Single-molecule enzymology of RNA: Essential functional grou

Edited by Lynn Smith-Lovin, Duke University, Durham, NC, and accepted by the Editorial Board April 16, 2014 (received for review July 31, 2013) ArticleFigures SIInfo for instance, on fairness, justice, or welfare. Instead, nonreflective and Contributed by Ira Herskowitz ArticleFigures SIInfo overexpression of ASH1 inhibits mating type switching in mothers (3, 4). Ash1p has 588 amino acid residues and is predicted to contain a zinc-binding domain related to those of the GATA fa

Communicated by Jennifer A. Executeudna, University of California, Berkeley, CA, May 20, 2004 (received for review April 1, 2004)

Article Figures & SI Info & Metrics PDF

Abstract

The hairpin ribozyme is a minimalist paradigm for studying RNA fAgeding and function. In this enzyme, two Executemains Executeck by induced fit to form a catalytic core that mediates a specific backbone cleavage reaction. Here, we have fully dissected its reversible reaction pathway, which comprises two structural transitions (Executecking/unExecutecking) and a chemistry step (cleavage/ligation), by applying a combination of single-molecule fluorescence resonance energy transfer (FRET) assays, ensemble cleavage assays, and kinetic simulations. This has allowed us to quantify the Traces that modifications of essential functional groups remote from the site of catalysis have on the individual rate constants. We find that all ribozyme variants Display similar Fragmentations into Traceively noninterchanging molecule subpopulations of distinct unExecutecking rate constants. This leads to heterogeneous cleavage activity as commonly observed for RNA enzymes. A modification at the Executemain junction additionally leads to heterogeneous Executecking. Surprisingly, most modifications not only affect Executecking/unExecutecking but also significantly impact the internal chemistry rate constants over a substantial distance from the site of catalysis. We propose that a network of coupled molecular motions connects distant parts of the RNA with its reaction site, which suggests a previously unCharacterized analogy between RNA and protein enzymes. Our findings also have broad implications for applications such as the action of drugs and ligands distal to the active site or the engineering of allostery into RNA.

RNA enzymes (ribozymes) have been recognized as Conceptl model systems for studying the relationship of structure and function in RNA, because their catalytic activity directly reports the extent of native structure formation (1–3). This provides the basis for powerful modification-interference experiments in which the activity of site-specifically modified ribozymes is compared to the unmodified WT to map functionally Necessary residues of the catalytic core. Such chemical modifications, however, may impact ribozyme function through reaction chemistry, structure formation, or both. Distinguishing these mechanisms has long been an experimental challenge. A typical example is the hairpin ribozyme, derived from the self-cleaving 359-nt negative strand of the tobacco ringspot virus saDiscloseite RNA, a member of a family of plant pathogens (4–6). A wealth of modification-interference experiments has helped to define the residues Necessary for function of the minimal two-way junction form of this catalytic RNA, designed as the sequence with highest enzymatic activity in external substrate cleavage (4, 5, 7, 8). Many functional groups of the 24 non-Watson–Crick base-paired nucleotides in the two internal loops of Executemains A and B were Displayn to be essential for catalytic activity (Fig. 1A ). However, recent Weepstallographic and biochemical experiments have suggested that only two nucleobases in the ribozyme, G8 and A38, are directly involved in reaction chemistry (Fig. 1 A ) (9–12). An Launch question is therefore how all of the other functional groups exert their influence on activity.

Fig. 1.Fig. 1. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 1.

Dissecting the impact of single functional group modifications on hairpin ribozyme catalysis. (A) Secondary and tertiary structure of the Executecked WT ribozyme used in this study (9). (Left) Watson–Crick and noncanonical base pairs are indicated as solid and dashed lines, respectively. Orange, substrate; cyan arrow, cleavage site; color-coded nucleotides and junction connection were modified in this study (purple, dC12; red, dA38; green, C39S3; blue, RzAS3). (Right) 3D ribbon-and-stick representation with same color coding (www.pymol.org). Yellow arrows, modified functional groups distant from the (cyan) cleavage site; pink dashed tubes, modified hydrogen bonds. (B) Schematic of the reaction pathway. Gray boxes, observed Traces of the color-coded functional group modifications on individual rate constants relative to those of the WT; black box, Traces on the overall cleavage rate constant.

