Lariat structure

In group II introns the reaction pattern is similar except for the nucleophile in the first step, which in this case is the 2 -hydroxyl group of an A residue within the intron (Fig. 26-15). A branched lariat structure is formed as an intermediate. 

The 2 OH of a specific adenosine in the intron acts as a nucleophile, attacking the 5 splice site to form a lariat structure. 

Adenosine in the lariat structure has three phosphodiester bonds. 

Ruskin, B., Krainer, A. R., Maniatis, T., and Green, M. R. (1984). Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell 38, 317—331. 

Figure 2 Details of two successive trans-esterification reactions. In the first step, the 2 -OH group of the branch point adenosine nucleophilically attacks the phosphate at the junction of the S exon and intron (S splice site), resulting in the formation of a new S -2 phosphodiester bond between the first nucleotide of the intron and the branch point adenosine (lariat structure formation) and breakage of an old 3 -S phosphodiester bond between the last nucleotide of the S exon and the first nucleotide of the intron (cut-off S exon formation). In the second step, the 3 -OH group of the cut-off S exon nucleophilically attacks the phosphate at the junction of the intron and 3 exon, ligating the two exons (mRNA formation) and releasing the lariat intron. The phosphates at the S splice site (red) and at the 3 splice site (green) and the branch point adenosine and its 2 -OH group are pictured. The lines represent the intron and boxes depict exons (El and E2).

Domdey H, Apostol B, Lin RJ, Newman A, Brody E, Abelson J. Lariat structures are in vivo intermediates in yeast pre-mRNA splicing. Cell 1984 39 611-621. 

Small nuclear RNAs complexed with protein (snRNPs) [e.g., U1 and U2] are involved in the cleavage and splicing process. A lariat structure may be generated during the splicing reaction (see Figure 3-20). 

As RNA synthesis has become routine, the synthesis of more complex oligomers has been investigated. One particular area of interest in RNA synthesis is the formation of cyclic and lariat RNA. The use of a protected universal building block containing the selectively activated 2 -H-phosphonate and 3 -chlorophenylphosphate has been used to prepare branched oligoribonucleotides and lariat structures."" The synthesis of small to medium cyclic RNA can be carried out, providing that the linear precursor attached to the support has a... 

Five different snRNPs interact via base pairing with one another and with pre-mRNA to form the spliceosome (see Figure 12-9). This very large ribonucleoprotein complex catalyzes two transesterification reactions that join two exons and remove the intron as a lariat structure, which is subsequently degraded (see Figure 12-7). 

This reaction is chemically similar to group II splicing in that an adenylate residue in the intron acts as a nucleophile to attack the 50 exon. This results in the formation of a lariat structure in the first step, which is followed by a second transesterification step that joins the 50 and 30 exons and releases the intron (Fig. 25.5). 

Figure 11.36 shows how splicing occurs. The G that is always present on the 5 end of the intron loops back in close contact with the invariant A from the branch point. The 2 hydroxyl of the A performs a nucleophilic attack on the phosphodiester backbone at the 5 splice site, forming a lariat structure and releasing exon 1. The AG at the 3 end of the exon then does the same to the G at the 3 splice site, fusing the two exons. These lariat structures can be seen with an electron microscope, although the structure is inherently unstable and soon is linearized. 

Figure 11.23 The fomation of a lariat in group II intron splicing The 5 -phosphate at the scissile bond of Nj is transferred to 2 -hydroxyl of N, (the lariat A residue) to form a lariat structure in the initial step of splicing reaction mediated by group II intron and spliceosome.

The formation of a 2, 5 -phosphodiester bond between an intron A residue and its 5 -terminal phosphate group forms a lariat structure (Figure 11.23) and release the 5 exon. 

A 2-5A analogue which is deoxygenated at C-3 in both end units has been synthesised (see also Vol.21, p.215),176 and 2 -5 -linked oligoadenylates with a nucleotide branch at the 3 -position have also been reported. 177 Four different strategies for synthesis of related branched-chain ( lariat ) structures have been reviewed. 178... 

Following these findings, chemical routes to such lariat structures have been explored (128-136), recently progressing to branched nona- and decanucleotides as well as cyclic lariat structures in work reported from the laboratory of J. B. Chattopadhyaya (137) (Fig. 6). Various studies, mainly of a spectroscopic nature, have been done to establish the correct structure and investigate the conformation of these compounds (138-141) in order to elucidate effects operational in the splicing mechanism (131). 

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