Describe an experiment to determine the region of RNA that a

Describe an experiment to determine the region of RNA that a certain protein would bind to assuming the following are available: a. the purified protein, b. a long piece of purified RNA with a recognizable region by the protein c. RNAse d. Gel-run reagents (Assume image is the result of the gel that was run).

Solution

Gel shift assay or gel retardation assay used to recognise the protein binding portion of RNA or proteins and RNA interactions. To proveknow this, take 3 appendrof tubes and marked as 1, 2 & 3. In tube 1, add RNA and RNA ase, in tube 2 add proteins and RNA ase. Where as in tube 3, add Protein, RNA and RNAase. Then all threeyour tubes subjected to incubation. After incubation, take outa each sampleamino and. Load in high % agarose gel. In first tube well, no bands appear due to degradation of RNA by RNA ase. In the second tube, single band, which is far from wells appear. Where as in 3 rd tube well, less distance migrated, PROTEIN AND RNA Complex band appear. In this way we can findout RNA Protein interactions.

This method is also called Foot printing techniques