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Crystallization of Protein–DNA Complexes

  1. Danaya Pakotiprapha,
  2. David Jeruzalmi

Published Online: 15 DEC 2009

DOI: 10.1002/9780470015902.a0002720.pub2



How to Cite

Pakotiprapha, D. and Jeruzalmi, D. 2009. Crystallization of Protein–DNA Complexes. eLS. .

Author Information

  1. Harvard University, Cambridge, MA, USA

Publication History

  1. Published Online: 15 DEC 2009

This is not the most recent version of the article. View current version (14 NOV 2014)


Determination of atomic resolution structures of protein–deoxyribonucleic acid (DNA) complexes using X-ray crystallography requires preparation of high-quality crystalline specimens. The preparation of such samples remains an empirical endeavour, more art than science. Nonetheless, decades of experience have yielded a large body of practical strategies and techniques towards this end. Such efforts with protein–DNA complexes enjoy special advantages, but also involve control of a larger set of variables. High purity, chemical and conformational, preparations of both macromolecules are important. Crystallogenesis of protein–DNA complexes is favoured by careful choice of the sequence and the terminal bases and/or base pairs of the DNA target. Modern crystallization screens, which encapsulate the accumulated wisdom of prior investigations, serve as an excellent starting point for experimentation.

Key Concepts

  • An atomic level analysis of a macromolecule by X-ray crystallography requires preparation of high-quality crystals of the entity of interest.

  • Preparation of crystalline specimens requires highly concentrated solutions of the molecules of interest. Success is favoured when high chemical and conformational purity has been achieved.

  • Extensive experience in preparation of protein crystals can be applied to growth of protein–DNA crystals. Additionally, the length, composition and identity of the termini of the DNA molecule play significant roles in crystallization.

  • Initial crystallization trials are set up using a concentrated stock of protein–DNA complex of interest with pre-made formulations that sparsely sample crystallization space. Precipitation and crystal formation under these conditions are used to direct efforts for further crystallization experiments. The experiments are repeated until crystals suitable for X-ray diffraction are obtained.


  • crystallization;
  • protein–DNA complex;
  • X-ray crystallography