DNA tertiary structure

Angelov, D., Vitolo, J.M., Mutskov, V., Dimitrov, S., and Hayes, J.J. (2001) Preferential interaction of the core histone tail domains with linker DNA. Proc. Natl. Acad. Sci. USA 98, 6599-6604. Tobias, I., Coleman, B.D., and Olson, W. (1994) The dependence of DNA tertiary structure on end conditions theory and implications for topological transitions. J. Chem. Phys. 101, 10990-10996. Coleman, B.D., Tobias, I., and Swigon, D. (1995) Theory of the influence of end conditions on selfcontact in DNA loops. J. Chem. Phys. 103, 9101-9109. 

Fig. 1. The three structural levels of DNA-based Immunomodulatory sequence (DIMS). G-rich motifs are shown in blacK, sequences containing unmethylated CpG motifs shown in grey (corresponding to the color of motif background in Table 1) thin grey/mes indicate hydrogen bonds formed by Watson-Crick nucleotide pairs (DNA secondary structure level) or by Floogsteen hydrogen bonding (DNA tertiary structure level).

Reactions of nitrenium ions with DNA. Most of what is known about their reactions with DNA bases is derived from studies with monomeric bases. Some work with DNA oligomers has been reported, but tittle is known of the effects of DNA tertiary structure on these reactions. 

That DNA would bend on itself and become super-coiled in tightly packaged cellular DNA would seem logical, then, and perhaps even trivial, were it not for one additional fact many circular DNA molecules remain highly supercoiled even after they are extracted and purified, freed from protein and other cellular components. This indicates that supercoiling is an intrinsic property of DNA tertiary structure. It occurs in all cellular DNAs and is highly regulated by each cell. 

Pure DNA folds randomly in solution depending on its natural stiffness and the tendency of some sequences to produce bends. B-DNA is quite flexible and a sequence of 200 bp can readily flex through 90°. Stable DNA bends are a common feature of DNA bound to proteins and, in general, when complexed with proteins, DNA takes up specific folded structures which are essential to its function. Examples include the folding of DNA in the nucleosome (Chapter 5) and its interaction with recombination enzymes (Chapter 23). Also, DNA tertiary structure may be important in the control of transcription (Chapter 29). The folding of DNA in chromosomes is a remarkable feat and is discussed further in Chapter 5. 

DNA supercoiling provides conformational potential energy for DNA tertiary structure formation such as the development of DNA cruciform structures (Figure 1.77). Supercoiling also leads to the creation of DNA triple helix (DNA triplex) structures, which form when an oligodeoxynucleotide chain, with an appropriately complementary deoxynucleotide residue... 

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