內環結構

內環結構（Internal loop）是一種RNA的高級結構，是RNA雙鏈中兩條鏈上對位的核苷酸殘基的鹼基無法配對產生的膨起環。內環分爲對稱和不對稱兩種。其中，對稱的內環是兩條鏈上對位的核苷酸殘基同時膨起產生的，而不對稱的內環結構中，只有一條鏈上有幾個核苷酸殘基膨起。對稱內環結構不是很穩定，一般只出現在RNA分子的移動過程中。而不對稱內環相對穩定。在核糖體RNA（rRNA）中就有較豐富的內環結構^[1]^[2]。

內環結構和莖環結構（髮卡結構）的區別在於，內環結構出現在RNA雙鏈的內部，「環」兩端都是閉合雙鏈。而莖環結構的「環」出現在雙鏈的一端^[2]^[1]。

內環可分為對稱或不對稱，其中一些不對稱的內環也稱為凸起(bulge)。許多重要的結構圖案均由內環組成，例如 C-環^[3]、對接彎頭(the docking-elbow)^[4]、扭結轉彎（k 轉彎）(kink-turns, k-turn)^[5]^[6]、直角^[7]、 sarcin/ricin 環（也稱為為凸起-G, bulged-G 基序）^[8]^[9]^[10]、扭曲基序^[11]、和UAA/GAN 內環基序^[12]。

參見

參考

^ ^1.0 ^1.1 RNA二级结构的预测. 東南大學生物信息學實驗室. [2018-01-27]. （原始內容存檔於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.

[SEU-1] 1.0 ^1.1 RNA二级结构的预测. 東南大學生物信息學實驗室. [2018-01-27]. （原始內容存檔於2018-01-27）.

[KnippenbergHilbers2013-2] 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.

[Lescoute2005-3] 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.

[Lehmann2013-4] 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.

[Klein2001-5] 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.

[6] 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.

[7] 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.

[Szewczak1995-8] 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  .

[9] 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.

[10] Moore PB. Structural motifs in RNA. Annu. Rev. Biochem. 1999, 68: 287–300. PMID 10872451. doi:10.1146/annurev.biochem.68.1.287.

[Zhong2012-11] 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.

[Lee2006-12] 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.

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