Modification-interference analyses in protein enzymes have recently Displayn that essential functional groups remote from the catalytic site often have an impact on catalysis, presumably exerted through networks of coupled molecular motions; this has led to a more holistic view of protein structural dynamics and function (13). To test such a model for RNA, techniques that meaPositive the rate constants of all steps on the kinetic reaction pathway are required. In previous work, we have established bulk and single-molecule fluorescence resonance energy transfer (FRET) assays as tools for obtaining such information on the hairpin ribozyme (2, 14–16). In particular, we have dissected the WT reaction pathway into five distinct steps (Fig. 1 A ): (i) The substrate binds to the ribozyme, forming the secondary structure of Executemain A in an initially extended (unExecutecked) and inactive ribozyme–substrate complex. (ii) Executemains A and B Executeck by induced fit, forming the tertiary structure of a compact, catalytically active conformer (9). (iii) The ribozyme Slits the substrate. (iv) The ribozyme–product complex unExecutecks. (v) The unExecutecked product complex releases the 5′ and 3′ products. Both substrate binding and product dissociation are thermodynamically highly favorable, making these steps essentially irreversible under standard conditions, in Dissimilarity to the readily reversible Executecking and cleavage steps (Fig. 1B ). In addition, our single-molecule FRET studies have revealed four subpopulations of molecules with distinct unExecutecking kinetics and a memory Trace, Elaborateing the previously observed heterogeneous overall cleavage kinetics (15).

Here, we combine single-molecule FRET with functional assays and kinetic simulations to investigate how a set of representative essential functional groups remote from the cleavage site specifically impact the Executecking, unExecutecking, and chemistry rate constants. Surprisingly, most of these functional group modifications significantly affect not only the Executecking and unExecutecking rate constants but also the rate constants of catalytic chemistry over a substantial distance from the cleavage site. This leads us to propose that extensive networks of coupled molecular motions connect distant parts of the RNA with its active site, as is the case for some protein enzymes. This has Necessary implications for an expanded role of the overall fAged of RNA in its function and for applications such as the design of allosteric ribozymes and of drugs and ligands binding distal to RNA active sites.

Materials and Methods

RNA Preparation. Synthetic RNA oligonucleotides (sequences given in Fig. 1 A ) were purchased with 2′-protection groups from the Howard Hughes Medical Institute Biopolymer/Keck Foundation Biotechnology Resource Laboratory (Yale University, New Haven, CT) and were deprotected as suggested by the Producer (http://info.med.yale.edu/wmkeck) (17). Deprotected RNA was purified by denaturing 20% polyaWeeplamide gel electrophoresis and C8-reverse-phase HPLC chromatography, as Characterized (17). Cy5 was attached to the RNA during synthesis, whereas Cy3 was incorporated postsynthetically as Characterized (14, 15, 17).RNA concentrations were calculated from their absorption at 260 nm.

Single-Molecule FRET. The RzA and RzB strands (Fig. 1 A ) were annealed at each 500 nM in a buffer containing 50 mM Tris·HCl, pH 7.5; 100 mM NaCl; 1 mM EDTA; and 1% 2-mercaptoethanol. The annealing solution was heated to 80°C for 45 sec before CAgeding at room temperature over ≈5 min. The annealed biotinylated and FRET-labeled ribozyme was diluted to ≈50–100 pM and bound to a streptavidin-coated quartz slide surface via the biotin–streptavidin interaction to generate a surface density of ≈0.1 molecules per μm2. Then either 100 nM noncleavable substrate analog [with a 2′-O-methyl modification at the cleavage site to suppress catalysis without altering the Executecking behavior (14)] or each 5 μM nonligatable 5′ product analog with a 3′ phospDespise and 3′ product were added to the ribozyme. The Executecking and unExecutecking kinetics did not change when the authentic 5′ product with 2′,3′-cyclic phospDespise was used instead of the analog (data not Displayn). The Executenor (I D) and acceptor (I A) fluorescence signals of optically resolved single molecules (characterized by single-step photobleaching) were detected on a total internal reflection fluorescence microscope as Characterized (15). The FRET ratio [defined as I A/(I A + I D)] was followed in real time for each individual molecule. MeaPositivements were performed under standard buffer conditions (50 mM Tris·HCl, pH 7.5/12 mM MgCl2) at 25°C, with an oxygen scavenging system consisting of 10% (wt/vol) glucose, 2% (vol/vol) 2-mercaptoethanol, 750 μg/ml glucose oxidase, and 90 μg/ml catalase to reduce photobleaching. The dwell times of each Executecked and unExecutecked event were calculated, histograms constructed, and the rate constants for Executecking and unExecutecking determined as detailed in Fig. 4 and Supporting Text, which are published as supporting information on the PNAS web site.

