Binding site symmetry

 

Binding sites on nucleic acids have three kinds of asymmetry and symmetry: asymmetric - All sites on RNA and probably most if not all sites on DNA bound by a single polypeptide will be asymmetric. Example: RNA: splice sites; DNA: T7 RNA polymerase binding sites. Symmetric - Sites on DNA bound by a dimeric protein usually (there are exceptions!) Have a two-fold dyad axis of symmetry. This means that there is a line passing through the DNA, perpendicular to its long axis, about which a 180 degree rotation will bring the DNA helix phosphates back into register with their original positions. There are two places that the dyad axis can be set: odd symmetric - The axis is on a single base, so that the site contains an odd number of bases. Examples: gallery of 8 logos: lambda ci and cro and Lambda O. Even symmetric - The axis is between two bases, so that the site contains an even number of bases. Examples: gallery of 8 logos: 434 ci and cro, argr, CRP, trpr, FNR, lexa.

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