In the article “One- pot pentaknot,” published by Advance Online Publishers and submitted to the Nature Chemistry Journal in November, 2011, Ayme Et. Al., (2011) describes DNA as one of the biological macromolecules that contain knots. The report states that knots are also found in proteins and are important structural components of deoxyribonucleic acids.
Similarly, the report, “New Motifs in DNA nanotechnology” by Seeman et al, (1998) outlines the importance of knots in DNA and the ability of various types of DNA to form knots. The report also states that the DNA molecule has a unique ability to pair with other DNA molecules through specific nucleotide base pairing. The report also describes ways in which this unique ability of DNA makes it an important construction material as well as outlining techniques of constructing DNA knots, polyhedrals and catenanes.
Finally, this article outlines the ideas and techniques of supra-molecular knot formation described in the article, “Metallo-supra-molecular self-assembly of a universal 3-ravel”, by Feng et. al, (2011). The report uses the twenty-component Fe8L12 supra-molecule to describe the techniques of branched knot formation through metallo-supra-molecular assembly.
DNA Knots and Polyhedrals in DNA Nanotechnology
DNA is a double stranded polynucleotide. It contains biological information and regulates the functions of a cell as well as determining an organism’s phenotype. Knots are found in both DNA and some proteins (Jean.F et al. 2011). In the recent past, scientists have been using unusual DNA motifs to make molecular building blocks. This is done though the joining of DNA sticky ends to form B- DNA. In their report on ‘New motifs in DNA nanotechnology,’ (Seeman et al. 1998) stated that they had used the same strategy in the construction of a supra-molecular DNA cube as well as an octahedron. They also reported on their use of the DNA polynucleotide to make trefoil folds.
In branched DNA, the angles formed between the branching arms in junctions vary. To construct a DNA cube, pairs of unique sticky ends are used. Since there is little control over DNA synthesis when constructing the cube in solution, a solid support is used. This way, it is easy to remove impurities from the growing chain. It also allows separation of growing chains preventing ligation of symmetric sticky ends. The polyhedral are made of topologically specified objects. Restriction sites are incorporated in appropriate sites and then broken to target catenanes whose electrophoretic properties can be compared against standards. 3- Arm branched junctions are used during the construction of the cube while 4-arm junctions are used when constructing an octahedron.
Construction of knots is one of the features of DNA nanotechnology. For these knots to be created, a node must first be created on the target DNA. A node can either be positive or negative. Positive and negative nodes are mirror images. Negative nodes are...