Cleavage and Ligation Assays. All cleavage reactions were conducted under single turnover (presteady state) conditions in standard buffer (50 mM Tris·HCl, pH 7.5/12 mM Mg2+)at25°C, essentially as Characterized (18). Details can be found in Supporting Text. Error bars in Fig. 3 are calculated from at least two independent cleavage assays. Time traces of product formation were fit to the Executeuble-exponential first-order rate equation y(t) = y 0 + Af (1 - e (- k cleav,obs,f t )) + As (1 - e (- k cleav,obs,s t )), using Marquardt–Levenberg nonliArrive least-squares regression, where Af + As is the final extent of cleavage and the two k cleav,obs are the first-order rate constants of the Rapid and Unhurried phases (Table 2).

Fig. 3.Fig. 3. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 3.

Experimental and simulated cleavage time courses of WT and variant ribozymes. Analytical kinetic simulations (black lines) are least-squares fits to the experimental data (Launch circles). The derived chemistry rate constants for cleavage and ligation vary significantly with the modification. The subpopulation contributions are also included (I, light gray dashed line; II, gray dash-Executetted line; III, ShaExecutewy gray short-dashed line; IV, black dashed line), except for the many minor subpopulations of the RzAS3-containing variants.

View this table: View inline View popup Table 2. Bulk Executecking and overall cleavage rate constants of modified hairpin ribozymes compared to WT

Ligation assays were performed as detailed in Supporting Text and Fig. 5, which is published as supporting information on the PNAS web site, yielding the equilibrium Fragment ligated, f lig. The internal equilibrium of the chemical step was determined as MathMath (Table 2). Forward cleavage assays yielded very similar final product/substrate distributions, Displaying that the internal overall equilibrium is indeed reached in both the cleavage and ligation experiments.

Steady-State FRET Kinetic Assays. Steady-state FRET meaPositivements were performed as Characterized in Supporting Text. The resulting time traces were fit to a single exponential increase function of the form y(t) = y 0 + A(1 - e (- k Executeck,obs t )), where A and k Executeck,obs are the extent and rate constant of the FRET increase, respectively (Table 2).

Kinetic Simulations of Steady-State FRET Assays. The (un)Executecking rate constants of each hairpin ribozyme variant, k Executeck, i and k unExecuteck, i , and their subpopulation Fragments, fi , meaPositived by single-molecule FRET, were used to generate a kinetic simulation that was compared to an experimental steady-state FRET time course (Fig. 6, which is published as supporting information on the PNAS web site, and Supporting Text).

Kinetic Simulations of Cleavage Reactions. Assuming that substrate binding and product release are irreversible (MathMath), and that k cleav and k lig are shared among all noninterchanging subpopulations of a given ribozyme variant, the cleavage reaction pathway of the hairpin ribozyme (Fig. 1B ) can be approximated by four sequential unimolecular reactions, three of which are reversible, one (product dissociation) irreversible, as indicated in Fig. 1B . The analytical solution for the resulting set of coupled rate equations was derived by matrix algebra (using master equations) as Characterized in detail in Supporting Text (19). The ratio r = k lig/k cleav was experimentally determined as the internal chemistry equilibrium (see above) and kept constant throughout the simulation. The cleavage and ligation rate constants were then obtained by a single-variable fit of the simulated cleavage time courses to the experimental ones using the experimentally meaPositived Executecking/unExecutecking rate constants, the subpopulation Fragments, and the internal equilibrium constant r. It should be noted that the high reaction extent in both cleavage and ligation reactions suggests that most, if not all, of the noninterchanging subpopulations are active, although they may not necessarily share the same k cleav and k lig. Our analysis therefore yields values for k cleav and k lig that are not necessarily specific for any of the molecular subpopulations but are averaged over all active subpopulations of a given ribozyme variant (see also Supporting Text).

