Exon trapping

Overview of exon trapping. An RNA is transcribed from the plasmid shown which contains an intron (blue line) flanked by two exons (yellow boxes). Splicing removes the intron. If there is any additional DNA sequence in the plasmid that contains another exon (orange box) with flanking sequences (orange line), this can be "captured" and identified in the later product (hence "trapping")

Exon trapping is a method to detect the information-carrying parts of DNA, the exons , in the laboratory and to differentiate them from the non- information- carrying parts, the introns .

The algorithmic prediction of exons on the basis of data obtained by DNA sequencing turns out to be extremely difficult, since the boundaries of the exons and introns - the so-called splice sites - are strongly degenerated. In addition, other cis elements , so-called splicing enhancers or splicing silencers , influence the processing of the primary transcripts (see also splicing ).

Because of these problems, the method of exon trapping was developed in order to be able to detect exons experimentally.

The basis for this is a plasmid that, after being introduced into eukaryotic cells (see transfection ) , leads to the expression of an RNA . This RNA itself usually contains an intron, which the cell then removes in the course of splicing. In order to find an exon (or a part of it), DNA fragments can now be cloned randomly into this intron of the plasmid . If there is an exon (or parts of it) in this DNA fragment, the cellular machinery recognizes this and takes it into account during splicing. This leads to the fact that the exon can finally be found in the finished product and sequenced from it (see adjacent figure). Disadvantages: On the one hand, the cloning of the DNA fragments in the vector and the subsequent analysis represent a not inconsiderable amount of work. On the other hand, exons (or parts of them) are torn out of their natural context, which can lead to important elements (such as splicing enhancers) being lost and exons not always being reliably recognized.

There are a number of modifications to these exon trapping vectors, but the principle is based on the theory described above. Due to the extensive cDNA and EST databases that have now emerged, exon trapping is becoming increasingly less important.