title: The GA-minor submotif as a case study of RNA modularity, prediction, and design.
abstract: Complex natural RNAs such as the ribosome, group I and group II introns, and RNase P exemplify the fact that three-dimensional (3D) RNA structures are highly modular and hierarchical in nature. Tertiary RNA folding typically takes advantage of a rather limited set of recurrent structural motifs that are responsible for controlling bends or stacks between adjacent helices. Herein, the GA minor and related structural motifs are presented as a case study to highlight several structural and folding principles, to gain further insight into the structural evolution of naturally occurring RNAs, as well as to assist the rational design of artificial RNAs.
authors: Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA.
authors: Wade W
authors: WW
authors: Grabow
authors: Zhuoyun
authors: Z
authors: Zhuang
authors: Joan-Emma
authors: JE
authors: Shea
authors: Luc
authors: L
authors: Jaeger
mesh_terms: D000818:Animals; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D012313:RNA
references: J Mol Biol. 1990 Dec 5;216(3):585-610
references: 2258934
references: J Mol Biol. 2004 Jun 25;340(1):141-77
references: 15184028
references: Nucleic Acids Res. 2009 Apr;37(7):2294-312
references: 19240142
references: J Mol Biol. 2003 Jan 3;325(1):65-83
references: 12473452
references: Proc Natl Acad Sci U S A. 1990 Nov;87(21):8467-71
references: 2236056
references: Nat Struct Biol. 2001 Dec;8(12):1064-8
references: 11702070
references: Nat Struct Mol Biol. 2008 Feb;15(2):177-82
references: 18204466
references: J Mol Biol. 1999 Oct 22;293(2):271-81
references: 10550208
references: RNA. 2010 Apr;16(4):762-8
references: 20145044
references: Nature. 1990 Oct 11;347(6293):578-80
references: 2215683
references: Nucleic Acids Res. 2006 Mar 10;34(5):1481-91
references: 16531589
references: Nucleic Acids Res. 2001 Jan 15;29(2):455-63
references: 11139616
references: RNA. 2002 Jul;8(7):873-7
references: 12166642
references: J Mol Biol. 2009 Jul 17;390(3):547-59
references: 19445952
references: Science. 2005 Sep 2;309(5740):1508-14
references: 16141058
references: Biochemistry. 1996 Feb 27;35(8):2577-85
references: 8611561
references: Nat Struct Biol. 2000 Jan;7(1):53-7
references: 10625428
references: Nucleic Acids Res. 2007;35(20):6995-7002
references: 17940098
references: RNA. 2003 Jun;9(6):640-3
references: 12756321
references: Nano Lett. 2011 Feb 9;11(2):878-87
references: 21229999
references: J Mol Biol. 2001 Jul 20;310(4):735-53
references: 11453684
references: Structure. 2006 May;14(5):825-35
references: 16698544
references: Nucleic Acids Res. 2008 Jun;36(11):3539-51
references: 18456707
references: Biochemistry. 1993 Dec 28;32(51):14220-8
references: 8260508
references: Nucleic Acids Res. 2008 Mar;36(4):1138-52
references: 18158305
references: RNA. 2003 Mar;9(3):355-63
references: 12592009
references: Nature. 2000 Sep 21;407(6802):327-39
references: 11014182
references: Nucleic Acids Res. 2006 Mar 06;34(5):1381-92
references: 16522648
references: Nat Nanotechnol. 2011 Feb;6(2):116-20
references: 21240283
references: RNA. 2002 Sep;8(9):1112-9
references: 12358430
references: Curr Opin Struct Biol. 2005 Jun;15(3):302-8
references: 15963891
references: RNA. 2010 Aug;16(8):1463-8
references: 20562215
references: Curr Opin Chem Biol. 2005 Apr;9(2):104-9
references: 15811793
references: RNA. 2009 Feb;15(2):189-99
references: 19144906
references: Biochemistry. 1992 Dec 29;31(51):12733-41
references: 1463745
references: Chem Biol. 1996 Dec;3(12):993-1009
references: 9000010
references: Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13953-8
references: 18768810
references: Annu Rev Biophys. 2008;37:445-64
references: 18573090
references: Biophys J. 2005 May;88(5):3466-85
references: 15722438
references: RNA Biol. 2012 Mar;9(3):254-60
references: 22336704
references: Q Rev Biophys. 2005 Aug;38(3):221-43
references: 16817983
references: RNA Biol. 2006 Oct;3(4):133-9
references: 17172877
references: Curr Opin Struct Biol. 2002 Jun;12(3):301-10
references: 12127448
references: Biochimie. 2002 Sep;84(9):961-73
references: 12458088
references: Nano Lett. 2009 Mar;9(3):1270-7