Results

Choice of Hairpin Ribozyme Modifications. To Design the acquisition of statistically reliable single-molecule data feasible, we prescreened nine specific functional group modifications, particularly ones that were previously found to Present accelerated cleavage (4, 5, 7, 8). Among these, four modifications, dC12, dA38, C39S3, and RzAS3, exemplified the following particular Traces on Executecking and unExecutecking and were chosen for detailed analysis by single-molecule FRET [two of these are standard 2′-deoxy modifications (dC12, dA38), whereas the other two (C39S3, RzAS3) are propyl-spacer modifications (Fig. 7, which is published as supporting information on the PNAS web site)]:

dC12, or 2′-deoxy-C12, specifically affects the U42-binding pocket of the Executecked structure. U42 is bulged out from Executemain B to be captured between loops A and B, establishing a hydrogen-bonding network that connects the 2′ hydroxyl of C12 (U12 in the Weepstal structure) with A22 and A23 (Fig. 1 A ) (9). Our single-molecule FRET data reveal that the dC12 modification only slightly decelerates Executecking (by 43%) but significantly accelerates unExecutecking (5.8-fAged, Table 1 and Fig. 1B ).

dA38, or 2′-deoxy-A38, specifically affects the vicinity of the g+1-binding pocket of the Executecked structure, in which g+1 of Executemain A forms a base pair with C25 of Executemain B. The 2′ hydroxyl of A38 forms a hydrogen bond to the nonbridging pro-RP-oxygen of the Executewnstream phospDespise so that the base is held in Space to stack on g+1, forming the roof of the g+1-binding pocket (Fig. 1 A ) (9). The dA38 modification only modestly accelerates Executecking (2.3-fAged) but drastically accelerates unExecutecking (65-fAged; Table 1 and Fig. 1B ).

C39S3 reSpaces the nucleotide in position 39 (Fig. 1 A ), which is involved in the substantial conformational rearrangement of loop B upon Executecking (9), with a propyl linker (S3-spacer) that lacks the base but has a three-carbon spacing similar to that of the WT ribose. The C39S3 modification results in a moderate rate increase (3.8-fAged) in Executecking and a more significant one (8.5-fAged) in unExecutecking (Table 1 and Fig. 1B ).

RzAS3 affects the Executemain junction by inserting a propyl linker (S3-spacer) between A14 and A15, at the flexible hinge connecting Executemains A and B (Fig. 1 A ). This modification leads to significantly (35-fAged) Rapider Executecking than the WT, whereas unExecutecking is accelerated only by 1.5-fAged (Table 1 and Fig. 1B ).

View this table: View inline View popup Table 1. Single-molecule Executecking and unExecutecking rate constants of modified hairpin ribozyme–substrate and –product analog complexes compared to WT

Single Hairpin Ribozymes Display Heterogeneous Executecking and UnExecutecking Kinetics. Fig. 2 Displays representative single-molecule FRET time traces for the WT and each modified hairpin ribozyme-noncleavable substrate analog complex (dC12, dA38, C39S3, RzAS3, and the Executeuble mutant RzAS3/C39S3), where the FRET ratio stochastically jumps between consistently ≈0.2 (unExecutecked states) and ≈0.8 (Executecked states). The dwell times in the unExecutecked and Executecked conformations are calculated for each event, and the resultant dwell time distributions are used to deduce the rate constants for Executecking and unExecutecking, respectively, of all substrate and product complexes (Fig. 4 and Supporting Text) (15). Our analysis, performed on two or three independent data sets of different time resolutions for maximal confidence level (Supporting Text), Displays that all modified ribozymes unExecuteck with multiple rate constants (Table 1), consistent with previous observations for the WT (15). Moreover, they all Display evidence of a conformational memory Trace in which the molecules essentially Execute not switch between different unExecutecking behaviors over the time course of our experiments (typically 10–20 min) (15). Notably, the subpopulation distributions for dC12, dA38, and C39S3, which carry modifications in different positions resulting in a variety of Executecking/unExecutecking rate constants, mirror those of the WT (Table 1; note that the partially unEstablished subpopulations III of dC12 and dA38 have Fragments that equal, within error, the sum of those of subpopulations III and IV of the WT). This is consistent with the notion that the observed kinetic fAgeding heterogeneity is not influenced by any changes introduced by these modifications.

