DNA knots

In a recent paper, Krasnow and co-workers (120) applied a Rec A protein coating to DNA knots and catenanes to enhance visualization of the helical DNA segments and, in particular, to determine the absolute handedness of the knots. The Rec A protein is known to bind cooperatively to duplex DNA, forming a stiffened complex about 100 A in diameter in the presence of ATPase (121). 

Methods have been devised for synthesis of even very complex DNA knots.185 186 Let s look briefly at the topology of knots. The three simple knots shown here have a chirality beyond that of the nucleotide... 

Figure 10.86 Electron microscope image of a loose DNA knot (reproduced from [99] with per mission from AAAS).

Wasserman, S. A., Dungan, J. M., Cozzarelli, N. R., Discovery of a predicted DNA knot substantiates a model for site-specific recombination. Science 1985, 229, 171-174. 

Careful design was used by Seeman to prepare complementary DNA strands that self assemble into a cube with 20 nucleotide pairs along each edge. Other derivatives include nylon DNA , through the synthesis of peptide nucleic acids (PNA), and polyethylene glycol derivatized DNA. Figure 8.1 illustrates the DNA knots that can be prepared using these techniques. 

Almost 20 years after theoretical estimations of the probability of DNA knotting were first published (Vologodskii et al., 1974 [76] Frank-Kamenetskii et al., 1975 [21]), quantitative experimental data have been reported (Rybenkov et al., 1993 [61] Shaw and Wang, 1993 [65]) which fully agreed with the theory. In these experiments, the equilibrium fraction of knotted DNA molecules at various ionic conditions was quantitatively measured while molecules carrying "cohesive" ends randomly closed, in the absence of any proteins. Comparing the fraction with theoretical predictions of Klenin et al. (1988) [36],... 

Arsuaga J, Vazquez M, Trigueros S, Sumncas D, Roca J (2002) Knotting probability of DNA molecules confined in restricted volumes DNA knotting in phage capsids. Proc Natl Acad Sci 99 5373-5377... 

Fig. 5 Seeman .s synthesis of DNA knots. (From Du. S.M. Stollar, B.D. Seeman, N.C. A synthetic DNA molecule in three knotted topologies. J. Am. Chem. Soc. 1995. 117. 1194-1200.)...

We want to note in passing that this creates a situation somewhat unprecedented in the whole of history of science researchers claim a rather complete understanding of DNA knotting, based on the agreement between simulations and experiments, but we have no theory. Will it stay that way, or somebody will eventually be able to crack a theory — remains to be seen. 

Dean, F. B., Stasiak, A., Roller, T., and Cozzarelli, N. R., 1985. Duplex DNA knots produced by Escherichia coli topoisomerase I. Structure and requirements for formation, /. Biol. Chem., 260(8) 4975 983. 

Dobrowolski JCz (2003) DNA knots and links (wgzly i sploty DNA). Polimery 48 3-15... 

The winding of DNA in higher-order forms such as knots and catenanes was also shown in electron micrographs of DNA molecules coated with Escherichia coli RecA protdn. It was found that DNA topoisomerase I of E. coli generates an equal mixture of (+) and (-) duplex DNA knots, and that one product was a catenane. It was later shown that RecQ helicase and topoisomerase III (Topo III) of E. coli together mediate a potent DNA strand passage activity that can catenate covalendy dosed DNA." The structure of the catenated DNA spedes formed by... 

Figure 19 Synthesis of DNA knots, (a) Positive and negative nodes generated from Z- and B-DNAs, respectively ...

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