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Dependent Conformational Change of RNA Studied by Fluorescence Correlation and FRET on Immobilized Single Molecules

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Dependent Conformational Change of RNA Studied by Fluorescence Correlation and FRET on Immobilized Single Molecules Mg2؉-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules Harold D. Kim*, G. Ulrich Nienhaus†‡, Taekjip Ha*§, Jeffrey W. Orr¶, James R. Williamson¶, and Steven Chu*ʈ *Department of Applied Physics and Physics, Stanford University, Stanford, CA 94305-4060; †Department of Biophysics, University of Ulm, D-89069 Ulm, Germany; ‡Department of Physics, University of Illinois, Urbana, IL 61801-3080; and ¶Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037 Contributed by Steven Chu, February 9, 2002 Fluorescence correlation spectroscopy (FCS) of fluorescence reso- showed that various cations such as Mg2ϩ,Ca2ϩ,Co3ϩ, and nant energy transfer (FRET) on immobilized individual fluoro- spermidine alone also yield the same folded conformation of the phores was used to study the Mg2؉-facilitated conformational junction (8, 9). Crystallographic studies located 8 Mg2ϩ ions change of an RNA three-helix junction, a structural element that around the junction region that may be involved in stabilizing the initiates the folding of the 30S ribosomal subunit. Transitions of folded form (10). the RNA junction between open and folded conformations resulted When fluorescence resonance energy transfer (FRET) (14, in fluctuations in fluorescence by FRET. Fluorescence fluctuations 15) was applied to single molecules (16), we previously observed occurring between two FRET states on the millisecond time scale conformational changes of individual RNA junctions that con- ؉ ؉ were found to be dependent on Mg2 and Na concentrations. tained shortened helices 20, 21, and 22 (17). In the open Correlation functions of the fluctuations were used to determine conformation, the donor and acceptor are about 8.5 nm apart, transition rates between the two conformations as a function of whereas in the folded conformation they are about 5 nm apart 2؉ ؉ Mg or Na concentration. Both the opening and folding rates based on the three-dimensional structure (10, 11). The large were found to vary with changing salt conditions. Assuming difference in donor–acceptor distance between the open and 2؉ specific binding of divalent ions to RNA, the Mg dependence of folded state makes the two conformations easily distinguishable the observed rates cannot be explained by conformational change ͞ ϩ by their different FRET efficiencies defined as Ia (Ia Id), induced by Mg2؉ binding͞unbinding, but is consistent with a where Ia is the acceptor intensity and Id is the donor intensity. In model in which the intrinsic conformational change of the RNA our previous study, the binding equilibrium and slow dissociation junction is altered by uptake of Mg2؉ ion(s). This version of ͞ of S15 were observed. However, when we used a buffer exchange FCS FRET on immobilized single molecules is demonstrated to be technique with a mixing time of Ϸ10 ms, we were unable to a powerful technique in the study of conformational dynamics of measure the conformational dynamics of the RNA junctions in biomolecules over time scales ranging from microseconds to ϩ response to [Mg2 ] changes. seconds. In this work, we use fluorescence correlation spectroscopy (FCS) (18, 19) and FRET on immobilized single molecules to 2ϩ ϩ onovalent and divalent cations such as magnesium and measure the Mg - and Na -dependent folding rates (kf,obs) and Msodium play an important role in stabilizing nucleic acid opening rates (ko,obs) of the RNA junction. Conventional FCS on structure in vivo. Specific binding sites for magnesium ions (1) freely diffusing molecules is not applicable if the time scale of have been observed crystallographically in a number of systems, their molecular transition is longer than their diffusion time including tRNA (2), hammerhead ribozyme (3), the P4-P6 across the observation region. Also, impurities, dye degradation, domain of the Tetrahymena thermophila group I intron (4), and or incomplete labeling of one of the FRET pairs can be easily a 5S ribosomal RNA domain (5). Metal ions can also stabilize the identified with immobilized molecules. RNA structure nonspecifically by screening the negatively charged backbone (6). Furthermore, the role of counterions is Materials and Methods critical to understanding protein–nucleic acid interactions (7). Sample Preparation. A Cy3–Cy5 donor–acceptor pair was at- In the case of RNA–protein interactions, the situation can be tached to two ends of the three-helix junction (Fig. 1), and a even more complex when ion-dependent conformational biotin moiety attached to