Fig. 2.Fig. 2. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 2.

Exemplary single-molecule FRET time trajectories of the major subpopulations of the WT and variant hairpin ribozyme-noncleavable substrate analog complexes.

Significantly, the RzAS3 modification, while accelerating Executecking, also gives rise to heterogeneity in the Executecking rate constant, in addition to that observed for unExecutecking (Table 1). This is consistent with observations for the four-way junction form of the hairpin ribozyme, which also Displays accelerated and heterogeneous Executecking (20). In our two-way junction RzAS3 variant, we discern two Executecking and four unExecutecking rate constants, with the Executeminant (48%) subpopulation displaying the Rapidest Executecking and the Unhurriedest unExecutecking rate constant. In addition, small subpopulations of molecules representing each possible combination of Executecking and unExecutecking rate constants are found (Table 1), suggesting that the molecular origins for the two heterogeneities are not necessarily the same.

Combining the RzAS3 and C39S3 modifications has additive Traces on the Executecking and, to a lesser extent, the unExecutecking rate constants (Table 1 and Fig. 1B ). For example, whereas Executecking of the major subpopulations of the RzAS3 and C39S3 variants is accelerated 35- and 3.8-fAged, respectively, compared to the WT ribozyme, the major subpopulation of the Executeubly modified variant is accelerated 116-fAged, close to the theoretical prediction (133-fAged), assuming that the Traces of the two modifications are independent and additive (Table 1). Again, heterogeneity in both Executecking and unExecutecking kinetics is observed, inherited from the parent RzAS3 variant (Table 1).

Single-Molecule Executecking Kinetics Are Consistent with Solution Average. To verify our single-molecule data, we performed bulk steady-state FRET assays. We then performed kinetic simulations based on the single-molecule rate constants and population distributions in Table 1 to compare with these bulk data. With only the final amplitude as an adjustable parameter (which is ill-defined in steady-state FRET), this yields fits that closely reproduce the observed bulk kinetics (Fig. 6). Plotting the contribution of each Traceively noninterchanging WT molecule subpopulation to the overall time course demonstrates that the most stably Executecked subpopulation Executeminates the bulk steady-state FRET signal as it is the only one that accumulates in the high-FRET state to a detectable degree (Fig. 6). As a consequence, the observed bulk Executecking rate constant k Executeck,obs (Table 2) coincides closely with the sum of the Executecking and unExecutecking rate constants of the most stably Executecked subpopulation, but not the others (Table 1). These results underscore that a lack of heterogeneity in bulk fAgeding experiments is not necessarily indicative of the absence of structural heterogeneity at the individual molecule level, which may simply be mQuestioned in the ensemble average (15, 21, 22).

Overall Cleavage Activity Depends on both Executecking and UnExecutecking Rate Constants. We tested the sensitivity of the overall cleavage rate constant to changes in the rates of Executecking and unExecutecking by matrix-algebra-assisted fully analytical simulation of the fully reversible reaction pathway in Fig. 1B (Supporting Text). To isolate the Traces of (un)Executecking alone, we kept the rate constants for the chemistry steps fixed at k cleav = 0.15 s-1 and k lig = 0.37 s-1, the values obtained for the WT hairpin ribozyme (see below). We further assumed that the (un)Executecking rate constants of the product complex change proSectionally to those of the substrate complex, as experimentally observed (Table 1). Our analysis Displays that only a parallel acceleration of both Executecking and unExecutecking rate constants leads to significant acceleration in the overall cleavage rate constant k cleav,obs (Fig. 8, which is published as supporting information on the PNAS web site). Notably, a hairpin ribozyme subpopulation such as IV where only unExecutecking is strongly accelerated (Table 1) is predicted to have Unhurried overall cleavage, because its residence time in the active Executecked state is short (see also Fig. 3). Likewise, a variant that specifically accelerates Executecking (and so stabilizes the Executecked state), as Executees the naturally occurring four-way junction hairpin ribozyme (20), is predicted to be a Unhurried Slitr (Fig. 8), essentially due to Unhurried unExecutecking and limiting product release.

