Catenanes, and Knots

Both catenanes and knots can bring together remote DNA sequences and may be important in transcription regulation and genetic recombination... 

For a review of chirality in Mobius-strip molecules catenanes, and knots, see Walba, D.M. Tetrahedron, 1985, 41, 3161. 

A useful summary of the various and numerous types of rotaxanes, catenanes, and knots can be found in a review of template routes to interlocked molecular structures 468). Inorganic chemistry is centrally involved in the templating involved in self-assembly and in controlled synthesis of such species. 

Thus there is an essential difference between classical homogeneous reactions in organic chemistry and reactions such as those in which catenanes and knots are formed. In the latter, there are heterogeneities on the micro scale. Thus supramolecular chemistry lies also in the border area between classical organic chemistry and surface chemistry. 

The molecules with distinct topological properties are not a mere curiosity, since they can be found in Nature. Circular DNA schematically presented as 42 are sometimes found in living organisms in the form of catenanes and knots [38], and special enzymes topoisomerases take part in their formation and transformations [39]. Circular DNA molecules can even form nets of catenated structures like that schematically presented in Figure 2.7 [40]. A discussion of biological topological structures falls outside the scope of this monograph it should be stressed, however, that their role in Nature is not understood and warrants an explanation. 

This route provides access to catenanes (and knotted rings) without having to thread closed cycles, sharing an important feature of the Mobius path. The more complex ring structures arise from the tangling motions of the pendant chain before formation of the four-membered ring 6 (Scheme 2). 

The discovery that DNA forms catenanes and knots, some of them extremely complex, initiated a new field of research which has been called Biochemical Topology [21]. In 1967, Vinograd and co-workers detected in HeLa cell mitochondria isolable DNA molecules that consist of independent, double-stranded, closed circles that are topologically interlocked or catenated like the links in a chain [22, 23]. A few years later, catenanes had been observed everywhere that circular DNA molecules were known [24] and the first knot was found by Liu and coworkers in single-stranded circular phage fd DNA treated with Escherichia coli co-protein [25]. In 1980, knots could also be generated in double-stranded circular DNA [26]. 

The ever-increasing interest in the catenanes and knots of DNA stems not only from their widespread occurrence or from their topological novelty determination of their structures provides precious information about the biological processes which generate them. A whole class of enzymes - topoisomerases - effects these topological transformations perfectly [30, 31]. Their possible role in a large vari-... 

The plectonemic nature of the DNA double-helix makes it a tractable molecule for experiments in molecular topology. This is a very rich vein for the exploration of the topological properties of matter. In this chapter, we have tried to illuminate some of the techniques by which the single-stranded topology of DNA can be directed in synthetic molecules. Catenanes and knots, periodic braids, and Borro-mean rings are available from simple protocols, and it is to be hoped that the physical properties associated with complex topologies (Moffatt 1990) will become available through the medium of DNA constructions. 

White, J.H., Millett, K.C., Cozzarelli, N.R. (1987) Description of the topological entanglement of DNA catenanes and knots by a powerful method involving strand passage and recombination. J. Mol. Biol. 197, 585-603. 

III. Template Effects for the Syntheses of Rotaxanes, Catenanes, and Knots 177... 

This process involves the covalent locking in of structures formed by reversible self-assembly. The irreversible, post-assembly step switches off the equilibrium process involved in the self-assembly. As we will see in the following sections, self assembly with covalent postmodification is involved in a range of biochemistry (e.g. insulin synthesis) and elegant abiotic supramolecular synthesis as in the formation of catenanes and knots. 

Jean-Pierre Sauvage is a CNRS director of research and is located at the Universite Louis Pasteur in Strasbourg, France. His current research interests include the development of models of the photosynthetic reaction centre using transition metals and porphyrins [5], topology (synthetic catenanes and knots) [6], and molecular machines [7]. 

Schalley, C.A, Reckien, W., Peyerimhoff, S., Vogtle, F. Theory and experiment in concert templated synthesis of amide rotaxanes, catenanes and knots, Chem. Eur. J. in press. 

The amide-based template synthesis of rotaxanes, catenanes and knots were first discovered by Vogtle and coworkers when they tried to synthesize macrocycle 3 [13], The cyclization to yield the tetralactam ring was carried out under high-dilution... 

A. Topological Stereochemistry Catenanes and Knots, the Topological Link... 

Scheme 1 illustrates the simplest structures of rotaxane, catenane, and knot besides polyrotaxane and polycatenane. From the fact that the main chain-type polyrotaxane at the left side is the only interlocked polymer synthesized so far among the three polymers shown at the bottom of the scheme, progress in synthesis of interlocked polymers appears to be sluggish judging from the level of activity in synthetic polymer chemistry in the world. 

A more accurate treatment requires to reduce the size of the system and to use model compounds. E.g. Schalley and coworkers [125, 126] carried out DFT calculations in order to gain insight into the details of the hydrogen bond patterns involved in the formation of mechanically interlocked species such as amide rotax-anes, catenanes, and knots. 

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