<P> Designing DNA - binding proteins that have a specified DNA - binding site has been an important goal for biotechnology . Zinc finger proteins have been designed to bind to specific DNA sequences and this is the basis of zinc finger nucleases . Recently 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 . </P> <P> 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: </P> <Ul> <Li> Electrophoretic mobility shift assay is a widespread technique to identify protein--DNA interactions . </Li> <Li> DNase footprinting assay can be used to identify the specific site of binding of a protein to DNA . </Li> <Li> 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 . </Li> <Li> Yeast One - hybrid System (Y1H) is used to identify which protein binds to a particular DNA fragment . </Li> <Li> Bacterial one - hybrid system (B1H) is used to identify which protein binds to a particular DNA fragment . </Li> <Li> Structure determination using X-ray crystallography has been used to give a highly detailed atomic view of protein--DNA interactions . </Li> </Ul> <Li> Electrophoretic mobility shift assay is a widespread technique to identify protein--DNA interactions . </Li>

Proteins always interact with dna in a sequence-specific manner