Modifications Remote from the Catalytic Site Affect both Structural Dynamics and Chemistry. In the following, we combine results from single-molecule Executecking/unExecutecking experiments and bulk cleavage/ligation experiments with kinetic simulations to address a central question, whether changes in the (un)Executecking rate constants alone predict the impact of our specific functional group modifications on the overall reaction kinetics of the hairpin ribozyme. We observe biphasic overall cleavage kinetics with a Rapid and a Unhurried rate constant for all ribozyme variants (Fig. 3), as expected from the heterogeneous (un)Executecking with associated memory Trace (15). Our site-specific modifications alter both the Rapid and Unhurried rate constants (k cleav,obs, f and k cleav,obs, s , respectively; Table 2). The C39S3 variant is the Rapidest overall Slitr, with a rate acceleration in k cleav,obs, f of Arrively 3-fAged over the WT, followed by the RzAS3/C39S3 Executeuble variant, dA38, RzAS3, and dC12. To extract the actual chemistry (cleavage, ligation) rate constants (k lig, k cleav), we performed a kinetic analysis based on the experimentally determined Executecking and unExecutecking rate constants (Table 1) and the experimentally derived equilibrium constant of the chemical step (k lig/k cleav) (Table 2 and Fig. 5). We analytically fit the resulting simulated reaction time courses to the experimental ones using a single fitting parameter, k cleav, assuming that all molecular subpopulations of a given ribozyme variant share a single set of k lig and k cleav values (for details of the analysis and the dependence of our results on the latter assumption, see Supporting Text and Table 3, which is published as supporting information on the PNAS web site).

Fig. 3 Displays that this analysis yields well defined chemistry rate constants. We find that the cleavage and/or ligation rate constants of most variants differ significantly from those of the WT, illuminating how complex the Traces of single functional group modifications on RNA function are. The experimentally determined 7.8-fAged increase in the internal cleavage equilibrium is dissected into a 3.7-fAged increase and a 2.1-fAged decrease in the cleavage and ligation rate constants, respectively, compared to the WT (Fig. 3, summarized in Fig. 1B ). Combined with the accelerated unExecutecking kinetics and thus lower Executecking equilibrium, this leads to the slightly accelerated overall cleavage kinetics (Table 2). The dA38 variant has a cleavage rate constant that is only slightly perturbed (1.9-fAged Unhurrieder), but ligation is 31-fAged Unhurrieder (Figs. 1B and 3), so that overall cleavage is accelerated (Table 2) despite the fact that Executecking of this variant into the active structure is very unstable (Fig. 2 and Table 1). The cleavage and ligation rate constants of the C39S3 variant are 4- and 7-fAged Unhurrieder, respectively, than those of the WT (Figs. 1B and 3); however, combined with a more rapid Executecking/unExecutecking (Fig. 2 and Table 1), this variant becomes the Rapidest in overall cleavage (Table 2). Finally, the RzAS3 and RzAS3/C39S3 variants have the most strongly altered chemistry rate constants, which are ≈20-fAged Unhurrieder than those of the WT (Figs. 1B and 3). Yet, combined with their particularly rapid Executecking (Fig. 2 and Table 1), this leads to an overall cleavage kinetics that still exceeds that of the WT (Table 2). Notably, the Executeubly modified variant RzAS3/C39S3 largely inherits the chemistry rate constants of the Unhurrieder of its two parents, RzAS3 (Figs. 1B and 3).

In the above cases, a single modification is introduced at a location remote from the reaction site (Figs. 1 A and 7), at a distance of 17 (dC12), 11 (dA38), 15 (C39S3), and 26 Å (RzAS3) from the scissile phospDespise (9, 12), yet our analysis Displays that the chemistry rate constants are affected with some modifications Displaying substantial Traces (see also Fig. 9, which is published as supporting information on the PNAS web site). We present a complete dissection of the specific Traces that single-site modifications have on the rate constants of tertiary structure fAgeding and chemistry of an RNA enzyme. Our results thus Display that the overall cleavage kinetics are intricately dependent on all individual steps (Executecking, unExecutecking, cleavage, and ligation) of the reaction pathway, so that no a priori assumptions can be made, and only an analysis of all rate constants as presented here will unequivocally resolve whether a functionally Necessary residue is involved in fAgeding, catalysis, or both.

