Linker Scanning Mutations

To locate promoter proximal elements in a short stretch of DNA up to around 100 base pair upstream of the TATA box, an experiment involving linker-scanning mutations can be used. A region of DNA that sequences a reporter gene is cloned several times. The clones are altered by addition of scrambled nucleotide sequences known as linker scanning mutations that are introduced from one end of the region of the sequence to the other. This is only done in a short stretch of the DNA to pinpoint the exact region of the promoter proximal elements. Then when the sequence is placed back into the cell via a plasmid vector, the rate of transcription (how much mRNA is produced) is measured by the amount of proliferation of the reporter gene. If transcription occurs, the region does not contain a promoter proximal element. If transcription has stopped or is reduced, the region of the linker mutation is that of a promoter proximal element, and the bases can then be identified.