Shen Z, Hagerman P J
Department of Biochemistry, Biophysics and Genetics University of Colorado Health Sciences Center, Denver 80262.
J Mol Biol. 1994 Aug 19;241(3):415-30. doi: 10.1006/jmbi.1994.1517.
The current investigation has focused on the structure of the central, three-helix junction of the 5 S ribosomal RNA from Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium. The 5 S molecule from S. acidocaldarius represents a paradigm for the study of the 5 S junction (and branched RNA structures in general) due to its unusually high degree of predicted secondary structure and stability. In order to study the junction in isolation, a set of three RNA heteroduplex molecules was assembled in which pairs of helices bounding the junction were extended by 70 base-pairs per helix. Since the extended helices comprise more than 95% of the heteroduplex structure, the relative solution conformations of the heteroduplex molecules, in effect, "report" the interhelix (branch) angles bounded by the extended pairs of helices. Examination of these heteroduplex molecules, using a combination of gel electrophoresis and transient electric birefringence measurements, has revealed a tertiary structure for the central branch in which helices I and V are essentially collinear, and in which helix II is relatively free to reorient with respect to the I-V axis.
目前的研究聚焦于嗜酸热硫化叶菌（一种嗜热嗜酸古细菌）5S核糖体RNA的中心三螺旋连接结构。嗜酸热硫化叶菌的5S分子因其预测的二级结构程度异常高且稳定性强，成为研究5S连接结构（以及一般的分支RNA结构）的范例。为了单独研究该连接结构，组装了一组三个RNA异源双链分子，其中界定连接结构的每对螺旋都延伸了70个碱基对。由于延伸的螺旋占异源双链结构的95%以上，异源双链分子的相对溶液构象实际上“报告”了由延伸的螺旋对界定的螺旋间（分支）角度。通过结合凝胶电泳和瞬态电双折射测量对这些异源双链分子进行研究，揭示了中心分支的三级结构，其中螺旋I和V基本共线，并且螺旋II相对于I-V轴可以相对自由地重新定向。
