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Protein–Oligonucleotide Interactions

Peptides and Proteins

  1. Odd Stokke Gabrielsen,
  2. Vilborg Matre,
  3. Stine Bergholtz

Published Online: 15 SEP 2006

DOI: 10.1002/9780470027318.a1628

Encyclopedia of Analytical Chemistry

Encyclopedia of Analytical Chemistry

How to Cite

Gabrielsen, O. S., Matre, V. and Bergholtz, S. 2006. Protein–Oligonucleotide Interactions. Encyclopedia of Analytical Chemistry. .

Author Information

  1. University of Oslo, Department of Biochemistry, Norway

Publication History

  1. Published Online: 15 SEP 2006


The specific binding of a protein to a nucleic acid is a first step in several central processes in a living cell. Sequence-specific protein–DNA interactions are crucial for the functional read-out of genetic information. Sequence recognition is the result of a concerted action of many weak chemical interactions of different types between the protein and its DNA target, including nonspecific electrostatic interactions, hydrogen bonding and van der Waals contacts. The precise complementarity of shape between the two macromolecules facilitates specific chemical recognition to be established. The electrophoretic mobility shift assay (EMSA) and several variants of footprinting are simple electrophoretic methods developed to study protein–DNA interactions. Because the specificity is determined by the nucleic acid sequence, the same methods can be exploited for a wide range of proteins simply by changing the sequence of the nucleic acid. EMSA detects sequence-specific DNA-binding activity in a protein sample as a separate migrating band in a nondenaturating gel. A footprinting method provides more detailed information on the precise location of a bound protein along the DNA fragment through the removal of specific bands in a pattern of cleaved fragments separated by electrophoresis. Both methods are highly sensitive due to the use of radioactively labeled oligonucleotides and can be performed with protein samples of low purity. When combined these methods are capable of providing a picture of the protein–DNA complex with a great deal of molecular detail, surpassed only by the more demanding methods of crystallography and nuclear magnetic resonance (NMR).