Boudvillain M, Pyle A M
The Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biophysics, 701 W. 168th Street, Room 616, Hammer Health Sciences Center, Columbia University, New York, NY 10032, USA.
EMBO J. 1998 Dec 1;17(23):7091-104. doi: 10.1093/emboj/17.23.7091.
Group II introns are self-splicing RNA molecules that are of considerable interest as ribozymes, mobile genetic elements and examples of folded RNA. Although these introns are among the most common ribozymes, little is known about the chemical and structural determinants for their reactivity. By using nucleotide analog interference mapping (NAIM), it has been possible to identify the nucleotide functional groups (Rp phosphoryls, 2'-hydroxyls, guanosine exocyclic amines, adenosine N7 and N6) that are most important for composing the catalytic core of the intron. The majority of interference effects occur in clusters located within the two catalytically essential Domains 1 and 5 (D1 and D5). Collectively, the NAIM results indicate that key tetraloop-receptor interactions display a specific chemical signature, that the epsilon-epsilon' interaction includes an elaborate array of additional features and that one of the most important core structures is an uncharacterized three-way junction in D1. By combining NAIM with site-directed mutagenesis, a new tertiary interaction, kappa-kappa', was identified between this region and the most catalytically important section of D5, adjacent to the AGC triad in stem 1. Together with the known zeta-zeta' interaction, kappa-kappa' anchors D5 firmly into the D1 scaffold, thereby presenting chemically essential D5 functionalities for participation in catalysis.
II类内含子是自我剪接的RNA分子，作为核酶、移动遗传元件和折叠RNA的实例，它们备受关注。尽管这些内含子是最常见的核酶之一，但关于其反应性的化学和结构决定因素却知之甚少。通过使用核苷酸类似物干扰图谱（NAIM），已经能够确定对于构成内含子催化核心最为重要的核苷酸官能团（Rp磷酸基团、2'-羟基、鸟苷外环胺、腺苷N7和N6）。大多数干扰效应发生在位于两个催化必需结构域1和5（D1和D5）内的簇中。总体而言，NAIM结果表明，关键的四环-受体相互作用呈现出特定的化学特征，ε-ε'相互作用包含一系列复杂的附加特征，并且最重要的核心结构之一是D1中一个未表征的三向连接。通过将NAIM与定点诱变相结合，在该区域与D5最具催化重要性的部分（与茎1中的AGC三联体相邻）之间鉴定出一种新的三级相互作用，κ-κ'。与已知的ζ-ζ'相互作用一起，κ-κ'将D5牢固地锚定到D1支架中，从而使化学上必不可少的D5官能团参与催化作用。
