title: Role of ion valence in the submillisecond collapse and folding of a small RNA domain.
abstract: Following the addition of ions to trigger folding, RNA molecules undergo a transition from rigid, extended states to a compact ensemble. Determining the time scale for this collapse provides important insights into electrostatic contributions to RNA folding; however, it can be challenging to isolate the effects of purely nonspecific collapse, e.g., relaxation due to backbone charge compensation, from the concurrent formation of some tertiary contacts. To solve this problem, we decoupled nonspecific collapse from tertiary folding using a single-point mutation to eliminate tertiary contacts in the small RNA subdomain known as tP5abc. Microfluidic mixing with microsecond time resolution and Förster resonance energy transfer detection provides insight into the ionic strength-dependent transition from extended to compact ensembles. Differences in reaction rates are detected when folding is initiated by monovalent or divalent ions, consistent with equilibrium measurements illustrating the enhanced screening of divalent ions relative to monovalent ions at the same ionic strength. Ion-driven collapse is fast, and a comparison of the collapse time of the wild-type and mutant tP5abc suggests that site binding of Mg(2+) occurs on submillisecond time scales.
authors: School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.
authors: Suzette A
authors: SA
authors: Pabit
authors: Julie L
authors: JL
authors: Sutton
authors: Huimin
authors: H
authors: Chen
authors: Lois
authors: L
authors: Pollack
mesh_terms: D001483:Base Sequence; D031541:Fluorescence Resonance Energy Transfer; D007477:Ions / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009994:Osmolar Concentration; D017354:Point Mutation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013768:Tetrahymena / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism
chemical_list: D007477:Ions; D016337:RNA, Catalytic
references: Biophys J. 2008 Jul;95(1):287-95
references: 18339743
references: Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2902-7
references: 22308376
references: Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11555-60
references: 9751704
references: RNA. 1999 Dec;5(12):1665-74
references: 10606276
references: RNA. 2009 Dec;15(12):2195-205
references: 19850914
references: Nat Rev Genet. 2001 Dec;2(12):919-29
references: 11733745
references: Cell. 2009 Feb 20;136(4):604-9
references: 19239882
references: J Biol Chem. 2011 Jun 3;286(22):19872-9
references: 21478155
references: Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):799-804
references: 22203973
references: RNA. 2004 Mar;10(3):335-43
references: 14970378
references: RNA. 2001 Feb;7(2):161-6
references: 11233973
references: Annu Rev Phys Chem. 2001;52:751-62
references: 11326079
references: Gene Ther. 2009 Oct;16(10):1189-201
references: 19587710
references: J Am Chem Soc. 2008 Sep 17;130(37):12334-41
references: 18722445
references: Curr Opin Chem Biol. 2005 Apr;9(2):104-9
references: 15811793
references: Biochemistry. 2000 Sep 12;39(36):10975-85
references: 10998234
references: Curr Opin Struct Biol. 2012 Jun;22(3):262-72
references: 22595008
references: Annu Rev Biophys. 2010;39:61-77
references: 20192764
references: Mol Cell. 2000 Mar;5(3):469-78
references: 10882132
references: Appl Phys Lett. 2008 Jun 2;92(22):223901-2239013
references: 19488404
references: Curr Opin Struct Biol. 2008 Jun;18(3):321-9
references: 18547802
references: J Phys Chem B. 2010 Jun 24;114(24):8207-20
references: 20518549
references: Nat Struct Biol. 1997 Jul;4(7):553-8
references: 9228948
references: Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4284-9
references: 11929999
references: Nucleic Acids Res. 2012 Sep;40(16):8011-20
references: 22641849
references: J Mol Biol. 2008 Jun 13;379(4):859-70
references: 18471829
references: RNA. 2007 Aug;13(8):1205-13
references: 17616553
references: Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10459-64
references: 17556539
references: Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 1):1571-5
references: 12351864
references: Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):542-7
references: 18178620
references: Nature. 2002 Jul 11;418(6894):222-8
references: 12110898
references: Science. 2010 Jan 8;327(5962):202-6
references: 20056889
references: J Am Chem Soc. 2010 Jul 28;132(29):10148-54
references: 20597502
references: Acc Chem Res. 2011 Dec 20;44(12):1302-11
references: 21899297
references: Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R17-29
references: 16651366
references: Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3695-700
references: 11274387
references: Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10115-7
references: 10468571
references: Fold Des. 1996;1(4):R78-88
references: 9079386
references: Curr Opin Chem Biol. 2008 Dec;12(6):619-25
references: 19081286
references: J Am Chem Soc. 2007 Mar 7;129(9):2676-82
references: 17295487
references: Anal Chem. 2006 Jul 1;78(13):4465-73
references: 16808455
references: RNA. 2010 Apr;16(4):708-19
references: 20194520
references: Phys Rev Lett. 2007 Jul 20;99(3):038104
references: 17678334
references: Nucleic Acids Res. 2009 Jul;37(12):3887-96
references: 19395592
references: J Mol Biol. 2006 Jan 13;355(2):282-93
references: 16303138