Question

Molecular Biology

Can you tell me what the difference between the functions of emsa/dna footprinting and chip-seq/chip-chip

Answer 1

EMSA vs DNA footprinting

EMSA (electrphoretic mobility shift assay) and DNA foot printing both assay are used to investigate sequence specific interaction of protein and DNA. However in EMSA protein DNA interaction is determined based on their charge, size and shape on agarose or poly acrylamide gel electrophoresis. While DNA foot printing is performed entirely in solution. It is possible to investigate interaction between DNA and protein in vivo and in vitro (inside cell and out side cell) in case of DNA foot printing but not possible in EMSA.

EMSA has one advantage, the specificity of EMSA is very high, if the small numbers of probe will bind to the complex, it will be easily observed in gel. Because unbounded probes are migrate faster in gel as compared to bound probe.So we can investigate even a smaller quantity of protein (bounded with DNA). While in DNA footprinting, higher binding affinity of probe to complex (DNA-protein complex) is primary requirement because it will detect bound as well as unbound probes as same. Hence if more probes are bind, more will be the accuracy.

Chip/seq vs Chip/chip

Chromatin immunoprecipitation followed by high through put sequencing is termed as Chip/seq. Whereas Chromatin immunoprecipitation followed by microarray hybridization (on glass chip) is termed as Chip/chip.

Chip on chip is used to investigate interaction between protein and DNA on the microarray platform. But functionally Chip on chip is limited to the smaller genomic region or used for organism with smaller genome. The efficiency of result is also poor as it is depends on immobalized probe, non specific bind will result in false positive result. On the other hand Chip-Seq is high thoughput and most advance technique. It investigates DNA protein interaction along with sequencing of DNA. It has higher genomic courage and wide range. It is more specific than Chip on Chip. chip-seq is used for the investigation of different protein factor and their targetted DNA sites along with the sequence identification of that particular DNA wich is not possible in Chip on chip.