内环结构
内环结构（Internal loop）是一种RNA的高级结构，是RNA双链中两条链上对位的核苷酸残基的碱基无法配对产生的膨起环。内环分为对称和不对称两种。其中，对称的内环是两条链上对位的核苷酸残基同时膨起产生的，而不对称的内环结构中，只有一条链上有几个核苷酸残基膨起。对称内环结构不是很稳定，一般只出现在RNA分子的移动过程中。而不对称内环相对稳定。在核糖体RNA（rRNA）中就有较丰富的内环结构[1][2]。
内环结构和茎环结构（发卡结构）的区别在于，内环结构出现在RNA双链的内部，“环”两端都是闭合双链。而茎环结构的“环”出现在双链的一端[2][1]。
内环可分为对称或不对称，其中一些不对称的内环也称为凸起(bulge)。 许多重要的结构图案均由内环组成，例如 C-环[3]、 对接弯头(the docking-elbow)[4]、 扭结转弯（k 转弯）(kink-turns, k-turn)[5][6]、 直角[7]、 sarcin/ricin 环（也称为为凸起-G, bulged-G 基序）[8][9][10]、 扭曲基序[11]、 和UAA/GAN 内环基序[12]。
承载内环结构的RNA基序图库 | |
|---|---|
|
![A consensus secondary structure and primary sequence for the 3` Sarcin-Ricin (or bulged-G) RNA motif.[8]](/wiki/File:Sarcin-ricin-1-secondary-structure.svg)
![A consensus secondary structure and primary sequence for the 5` Sarcin-Ricin (or bulged-G) RNA motif.[8]](/wiki/File:Sarcin-ricin-2-secondary-structure.svg)
![A consensus secondary structure and primary sequence for the twist-up RNA motif.[11]](/wiki/File:Twist_up-secondary-structure.svg)
![A consensus secondary structure and primary sequence for the UAA-GAN RNA motif.[12]](/wiki/File:UAA_GAN-secondary-structure.svg)
参见
[编辑]参考
[编辑]- ^ 1.0 1.1 RNA二级结构的预测. 东南大学生物信息学实验室. [2018-01-27]. （原始内容存档于2018-01-27）.
- ^ 2.0 2.1 P. H. van Knippenberg; C. W. Hilbers. Structure and Dynamics of RNA. Springer Science & Business Media. 8 March 2013: 197–199. ISBN 978-1-4684-5173-3.
- ^ Lescoute, A; Leontis, NB; Massire, C; Westhof, E. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments.. Nucleic Acids Research. 2005, 33 (8): 2395–409. PMC 1087784
. PMID 15860776. doi:10.1093/nar/gki535.
- ^ Lehmann, J; Jossinet, F; Gautheret, D. A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders.. Nucleic Acids Research. May 1, 2013, 41 (10): 5494–502. PMC 3664808 . PMID 23580544. doi:10.1093/nar/gkt219.
- ^ Klein, D.J. The kink-turn: a new RNA secondary structure motif. The EMBO Journal. 2001, 20 (15): 4214–4221. ISSN 1460-2075. PMC 149158 . PMID 11483524. doi:10.1093/emboj/20.15.4214.
- ^ Schroeder, KT; McPhee, SA; Ouellet, J; Lilley, DM. A structural database for k-turn motifs in RNA.. RNA. Aug 2010, 16 (8): 1463–8. PMC 2905746 . PMID 20562215. doi:10.1261/rna.2207910.
- ^ Grabow, WW; Zhuang, Z; Swank, ZN; Shea, JE; Jaeger, L. The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns.. Journal of Molecular Biology. Nov 23, 2012, 424 (1–2): 54–67. PMC 3488136 . PMID 22999957. doi:10.1016/j.jmb.2012.09.012.
- ^ 8.0 8.1 8.2 Szewczak, AA; Moore, PB. The sarcin/ricin loop, a modular RNA.. Journal of Molecular Biology. Mar 17, 1995, 247 (1): 81–98. PMID 7897662. doi:10.1006/jmbi.1994.0124 .
- ^ Leontis, NB; Westhof, E. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs.. Journal of Molecular Biology. Oct 30, 1998, 283 (3): 571–83. PMID 9784367. doi:10.1006/jmbi.1998.2106.
- ^ Moore PB. Structural motifs in RNA. Annu. Rev. Biochem. 1999, 68: 287–300. PMID 10872451. doi:10.1146/annurev.biochem.68.1.287.
- ^ 11.0 11.1 Zhong, C; Zhang, S. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.. Nucleic Acids Research. Feb 2012, 40 (3): 1307–17. PMC 3273805 . PMID 21976732. doi:10.1093/nar/gkr804.
- ^ 12.0 12.1 Lee, JC; Gutell, RR; Russell, R. The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.. Journal of Molecular Biology. Jul 28, 2006, 360 (5): 978–88. PMID 16828489. doi:10.1016/j.jmb.2006.05.066.