the third helix was used for immobi- changes accompany protein binding. An interesting example is 1 lization on a glass surface. Two coverslips (No. 1 ⁄2, VWR the three-helix junction located in the central domain of the 16S Scientific) were flamed with a propane torch and taped to each ribosomal RNA that is the binding site for protein S15 (Fig. 1). other. The narrow channel between two glasses guided by double Biochemical analysis of the binding of S15 from Bacillus stearo- stick tape was used as a flow cell for microscopy. Glass surface thermophilus has shown that a large conformational change was treated with 1 mg/ml of biotin-labeled bovine albumin occurs in the junction region (8, 9). Two different groups recently (Sigma), 0.2 mg/ml of streptavidin (Molecular Probes) and Ϸ50 solved the crystal structure of the ribo–nucleoprotein complex pM of biotinylated RNA junction, successively. Each step lasted including the junction region and S15 protein (10, 11), and the for 5 min and was followed by washing the flow cell with the structure of the entire 30S subunit has been solved (12, 13). ͞ In the open (unfolded) form of the junction, the three helices standard buffer (10 mM Tris 50 mM NaCl, pH 8). The biotin- 20, 21, and 22 are arranged with nearly equal Ϸ120° angles between them. The folded form of the junction is formed in the Abbreviations: FRET, fluorescence resonance energy transfer; FCS, fluorescence correlation presence of ions or upon the binding of S15, where helix 21 stacks spectroscopy. coaxially under helix 22, and helix 20 makes 60° angle with helix §Present address: Department of Physics, University of Illinois, Urbana, IL 61801-3080. 22. This unusual structure is stabilized in part by the noncanoni- ʈTo whom reprint requests should be addressed. E-mail: [email protected]. cal base-pairing between C754 and G654. S15 interacts with the The publication costs of this article were defrayed in part by page charge payment. This upper bulge region of helix 22 and the junction region. Solution article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. studies based on gel mobility of this RNA three-helix junction §1734 solely to indicate this fact. 4284–4289 ͉ PNAS ͉ April 2, 2002 ͉ vol. 99 ͉ no. 7 www.pnas.org͞cgi͞doi͞10.1073͞pnas.032077799 Downloaded by guest on September 29, 2021 ϩ ␶ ϭ at time t . Applying the initial condition, Nm(t) N and ϩ ␶ solving for Nn(t ) by using Eq. 4 leads to N ͑t ϩ ␶͒ k k ͑ ͉ ϩ ␶͒ ϭ n ϭ ͩ␦ Ϫ nͪ Ϫ ␭␶ ϩ n P m, t n, t ͑ ͒ mn ␭ e ␭ , Nm t [6] ␦ where mn is the Kronecker delta. If Im is the observable measured from a single molecule in state m, the autocorrelation of I can be derived from Eq. 1 as 2 2 ͸ ͸ ͑ ͒ ͑ ͉ ϩ ␶͒ ImInP m P m, t n, t ͗I͑t͒I͑t ϩ ␶͘ m ϭ 1 n ϭ 1 Ϫ ϭ Ϫ 2 1 1 ͗I͑t͒͘ 2 ͑ ͸ ͑ ͒͒2 ImP m Fig. 1. The secondary structure of a modified 16S ribosomal RNA junction. m ϭ 1 Bases in bold light gray are conserved above 95% across all known eubacterial sequences. On folding, rotation of helix 22 by 60° toward helix 20 decreases ͑ Ϫ ͒2 I2 I1 k1k2 Ϫ␭␶ the donor–acceptor distance from 8.5 nm to 5 nm, and the FRET efficiency ϭ ͑ ϩ ͒2 e . [7] increases markedly. Based on the crystal structure, it is likely that C754 switches k1I1 k2I2 base pairing from G587 to G654 in this transition. We assume that the donor (acceptor) signal fluctuates in an folded anticorrelated manner between two intensity levels Id and open folded open ylated end of an RNA junction then forms a specific binding to Id (Ia and Ia ). We further assume that two rate coeffi- the surface through the streptavidin linker. cients, the observed folding and opening rates, kf,obs and ko,obs apply to both signals. Applying these assumptions to Eq. 7, the Correlation of Fluorescence Intensities. Information on stochastic autocorrelations for donor and acceptor signals and the cross- processes underlying the fluctuations is contained in correlations correlation between the two signals become of fluorescence fluctuations. Even for shot-noise-dominated Ifolded 2 fluorescence fluctuations, rate constant for the fluctuations can ͩ a Ϫ ͪ open 1 be extracted with high accuracy by counting a large number of Ia ko,obs Ϫ␭␶ ␶ AC ͑␶͒ ϭ e , [8] photons. The autocorrelation AC( ) of a signal I(t) is defined by a Ifolded k 2 k ͩ a ϩ o,obsͪ f,obs open ͗␦I͑t͒␦I͑t ϩ ␶͒͘ ͗I͑t͒I͑t ϩ ␶͒͘ Ia kf,obs ͑␶͒ ϭ ϭ Ϫ AC ͗ ͑ ͒͗͘ ͑ ͒͘ ͗ ͑ ͒͗͘ ͑ ͒͘ 1, [1] I t I t I t I t Iopen 2 ͩ d Ϫ ͪ ͗ ͘ ␦ folded 1 where I(t) is the time average of I(t), and I(t) is the difference Id kf,obs Ϫ␭␶ ͗ ͘ ␶ AC ͑␶͒ ϭ e , and [9] of I(t) from I(t) . Similarly, the cross-correlation CC( )oftwo d Iopen k 2 k ͩ d ϩ f,obsͪ o,obs signals is defined by folded Id ko,obs ͗␦I ͑t͒␦I ͑t ϩ ␶͒͘ ͗I ͑t͒I ͑t ϩ ␶͒͘ ͑␶͒ ϭ d a ϭ d a Ϫ ͑␶͒ ϭ Ϫ͓ ͑␶͒⅐ ͑␶͔͒1/2 CC ͗ ͑ ͒͗͘ ͑ ͒͘ ͗ ͑ ͒͗͘ ͑ ͒͘ 1.
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