內環結構

编辑链接
维基百科，自由的百科全书
如圖，最上端的結構是莖環結構（髮卡結構），自上往下第二個結構是對稱內環結構，第三、第四、第五個結構是不對稱內環結構

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]。

承載內環結構的RNA基序圖庫
  • A consensus secondary structure and primary sequence for the C-loop RNA motif.
    A consensus secondary structure and primary sequence for the C-loop RNA motif.
  • A consensus secondary structure and primary sequence for the docking elbow RNA motif.
    A consensus secondary structure and primary sequence for the docking elbow RNA motif.
  • A consensus secondary structure and primary sequence for the kink-turn RNA motif.
    A consensus secondary structure and primary sequence for the kink-turn RNA motif.
  • A consensus secondary structure and primary sequence for the kink-turn RNA motif.
    A consensus secondary structure and primary sequence for the kink-turn RNA motif.
  • A consensus secondary structure and primary sequence for the right-angle RNA motif.
    A consensus secondary structure and primary sequence for the right-angle RNA motif.
  • A consensus secondary structure and primary sequence for the 3` Sarcin-Ricin (or bulged-G) RNA motif.[8]
    A consensus secondary structure and primary sequence for the 3` Sarcin-Ricin (or bulged-G) RNA motif.[8]
  • A consensus secondary structure and primary sequence for the 5` Sarcin-Ricin (or bulged-G) RNA motif.[8]
    A consensus secondary structure and primary sequence for the 5` Sarcin-Ricin (or bulged-G) RNA motif.[8]
  • A consensus secondary structure and primary sequence for the twist-up RNA motif.[11]
    A consensus secondary structure and primary sequence for the twist-up RNA motif.[11]
  • A consensus secondary structure and primary sequence for the UAA-GAN RNA motif.[12]
    A consensus secondary structure and primary sequence for the UAA-GAN RNA motif.[12]

參見

參考

  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]. （原始内容存档于2018-01-27）. 
  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. 
  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 可免费查阅. PMID 15860776. doi:10.1093/nar/gki535. 
  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 可免费查阅. PMID 23580544. doi:10.1093/nar/gkt219. 
  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 可免费查阅. 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 可免费查阅. 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 可免费查阅. PMID 22999957. doi:10.1016/j.jmb.2012.09.012. 
  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 可免费查阅. 
  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. 
  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 可免费查阅. PMID 21976732. doi:10.1093/nar/gkr804. 
  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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