Difference between revisions of "Part:BBa K1332005"

Revision as of 02:03, 11 October 2014

The 3' side of the intron(+exon fragment) from td gene of T4 phage

This part is a part of the mRNA circularization device (5’ side). The combination of this part, a promoter (lacI regulated) (BBa_R0010) and RBS (BBa_B0034) is the mRNA circularization device (5’ side) (BBa_K1332008).

The mechanism of mRNA circularization

This part is a part of group 1 intron. The group 1 intron is capable of self-splicing. The mRNA circularization device is based on the mechanism. We explain the circularization mechanism of groupⅠintron with td gene of T4 phage as an example. Td gene consists of an upstream exon, an upstream intron, an ORF, a downstream intron and a downstream exon. As the first step, a nucleophilic attack by a guanosine separates the upstream exon from the upstream intron and then the guanosine bond to the 5’ end of the upstream intron. As the second step, the downstream exon is separated from the downstream intron by a nucleophilic attack. The nucleophilic attack is taken place by a hydroxy group at the 3’ end of the upstream exon.(Figure 1)

Figure 1. Self-splicing in T4 phage: the first and second step (Blue: intron, Orange: exon)

As the third step, the upstream intron bond to the downstream intron by an attack on an adenine of the upstream intron. The attack is taken place by a hydroxyl group of an end of the downstream intron. And then a circular intron is formed.(Figure 2)

Figure 2. Self-splicing in T4 phage: the third step (Blue: intron, Orange: exon)

This part is involved in the second step of the mechanism of mRNA circularization.
The method that is based on the circularization mechanism is the PIE method. The PIE method stands for the Permuted Intron-Exon Method. The PIE method is a method to circularize an exon with permuting the exons and introns.(Figure 3)



Figure 3. The mechanism of the PIE method (Blue: intron, Orange: exon)

Sequence and Features