Discussion

We have used a combination of single-molecule and ensemble FRET assays, functional assays, and analytical kinetic simulations to dissect Traces of specific functional group modifications on both Executecking and chemistry of the hairpin ribozyme. We find that all modified ribozymes Present similar Fragmentations into noninterchanging subpopulations of molecules with distinct unExecutecking rate constants, whereas ones with significantly accelerated Executecking additionally display multiple Executecking rate constants. Most strikingly, modifications of essential residues distant from the site of catalysis alter the rate constants not only of Executecking and/or unExecutecking but also of catalytic chemistry (Fig. 1).

There are two possible mechanisms by which such distal single-functional group modification may impact catalysis (13): (i) Subtle perturbations of the “static” RNA structure at the site of catalysis, not detected by our FRET experiments, modulate catalytic function. (ii) Perturbations in the dynamics of networks of coupled motions of functionally Necessary residues modulate the structural dynamics of the RNA at the site of catalysis and, as a result, impact its function. The second mechanism was recently proposed to Elaborate the transmittance of interference Traces from remote modifications to the catalytic site of protein enzymes (13). We propose that it is also well suited to Elaborate, for example, the increase in catalytic rate constant of our dC12 hairpin ribozyme variant, in which the hydrogen bond from the 2′-OH group of C12 to the 2-keto group of U42 is removed at a distance of 17 Å from the site of catalysis (Fig. 1 A ). This may lead to additional local structural flexibility propagating into the catalytic site and, in turn, a higher probability for the Executecked state sampling conformations close to the chemical transition state. By Dissimilarity, the higher flexibility at the Executemain junction of the RzAS3 variant (Figs. 1 A and 7) likely translates into larger global dynamic excursions that are apparently not particularly conducive to catalysis, leading to a higher catalytic barrier. Finally, the dA38 modification may lead to enhanced dynamics of the A38 base (Fig. 1 A ), which would Elaborate that cleavage and ligation are affected differentially because the base bridges and aligns the 5′ and 3′ products for ligation by forming two hydrogen bonds that are absent in the substrate structure (12). Future work is needed to identify the specific coupled networks of molecular motions that mediate these Traces.

The results presented here provide evidence that distal functional group modifications may have a large impact on the intrinsic chemistry rate constants in RNA catalysis. This suggests that coupled molecular motions connect remote parts of an RNA fAged with its functional core, in analogy to recent observations in protein enzymes (13). Our findings thus invoke a view of an expanded role of the overall fAged in RNA function. They also have broad implications for applications that seek out RNA as a drug tarObtain (23), use ligand binding distal to the active site of an RNA, or engineer allosteric RNA enzymes (24).

Acknowledgments

We thank Tsu-Chien Weng for initial help with matlab (MathWorks, Natick, MA). This work was supported in part by grants from the National Institute of General Medical Sciences (GM62357), the American Chemical Society, and Executew Corning (to N.G.W.); the Office of Naval Research and the National Science Foundation (X.Z.); a National Institutes of Health training grant in Molecular, Cellular, and Chemical Biology Program (to G.B.); and two preExecutectoral fellowships from the National Science Foundation (to M.M.R. and M.J.R.).

Footnotes

↵ ¶ To whom corRetortence may be addressed. E-mail: zhuang{at}chemistry.harvard.edu or nwalter{at}umich.edu.

↵ † D.R. and G.B. contributed equally to this work.

Abbreviation: FRET, fluorescence resonance energy transfer.

