Conformational changes of DNA

Protein-DNA backbone interactions determine DNA conformation Conformational changes of DNA are... 

Schultz P, Olland S, Oudet P, Hancock R. Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy. Proc Natl Acad Sci USA 1996 93 5936-5940. 

Moreover, as will be shown below, electronic coupHngs are very sensitive to conformational changes of DNA fragments their magnitude can change... 

Fig. 26 Cartoon illustration of the temperature effect on conformational changes of DNA in solutions (up) and in gels (down). The green pendants represent cross-linker molecules named EGDE. Reproduced with permission from [110]...

A recent study has shown that two different kinds of conformational changes, helix-coil transition and the folding transition, mutually interfere with each other in a drastic manner (Mikhailenko et al., 2000). As the melting of the double stranded structure, or helix-coil transition, is an essential process in the genetic activity, further studies on the biological role of the conformational change of DNA are awaited. 

Minagawa, K., Matsuzawa, Y., Yoshikawa, K., Matsumoto, M. and Doi, M. (1991) Direct observation of the biphasic conformational change of DNA induced by cationic polymers. FEBS Lett., 295, 67-69. 

Wakizaka, A. and Okuhara, E. (1979) Immunochemical studies on the correlation between conformational changes of DNA caused by ultraviolet irradiation and manifestadon of andgeniciiy.y. Btochem. 86,1469-1478. 

The SANS data demonstrated that as a result of lipoplex formation, the SUVs were converted to multilamellar lipid-DNA complexes. This transition occurred via three stages. The first step, occurring on a millisecond timescale, was inaccessible to SANS as the smallest time slice used was 1 sec. This step was, however, observable by stopped-flow turbidity and fluorescence experiments. The next step, occurring on a timescale of seconds, which was observable by SANS, was found to correspond to the formation of an (unstable) intermediate with a locally cylindrical structure. The final step, occurring over minutes, involved the conversion of the unstable cylindrical intermediates to a multilamellar structure. As fluorescence measurements can only give information about the conformational changes of DNA, SANS measurements are necessary to probe the structure of the different intermediates that occur during the formation of the DNA-lipid complexes. No other technique lends itself to such studies. 

By itself, Cu (phen)2 is an efficient chemical tool to probe small conformational changes of DNA. Comparison of the digestion patterns... 

In order to confirm and study in situ the respective conformational changes of DNA in the adsorbed state, the SERS spectroscopy was applied later Native DNA exhibits some 30-40 normal solution Raman scattering bands in the spectral range of 200-1800 cm iss.ise) jj g more intense bands are caused by vibrations of the base residues adenine (A), guanine (G), cytosine (C) and thymine (T). 

The SERS spectrum of methylated DNA shows new Raman bands at 656 cm , 700 cm and 1360 cm" which correspond to characteristic vibrations of 7-MeGua residues in adsorbed methylated DNA (cf. Table 4). Furthermore, the decrease of the band at 1200 cm and the 13(K)cm" shoulder of the band centered at 1332 cm" in the SERS spectrum of native DNA upon methylation can be related to a conformational change of DNA at the location of modified nucleic base pairs 7-MeGua-cytosine. Thus, at a rather positively charged surface, the SERS spectra reveal substantial changes in the adsorption behaviour of methylated DNA. 

Tsoi, P. Y., and Yang, M. Surface plasmon resonance study of the molecular recognition between polymerase and DNA containing various mismatches and conformational changes of DNA-protein... 

The molecule with the charge distribution (73) can be considered as a model for a B-DNA hehx charges on the strands represent the phosphates and the cylinder charge corresponds to adsorbed cations, smeared on the DNA surface (for B-DNA, a 10 A, B 0.4 H [182]). Note that (74) could also be used for the description of electrostatically induced conformational changes of DNA, e.g., for the B- to Z-DNA transition at high salt concentrations [183]. Moreover, the exact theory of electrostatic interaction between two DNA duplexes predicts an attraction between them due to a correlated structure-driven zipper-like charge separation along the molecules [184]. 

PS. Spuhler, J. Knezevic, A. Yal9in, Q. Bao, E. Pringsheim, P. Drdge, et al.. Platform for in situ real-time measurement of protein-induced conformational changes of DNA, Proceedings of the National Academy of Sciences 107 (2010) 1397-1401. 

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