Nowakowski J, Tinoco I
Department of Chemistry, University of California at Berkeley, Berkeley, California 94720-1460, USA.
Biochemistry. 1996 Feb 27;35(8):2577-85. doi: 10.1021/bi952263p.
We present a three-dimensional structure of a 34-nucleotide RNA molecule determined by NMR spectroscopy. The molecule was designed to form a junction between two double-helical stems whose sequence was based on the P4/P6 domain from group I introns. There are 5' and 3' single-strand overhangs at the junctions of the stems. Contrary to our expectations, we found that the 3' end of the molecule is placed in the minor and not the major groove of the P4 helix. As a result of tertiary contacts and stacking interactions from nucleotides in the 3' end, the junction helices are rotated in a left-handed fashion and do not stack coaxially. This conformation is highly dependent on the presence of single-stranded nucleotides at the 3' overhang. When the 3' end is removed, the molecule assumes a radically different structure with 5' end in the minor groove of the P6 helix and overall right-handed rotation between the stems. Only one nucleotide at the 3' end is sufficient to change the geometry of the junction.
我们展示了一个通过核磁共振光谱法测定的34个核苷酸的RNA分子的三维结构。该分子被设计成在两个双螺旋茎之间形成一个连接点，其序列基于I组内含子的P4/P6结构域。在茎的连接处有5'和3'单链突出端。与我们的预期相反，我们发现该分子的3'端位于P4螺旋的小沟而非大沟中。由于3'端核苷酸的三级相互作用和堆积相互作用，连接螺旋以左手方式旋转，并且不同轴堆积。这种构象高度依赖于3'突出端单链核苷酸的存在。当3'端被去除时，该分子呈现出截然不同的结构，5'端位于P6螺旋的小沟中，茎之间整体呈右手旋转。3'端仅一个核苷酸就足以改变连接点的几何形状。
