Topology catenanes

The C fiscicuIata)sD h networitconsists of-5,000 minicircles of 2.5 kb and -25 maxicircles of 37 kb. Minidrcles in the network are relaxed and singly interlocked to each other forming a two dimensional DNA network. Maxicircles form independent topological catenanes, that are threaded into the minicircles network and are embedded in different panems within kDNA networks in the wious trypanosomatid species, to form network within a network . ... 

Singly and doubly interlocked [2]catenanes can exist as topological stereoisomers (see p. 144 for a discussion of diastereomers). Catenanes 35 and 36 are such stereoisomers and would be expected to have identical mass spectra. Analysis showed that 35 is more constrained and cannot readily accommodate an excess of energy during the mass spectrometry ionization process and, hence, breaks more easily. 

The template-directed preparation of cycloi is(paraquat-4,4 -biphenylene (a molecular square ) has been achieved the use of a macrocyclic hydroquinone-based polyether template incorporating an ester moiety in one polyether chain afforded a 1 1 mixture of two topologically stereoisomeric [3]catenanes <96CEJ877>. 

Some racemates (Figure 3.23) are more efficiently resolved on the bonded-type CSP than the coated-type CSP by using chloroform as a component of the eluent. On the bonded-type CSP of 24n, topologically interesting catenanes and molecular knots are successfully resolved using a hexane-chloroform-2-propanol mixture.185 The first direct HPLC resolution of the smallest chiral... 

Our definitions of the stereoisomeric center, line, and plane all stipulate the existence of bonds between the ligating element and its ligands. The exclusive use of these elements limits our analysis to classical stereochemistry and thus does not encompass the so-called topological isomerism (47) of interlocked rings—catenanes (48)—or of knots. As there is no bond between the rings of the catenanes we cannot expect to handle such compounds with a system based on connectedness. At the present stage of development, this limitation in scope... 

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. 

As stated above, simple catenanes were first obtained by a statistical approach. However, the successful syntheses of more complicated topological molecules would not have been possible without an enforcement of spatial orientation of reaction substrates called preorganization, introduced in Section 2.3. The latter effect can be achieved by... 

Out of many exciting recently obtained topologically distinct structures combined rotaxanes 41,400 [23], pretzel-molecule 35 [24a] and bis(pretzelane) 401 [24b], a topologically chiral [2]catenane [25] and an interestiig catenated... 

Another, more complicated topological structure represents a [2]catenane formed by two interlocked nanotube rings observed by Scanning Electron Microscope by Mattel and coworkers [35]. 

Besides their topology, rotaxanes and catenanes are also appealing systems for the construction of molecular machines because (i) the mechanical bond allows a large variety of mutual arrangements of the molecular components, while conferring stability to the system, (ii) the interlocked architecture limits the amplitude of the intercomponent motion in the three directions, (iii) the stability of a specific... 

So, when either replication fork encounters a functional Tus-Ter complex, it halts the other fork halts when it meets the first (arrested) fork. The final few hundred base pairs of DNA between these large protein complexes are then replicated (by an as yet unknown mechanism), completing two topologically interlinked (catenated) circular chromosomes (Fig. 25-17b). DNA circles linked in this way are known as catenanes. Separation of the catenated circles in E. coli requires topoi-somerase IV (a type II topoisomerase). The separated chromosomes then segregate into daughter cells at cell... 

Dr. L. Barash performed the Herculean labor of preparing the catenane, 3. Drs A.M. Trozzolo and H.L. Frisch were always willing to engage in thought-provoking conversation. More recently, discussion with Professors D.W. Sumners, S.G. Whittington, and J. Simon familiarized me with recent mathematical advances relevant to chemical topology. 

We can use this same approach to prove that other molecular knots and links are topologically chiral. For example, consider the molecular link illustrated in Figure 18. This catenane was synthesized by Nierengarten et al. [12]. For this molecule the set T(G) consists of many unlinks together with many copies of the (4,2)-torus link, illustrated as L in Figure 12. However we saw earlier that this unoriented link is topologically chiral. Therefore, the molecular (4,2)-torus link is topologically chiral as well. 

Another fascinating approach to catenanes via self-assembly involves metal-coordination which templates or directs the assembly of catenane frameworks. After brief discussions on the recent examples of metal-containing catenanes and related topologically interesting molecules (Sections 4.2.1-4.2.3), the focus will be on the self-assembly of Pd(II)-linked catenanes (Sections 4.2.4 and 4.2.5). 

For catenane formation from two separate rings, the most reasonable explanation involves dissociation of a ring, threading another ring on the thread, and reconnection of the ends of the thread (Scheme 2 a). However, careful mechanistic consideration of the rapid interconversion suggested a Mobius strip mechanism which involves molecular topology reminiscent of the well-known Mobius strip. 

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]. 

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