DNA grooves binding

Armitage BA (2005) Cyanine dye-DNA groove binding, and aggregation. Top Curr Chem 253 55-76... 

The dynamics of intercalation of small molecules with DNA, groove binding and binding to specific sites, such as base pair mismatches have been studied by stopped-flow,23,80 108 temperature jump experiments,26,27,94 109 120 surface plasmon resonance,121 129 NMR,86,130 135 flash photolysis,136 138 and fluorescence correlation spectroscopy.64 The application of the various techniques to study the binding dynamics of small molecules will be analyzed for specific examples of each type of binding. 

Figure 15.31 Synthesis of DNA-groove binding lipids (i) dodecyl or octadecyl isocyanate (1.5 eq), DIEA (excess), DMF, 50 °C, 18 hours, 41% yield.

Binding of Small Molecules to DNA - Groove Binding and Intercalation... 

W. Wierenga "DNA-Minor Groove Binding Anticancer Agents" in Cytotoxic Mnticancer Drugs Models and Conceptsfor Drug Discovey and Development, Kluwer Academic PubHshers, Boston, Mass., 1992, p. 105. 

Figure 8.22 The lac repressor molecule is a V-shaped tetramer in which each arm is a dimer containing a DNA-hinding site. The helix-tum-helix motifs (red) of each dimer bind in two successive major grooves and the hinge helices (purple) bind adjacent to each other in the minor groove between the two major groove binding sites. The four subunits of the tetramer are held together by the four C-terminal helices (yellow) which form a four helix bundle. The bound DNA fragments are bent. (Adapted from M. Lewis et al., Science 271 1247-1254, 1996.)...

Some of the procaryotic DNA-binding proteins are activated by the binding of an allosteric effector molecule. This event changes the conformation of the dimeric protein, causing the helix-tum-helix motifs to move so that they are 34 A apart and able to bind to the major groove. The dimeric repressor for purine biosynthesis, PurR, induces a sharp bend in DNA upon binding caused by insertion of a helices in the minor groove between the two... 

Schumacher, M.A., et al. Crystal structure of Lac 1 member, PurR, bound to DNA minor groove binding by a helices. Science 266 763-770, 1994. 

Some purely major groove-binding TFs, such as the basic-region leucine zipper (bZIP) protein GCN4, can co-occupy the DNA helix in the presence of polyamides [72]. Modified polyamides with an attached Arg-Pro-Arg tripeptide can interfere with major groove-binding proteins by disrupting key phosphate contacts, distort-... 

B. Dervan, and J.M. Gotteseeld. Importance of minor groove binding zinc fingers within the transcription factor lllA-DNA complex./. Mol. Biol. 1997, 274, 439-445. 

Electrostatic binding Groove binding Intercalative binding Fig. 5 Schematic representation of various binding modes of small molecules to DNA... 

Karlsson, H.J., Eriksson, M., Perzon, E., Akerman, B., Lincoln, P., and Westman, G. (2003) Groove-binding unsymmetrical cyanine dyes for staining of DNA Syntheses and characterization of the DNA-bind-ing. Nucleic Acids Res. 31(21), 6227-6234. 

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