references: 19239258
references: Trends Biochem Sci. 2006 Jan;31(1):41-51
references: 16356725
references: Science. 1996 Sep 20;273(5282):1696-9
references: 8781229
references: Nat Struct Biol. 1999 Dec;6(12):1139-47
references: 10581556
references: Curr Opin Struct Biol. 2006 Aug;16(4):531-43
references: 16843653
references: Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6854-9
references: 9618502
references: RNA. 2007 Sep;13(9):1537-45
references: 17652406
references: Nucleic Acids Res. 2009 Aug;37(15):4898-918
references: 19528080
references: Nat Struct Biol. 2001 Apr;8(4):339-43
references: 11276255
references: Biol Chem. 2005 Sep;386(9):833-44
references: 16164408
references: J R Soc Interface. 2008 Oct 6;5(27):1159-72
references: 18319208
references: J Mol Evol. 1999 Oct;49(4):411-2
references: 10485998
references: RNA. 2010 Feb;16(2):375-81
references: 20038632
references: Biochemistry. 1994 Feb 1;33(4):973-82
references: 7508262
references: J Biomol Struct Dyn. 2004 Oct;22(2):183-94
references: 15317479
references: Bioinformatics. 2000 Apr;16(4):334-40
references: 10869031
references: Nature. 2009 Mar 12;458(7235):233-7
references: 19169240
references: EMBO J. 2001 Aug 1;20(15):4214-21
references: 11483524
references: J Mol Biol. 2000 Jul 21;300(4):791-803
references: 10891269
references: Nucleic Acids Res. 2003 Dec 1;31(23):6806-18
references: 14627814
references: Nucleic Acids Res. 2011 Feb;39(3):1066-80
references: 20876687
references: Science. 2000 Aug 11;289(5481):905-20
references: 10937989
references: RNA. 2007 Aug;13(8):1256-67
references: 17585050
references: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903
references: 11296253
references: RNA. 2012 Apr;18(4):610-25
references: 22361291
references: EMBO J. 1995 Mar 15;14(6):1276-85
references: 7720718
references: J Mol Biol. 2012 Nov 23;424(1-2):54-67
references: 22999957
references: RNA. 2007 May;13(5):643-50
references: 17339576
references: Nucleic Acids Res. 2004 Dec 17;32(22):6650-9
references: 15608296
references: Nucleic Acids Res. 2007;35(5):1726-36
references: 17317683
references: Nature. 1989 Nov 23;342(6248):391-5
references: 2685606
references: Nature. 2009 Feb 19;457(7232):977-80
references: 19225518
references: Science. 2004 Dec 17;306(5704):2068-72
references: 15604402
references: Nature. 2008 Mar 6;452(7183):51-5
references: 18322526
references: J Mol Biol. 2002 Jul 12;320(3):455-74
references: 12096903
references: RNA. 2006 Jan;12(1):83-93
references: 16373494
references: EMBO J. 1997 Jun 2;16(11):3289-302
references: 9214644
references: Nucleic Acids Res. 2006 Mar 06;34(5):1326-41
references: 16522645
references: J Mol Biol. 2001 Jul 27;310(5):1109-23
references: 11501999
references: J Math Biol. 2008 Jan;56(1-2):215-52
references: 17694311
references: J Mol Evol. 1999 Oct;49(4):413-23
references: 10485999
references: RNA. 1995 Apr;1(2):219-22
references: 7585251
references: J Mol Biol. 1995 Jul 21;250(4):447-59
references: 7616567
references: Fold Des. 1996;1(4):R78-88
references: 9079386
references: RNA. 2001 Apr;7(4):499-512
references: 11345429
references: Nucleic Acids Res. 2005 Apr 28;33(8):2395-409
references: 15860776
references: Int J Mol Sci. 2009 Jun 30;10(7):2921-34
references: 19742176
references: J Mol Biol. 1998 Oct 30;283(3):571-83
references: 9784367
references: Biochimie. 2002 Sep;84(9):925-44
references: 12458085
references: RNA. 1998 Sep;4(9):1134-53
references: 9740131
references: PLoS Biol. 2005 Jan;3(1):e5
references: 15630477
references: J Mol Biol. 2006 Jul 28;360(5):978-88
references: 16828489
references: Curr Opin Struct Biol. 2006 Jun;16(3):279-87
references: 16713707
references: RNA. 2007 Jul;13(7):1036-42
references: 17507660
references: RNA. 2003 Jan;9(1):44-51
references: 12554875
references: Angew Chem Int Ed Engl. 2000 Jul 17;39(14):2521-2524
references: 10941124
references: Curr Opin Struct Biol. 2003 Jun;13(3):300-8
references: 12831880
references: Cold Spring Harb Symp Quant Biol. 1987;52:759-67
references: 3454288
references: Nucleic Acids Res. 2009 Jan;37(1):215-30
references: 19036788
references: Structure. 2004 Jul;12(7):1165-76
references: 15242593
references: RNA. 2007 Apr;13(4):549-54
references: 17283211