Chen Jonathan L, Kennedy Scott D, Turner Douglas H
†Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.
‡Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States.
Biochemistry. 2015 Jun 2;54(21):3269-85. doi: 10.1021/acs.biochem.5b00012. Epub 2015 May 21.
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 encode the 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 three-dimensional model of the hairpin derived from nuclear magnetic resonance spectra and simulated annealing with restrained molecular dynamics. Additional insight was provided by modeling based on (1)H chemical shifts. 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.
甲型流感病毒是一种RNA病毒，其基因组由八个负义片段组成。第7节段mRNA含有一个3'剪接位点，用于可变剪接以编码必需的M2蛋白。基于序列比对和化学图谱实验，当3'剪接位点处于暴露该位点的发夹构象时，其周围的二级结构具有一个内环、腺嘌呤凸起和发夹环。我们报告了通过核磁共振光谱和受限分子动力学模拟退火得到的发夹三维模型的结构特征。基于（1）H化学位移的建模提供了更多见解。包含3'剪接位点的内环有一个动态鸟苷和一个稳定的亚氨基（顺式沃森-克里克/沃森-克里克）GA对。腺嘌呤凸起似乎也是动态的，腺嘌呤要么堆积在茎中，要么与沃森-克里克GC对形成碱基三联体。发夹环是一个由AC对封闭的GAAA四环。
