ARCIMBOLDO on DNA

The crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein-DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods.
The potential of the structure-solution program ARCIMBOLDO for the solution of protein-DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE.
Whereas for typical proteins main-chain helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments.
Here you can find instructions on how to solve protein-DNA complexes with ARCIMBOLDO_BORGES and how to create a library for one of the protein-DNA complexes shown on the right, or alternatively download a prepared library.

Zinc-finger protein-DNA complex

Zipper-type protein-DNA complex

HTH-type protein-DNA complex