Minor groove binding ligands

Nguyen-Hackley DH, et al. Allosteric inhihition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands. Biochemistry 2004 43 3880-3890. 

Mote, J., Jr., Ghanouni, P., and Reines, D.A. (1994) DNA minor groove-binding ligand both potentiates and arrests transcription by RNA polymerase II. Elongation factor SII enables readthrough at arrest sites. /. Mol. Biol, 236, 725-737. 

There are also G4 ligands that bind at the grooves of quadruplexes, with structures similar to those for duplex DNA minor groove binding ligands [76, 77]. 

Jain AK, Bhattacharya S (2011) Interaction of G-quadruplexes with nonintercalating duplex-DNA minor groove binding ligands. Bioconjugate Chem 22 2355-2368... 

Figure 4 Examples of DNA and IWA binding sites, (a) A complex formed between DNA and a minor groove binding ligand the bis(benzimidazole)-DNA complex (PDB ID No. 109D) (b) a complex formed between DNA and a bis(intercalator) (the triostin-DNA complex (PDB ID No. ODAC) (c) Rev responsive element (RRE) RNA (d) TAR RNA ...

Misra, V. K., Sharp, K. A, Friedman, R. A., and Honig, B. (1994b). Salt effects on ligand-DNA binding. Minor groove binding antibiotics./. Mol. Biol. 238, 245-263. 

Figure 2 (A) ICD of a DNA intercalator calculated as a function of the transition moment in the plane of the intercalation pocket and centred on the helix axis, y is the angle between the transition moment and the DNA dyad axis. Reproduced with permission from Lyng, Hard and Norden (1987) Biopolymer 2Q 1327. (B) definition of geometrical parameters of a DNA-ligand system with r=0,a = 90° and p = 0°, then y corresponds to the orientation of an intercalator transition moment (see top figure). Typical minor groove binding geometry parameters are r= 7 A, a = 45°, = 0° and y = 0.

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