Protein–DNA interactions

Protein–DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological
function of DNA, usually the expression of a gene. Among the proteins that bind to DNA are transcription
factors that activate or repress gene expression by binding to DNA motifs and histones that form part of
the structure of DNA and bind to it less specifically. Also proteins that repair DNA such as uracil-DNA
glycosylase interact closely with it.

In general, proteins bind to DNA in the major groove; however, there are exceptions. Protein–DNA
interactions are of mainly two types:

1. Specific interaction.
2. Non-specific interaction.

Single-molecule experiments shows that DNA binding proteins undergo of rapid rebinding in order to bind in
correct orientation for recognizing the target site.

Designing DNA-binding proteins that have a specified DNA-binding site has been an important goal. Zinc
finger proteins have been designed to bind to specific DNA sequences and this is the basis of zinc finger
nucleases. Transcription activator-like effector nucleases (TALENs) have been created which are based on
natural proteins secreted by Xanthomonas bacteria via their type III secretion system when they infect
various plant species.

There are many in vitro and in vivo techniques which are useful in detecting DNA-Protein Interactions. The
following lists some methods currently in use:

1. Electrophoretic mobility shift assay is a widespread technique to identify protein–DNA interactions.

2. DNase footprinting assay can be used to identify the specific site of binding of a protein to DNA.
3. Chromatin immunoprecipitation is used to identify the sequence of the DNA fragments which bind to
a known transcription factor. This technique when combined with high throughput sequencing is
known as ChIP-Seq and when combined with microarrays it is known as ChIP-chip.
4. Yeast One-hybrid System (Y1H) is used to identify which protein binds to a particular DNA fragment.
5. Bacterial one-hybrid system (B1H) is used to identify which protein binds to a particular DNA
fragment.
6. Structure determination using X-ray crystallography has been used to give a highly detailed atomic
view of protein–DNA interactions.

The protein–DNA interactions can be modulated using stimuli like ionic strength of the buffer, macromolecular
crowding, temperature, pH and electric field. This can lead to reversible dissociation/association of the
protein–DNA complex.