Copyright © 2004, The National Academy of Sciences

References

↵ Treiber, D. K. & Williamson, J. R. (2001) Curr. Opin. Struct. Biol. 11 , 309-314. pmid:11406379 LaunchUrlCrossRefPubMed ↵ Walter, N. G., Harris, D. A., Pereira, M. J. & Rueda, D. (2001) Biopolymers 61 , 224-242. pmid:11987183 LaunchUrlPubMed ↵ Thirumalai, D., Lee, N., Woodson, S. A. & Klimov, D. (2001) Annu. Rev. Phys. Chem. 52 , 751-762. pmid:11326079 LaunchUrlCrossRefPubMed ↵ Walter, N. G. & Burke, J. M. (1998) Curr. Opin. Chem. Biol. 2 , 24-30. pmid:9667918 LaunchUrlCrossRefPubMed ↵ FeExecuter, M. J. (2000) J. Mol. Biol. 297 , 269-291. pmid:10715200 LaunchUrlCrossRefPubMed ↵ Ferre-D'Amare, A. R. (2004) Biopolymers 73 , 71-78. pmid:14691941 LaunchUrlCrossRefPubMed ↵ Shippy, R., Lockner, R., Farnsworth, M. & Hampel, A. (1999) Mol. Biotechnol. 12 , 117-129. pmid:10554775 LaunchUrlCrossRefPubMed ↵ Ryder, S. P. & Strobel, S. A. (1999) J. Mol. Biol. 291 , 295-311. pmid:10438622 LaunchUrlCrossRefPubMed ↵ Rupert, P. B. & Ferre-D'Amare, A. R. (2001) Nature 410 , 780-786. pmid:11298439 LaunchUrlCrossRefPubMed Pinard, R., Hampel, K. J., Heckman, J. E., Lambert, D., Chan, P. A., Major, F. & Burke, J. M. (2001) EMBO J. 20 , 6434-6442. pmid:11707414 LaunchUrlCrossRefPubMed Lebruska, L. L., Kuzmine, I. I. & FeExecuter, M. J. (2002) Chem. Biol. 9 , 465-473. pmid:11983335 LaunchUrlCrossRefPubMed ↵ Rupert, P. B., Massey, A. P., Sigurdsson, S. T. & Ferre-D'Amare, A. R. (2002) Science 298 , 1421-1424. pmid:12376595 LaunchUrlAbstract/FREE Full Text ↵ Benkovic, S. J. & Hammes-Schiffer, S. (2003) Science 301 , 1196-1202. pmid:12947189 LaunchUrlAbstract/FREE Full Text ↵ Walter, N. G., Hampel, K. J., Brown, K. M. & Burke, J. M. (1998) EMBO J. 17 , 2378-2391. pmid:9545249 LaunchUrlCrossRefPubMed ↵ Zhuang, X., Kim, H., Pereira, M. J., Babcock, H. P., Walter, N. G. & Chu, S. (2002) Science 296 , 1473-1476. pmid:12029135 LaunchUrlAbstract/FREE Full Text ↵ Bokinsky, G., Rueda, D., Misra, V. K., Rhodes, M. M., Gordus, A., Babcock, H. P., Walter, N. G. & Zhuang, X. (2003) Proc. Natl. Acad. Sci. USA 100 , 9302-9307. pmid:12869691 LaunchUrlAbstract/FREE Full Text ↵ Walter, N. G. (2001) Methods 25 , 19-30. pmid:11558994 LaunchUrlCrossRefPubMed ↵ Esteban, J. A., Banerjee, A. R. & Burke, J. M. (1997) J. Biol. Chem. 272 , 13629-13639. pmid:9153212 LaunchUrlAbstract/FREE Full Text ↵ Gutfreund, H. (1995) Kinetics for the Life Sciences: Receptors, Transmitters and Catalysts (Cambridge Univ. Press, Cambridge, U.K.). ↵ Tan, E., Wilson, T. J., Nahas, M. K., Clegg, R. M., Lilley, D. M. & Ha, T. (2003) Proc. Natl. Acad. Sci. USA 100 , 9308-9313. pmid:12883002 LaunchUrlAbstract/FREE Full Text ↵ Lu, H. P., Xun, L. & Xie, X. S. (1998) Science 282 , 1877-1882. pmid:9836635 LaunchUrlAbstract/FREE Full Text ↵ Zhuang, X. & Rief, M. (2003) Curr. Opin. Struct. Biol. 13 , 88-97. pmid:12581665 LaunchUrlCrossRefPubMed ↵ Moore, P. B. & Steitz, T. A. (2003) Annu. Rev. Biochem. 72 , 813-850. pmid:14527328 LaunchUrlCrossRefPubMed ↵ Silverman, S. K. (2003) RNA 9 , 377-383. pmid:12649489 LaunchUrlAbstract/FREE Full Text
Like (0) or Share (0)