 1990, Nature.

[23]  N C Seeman,et al.  Assembly and characterization of five-arm and six-arm DNA branched junctions. , 1991, Biochemistry.

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

[25]  Chung-Cheng Liu,et al.  Type II DNA topoisomerases: Enzymes that can unknot a topologically knotted DNA molecule via a reversible double-strand break , 1980, Cell.

[26]  Rac Jones,et al.  Tetraplex formation of a guanine-containing nonameric DNA fragment , 1990, Science.

[27]  N C Seeman,et al.  Three-arm nucleic acid junctions are flexible. , 1986, Nucleic acids research.

[28]  Alexander Rich,et al.  FORMATION OF A THREE-STRANDED POLYNUCLEOTIDE MOLECULE , 1957 .

[29]  Alfred Nordheim,et al.  THE CHEMISTRY AND BIOLOGY OF LEFT-HANDED Z-DNA , 1984 .

[30]  J. Wang,et al.  Knotted single-stranded DNA rings: a novel topological isomer of circular single-stranded DNA formed by treatment with Escherichia coli omega protein. , 1976, Journal of molecular biology.

[31]  G. Ashley,et al.  Chemical synthesis of oligodeoxynucleotide dumbbells. , 1991, Biochemistry.

[32]  N. Leontis,et al.  Stability and structure of three-way DNA junctions containing unpaired nucleotides. , 1991, Nucleic acids research.