Topology of three-way junctions in folded RNAs

被引:230
作者
Lescoute, A [1 ]
Westhof, E [1 ]
机构
[1] Univ Strasbourg, Inst Biol Mol & Cellulaire, UPR 9002, Architecture & React ARN,CNRS, F-67084 Strasbourg, France
关键词
RNA motif; folding; tertiary contact; junction; RNA topology;
D O I
10.1261/rna.2208106
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The three-way junctions contained in X-ray structures of folded RNAs have been compiled and analyzed. Three-way junctions with two helices approximately coaxially stacked can be divided into three main families depending on the relative lengths of the segments linking the three Watson-Crick helices. Each family has topological characteristics with some conservation in the non-Watson.-Crick pairs within the linking segments as well as in the types of contacts between the segments and the helices. The most populated family presents tertiary interactions between two helices as well as extensive shallow/minor groove contacts between a linking segment and the third helix. On the basis of the lengths of the linking segments, some guidelines could be deduced for choosing a topology for a three-way junction on the basis of a secondary structure. Examples and prediction based on those rules are discussed.
引用
收藏
页码:83 / 93
页数:11
相关论文
共 64 条
[1]   Crystal structure of a group I intron splicing intermediate [J].
Adams, PL ;
Stahley, MR ;
Gill, ML ;
Kosek, AB ;
Wang, JM ;
Strobel, SA .
RNA, 2004, 10 (12) :1867-1887
[2]   Structure of the S15,S18-rRNA complex: Assembly of the 30S ribosome central domain [J].
Agalarov, SC ;
Prasad, GS ;
Funke, PM ;
Stout, CD ;
Williamson, JR .
SCIENCE, 2000, 288 (5463) :107-112
[3]   The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution [J].
Ban, N ;
Nissen, P ;
Hansen, J ;
Moore, PB ;
Steitz, TA .
SCIENCE, 2000, 289 (5481) :905-920
[4]  
Batey RT, 1999, ANGEW CHEM INT EDIT, V38, P2327
[5]   Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15 [J].
Batey, RT ;
Williamson, JR .
RNA, 1998, 4 (08) :984-997
[6]   Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine [J].
Batey, RT ;
Gilbert, SD ;
Montange, RK .
NATURE, 2004, 432 (7015) :411-415
[7]   A SECONDARY-STRUCTURE MODEL FOR THE SELF-CLEAVING REGION OF NEUROSPORA VS RNA [J].
BEATTIE, TL ;
OLIVE, JE ;
COLLINS, RA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (10) :4686-4690
[8]   Hierarchy and dynamics of RNA folding [J].
Brion, P ;
Westhof, E .
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 1997, 26 :113-137
[9]   Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus:: Structure of the proteins and their interactions with 16 S RNA [J].
Brodersen, DE ;
Clemons, WM ;
Carter, AP ;
Wimberly, BT ;
Ramakrishnan, V .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 316 (03) :725-768
[10]   Fast cleavage kinetics of a natural hammerhead ribozyme [J].
Canny, MD ;
Jucker, FM ;
Kellogg, E ;
Khvorova, A ;
Jayasena, SD ;
Pardi, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (35) :10848-10849