Biology 5 catenane

Catenanes are formed when two or more closed-circular DNAs are linked together to form a chain. Catenanes were first isolated in human mitochondrial DNA and have since been identified in a number of biological systems. These stmctures often occur as intermediates during the repHcation of circular DNA molecules. 

In recent years, with increasing recognition of the roles played by specific noncovalent interactions in biological systems and chemical processes, the science of noncovalent assemblies- often called supramolecular science- has aroused considerable interest [76], The remaining part of this article reviews some important studies made on rotaxane and catenane, two classic types of supramolecular structure. 

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. 

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 nonionic template strategy based on hydrogen bonds and to a certain extent on n-n interactions has made catenanes and rotaxanes readily available. The molecular recognition and self-organization process which is responsible for the formation of intertwined and interlocked structures is founded upon the same weak interactions that govern many biological processes. Amide-based catenanes and rotaxanes can thus serve as valuable models for complex molecular recognition patterns in nature. 

Are there any other possible uses for the construction of complex topological species One possible application is in the mass production of DNA polyhedral catenanes by biological means, such as the polymerase chain reaction (PCR) (Saiki et al. 1986) or by production in vivo. Figure 21 illustrates that semi-conservative replication (the mechanism used by DNA polymerases) cannot reproduce a stable branch. The DNA with different sequences in the two arms of the branch (cartooned as dashed and solid lines) leads to two heterologous duplex DNA molecules, rather than a second branched molecule. 

Peptide ligation strategies used so far have mainly been used for protein total synthesis and protein engineering purposes. The ability to prepare perfectly mono-disperse and relatively high molar mass peptides with precise control over the a-amino acid sequence could also afford unprecedented opportunities for the development of novel biologically-inspired supramolecular architectures and materials. As a final, recent, example, the preparation of a protein[2]catenane using NCL is shown in Figure 6.6.5 [34]. 

In contrast to modem industry, where technology utilizes the mechanical bond far more ubiquitously on the macroscale than on the nanoscale, Nature depends more vitally on mechanical interlocking at the molecular level. To be certain, a few mechanical bonds can be identified in Nature s macroscale designs, such as the rotaxane-like mammalian spine (Fig. 3a) or a turtle s shell - a suitane in the molecular world [33] (Fig. 3b). But, mechanical bonds are being made and broken incessantly within the mesoscopic world of cells. DNA is foremost among the players in biological MIMs. DNA catenanes [34] and knots [35] are intermediate... 

Another area of NEMS that is receiving tremendous attention is the mimicry of biological systems, aptly referred to as biomimetics. For instance, in the development of linear molecular muscles that undergo contraction and extension movements. Initial work in this field utilized transition metal complexes containing rotaxanes and catenanes, due to the nondestructive redox processes occurring on the metal centers.Though these complexes were actuated by a chemical reaction, the movement was in a noncoherent manner. In order to better mimic skeletal muscle movement, one has to look at the mode of motion within the most efficient molecular machines - in our human bodies. 

As noted in a previous article in this Encyclopedia, self-assembly processes often generate compoimds and materials displaying hierarchies of stmcture. also known as higher stmctures. Self-assembled catenanes display similar stmctural hierarchies, although these are dififerent to the hierarchies common in biology and chemistry. 

Biological Models and Their Characteristics, p. 701 Catenanes and Other Interlocked Molecules, p. 206 Classification and Nomenclature of Supramolecular Compounds, p. 261... 

Because of their importance in naturally occurring biological systans and their aesthetic appeal, the synthesis of these topological structures also became the focus of interest of chemists. After the first synthesis of a [2]catenane (Hopf or 2 link) and subsequent relevant works based on the Mbbius ring concept, it was realized early that the step-by-step chemical approaches yielded only poor quantities of the expected knots and an alternative approach was necessary. 

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