Chiral helical groove

Weix DJ, Dreher SD, Katz TJ (2000) [5]HELOL phosphite a helically grooved senstn of remote chirality. J Am Chem Soc 122 10027... 

Fig. 7 Schematic view of the different approaches used to model the chiral interactions between DNA double helices, (a) DNA duplexes are viewed as clean cylinders with charged helical patterns of negative phosphates and positive adsorbed counterions. Reproduced with permission from [18], (b) Duplexes interact via steric interlocking of backbone and grooves and through electrostatic repulsion of the phosphate groups. Reproduced with permission from [14]...

DNA is an interesting supramolecular structure, as it provides different complexation sites for molecules. Planar and relatively small molecules intercalate between base pairs, whereas larger molecules can bind to the minor or major grooves of the DNA helix. Interaction can be rather specific due to the chirality of the helix [147,150]. In addition, the negatively charged phosphate backbone is able to anchor or bind cationic probes or quenchers. Most studies have been performed with calf thymus DNA in its native double helical form. 

Figure 6. Schematic drawings illustrating two RNA-RNA anchors. Both motifs introduce new chiralities. (Top) The single-stranded residues of a hairpin loop fonn Watson-Crick base pairs with an unpaired complementary sequence in another structural domain, thereby molding a pseudoknot. As in standard RNA helices, the base pairing occurs with antiparallel polarities of the strands. (Bottom) A -GNRA-tetraloop in a hairpin binds to the shallow groove of a helix belonging to another domain so that an A of the tetraloop interacts with either a G-C or an A-U pair and a G with only an A-U pair. The purines in the loop and in the helix are oriented with a parallel polarity.

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