DNA flexibility

Kdnig, P., Richmond, T.J. The x-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility. ]. Mol. Biol. 233 139-154, 1993. 

Taylor, W.H. and Hagerman, P.J. (1990) Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure I.NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212, 363-376. 

D. Shore, J. Langowski, and R. L. Baldwin. DNA flexibility studied by covalent closure of short DNA fragments into circles. Proc. Natl. Acad. Sci. USA, 78 4833 1837, 1981. 

A comparison of the flexibility properties of adenine tracts (found in MLP) and inosine tracts (found in I) indicated that the former are more rigid than the latter, making I a better substrate for TBP than MLP. Nevertheless, as discussed in the previous section, MLP coordinates more water molecules in the minor groove than I, compensating in excess the difference in rigidity of the purine tracts. In this particular comparison, hydration would appear to be a more important selectivity determinant than DNA flexibility. 

Grove, A., Galeone, A., Mayol, L. Geiduschek, E. P. (1996a). Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J. Mol. Biol. 206, 120-125. 

Knegtel, R. M. A., Boelens, R. Kaptein, R. (1994b). Monte Carlo docking of protein-DNA complexes incorporation of DNA flexibility and experimental data. Prot. Eng. 7, 761-767. 

CA runs increase DNA flexibility in the complex of lambda Cro protein with the OR3 site. Biochemistry, 32, 4121-4127. 

Whether the flexibility of DNA per se is important in biological function is harder to assess. Nonetheless, hydrodynamic measurements have suggested that damage increases DNA flexibility, with implications for recognition and... 

In modern experiments one is now able to place selectively spin labels in most any region of a biomolecule. This ability is stimulating an ever increasing usage of spin label EPR spectroscopy. In addition labeling of proteins and peptides, experiments have demonstrated that DNA may be labeled without perturbation of the double-helical structure. Analysis of DNA flexibility may provide important information toward the understanding of protein-DNA and drug-DNA interactions. 

Okonogi TM, Alley SC, Harwood EA, Hopkins PB, Robinson BH (2002) Phosphate backbone neutralization increases duplex DNA flexibility a model for protein binding. Proc Natl Acad Sci USA 99(7) 4156-4160... 

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