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 ...

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