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Publication Abstract from PubMed

Influenza A is an RNA virus with a genome of eight negative sense segments. Segment 7 mRNA contains a 3' splice site for alternative splicing to code for essential M2 protein. On the basis of sequence alignment and chemical mapping experiments, the secondary structure surrounding the 3' splice site has an internal loop, adenine bulge, and hairpin loop when it is in the hairpin conformation that exposes the 3' splice site. We report structural features of a 3D model of the hairpin derived from NMR spectra and simulated annealing with restrained molecular dynamics. The internal loop containing the 3' splice site has a dynamic guanosine and a stable imino (cis Watson-Crick/Watson-Crick) GA pair. The adenine bulge also appears to be dynamic with the A either stacked in the stem or forming a base triple with a Watson-Crick GC pair. The hairpin loop is a GAAA tetraloop closed by an AC pair.

Structural features of a 3' splice site in influenza A.,Chen JL, Kennedy SD, Turner DH Biochemistry. 2015 Apr 24. PMID:25909229^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.