Chapter

Crystallography in the study of protein–DNA interaction

Maninder K. Sohi and Ivan Laponogov

in Macromolecular Crystallography

Published in print August 2007 | ISBN: 9780198520979
Published online September 2007 | e-ISBN: 9780191706295 | DOI: http://dx.doi.org/10.1093/acprof:oso/9780198520979.003.0015
 Crystallography in the study of protein–DNA interaction

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In the living cell, protein-DNA interactions take place during genetic processes such as chromatin organization, recombination, replication, transcription, and DNA repair. In order to fully understand the mechanism of these processes, study of protein-DNA interactions at atomic level is required. Despite the wealth of knowledge and attempts of several investigators to classify protein-DNA complexes on the basis of structural analysis of well over 200 protein-DNA complexes, the prediction and modelling based on three-dimensional structure or amino acid sequence of a protein and nucleotide sequence of DNA is challenging. X-ray crystallography is the most powerful technique used for structural studies and the development of technology for the production and purification of large quantities of proteins and DNA is vital to its success. Advances in oligonucleotide synthesis have not only provided ease of synthesis of large quantities of pure DNA but also of any required DNA sequence. This has resulted in the crystallization and structure determination of a vast number of DNA oligonucleotides and protein-DNA complexes. Since 1994 there has been a dramatic increase in the number of the protein-DNA complex structures solved annually. The first and most difficult step in the X-ray crystallographic study is the growth of well-diffracting crystals of the protein-DNA complex under investigation. This chapter describes methods employed to purify proteins and DNA for cocrystallization, procedures for crystallization of protein-DNA, and characterization of cocrystals.

Keywords: protein-DNA interactions; oligonucleotide; X-ray crystallography; protein purification; cocrystals

Chapter.  11855 words.  Illustrated.

Subjects: Biochemistry

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