A single-molecule study of RNA catalysis and folding

The origins of RNA catalysis in ribozymes

The discovery of RNA catalysis provided a paradigm shift in biology, insight into the evolution of life on the planet and a challenge to understand its mechanistic origins. RNA has limited catalytic resources that must be used to maximal effect. Consequently, RNA catalysis tends to be multifactorial, with several processes contributing to an overall significant enhancement of reaction rate. These include general acid-base catalysis, electrostatic effects, and substrate orientation and proximity. The main players are the RNA nucleobases and bound metal ions. Although most ribozymes carry out phosphoryl transfer, the same considerations appear to apply to peptidyl transfer in the ribosome.

Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations

Vesicle fusion in eukaryotes is thought to involve the assembly of a highly conserved family of proteins termed soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) into a highly stable parallel four-helix bundle. We have used intermolecular single-molecule fluorescence resonance energy transfer to characterize preassembled neuronal SNARE complexes consisting of syntaxin, synaptobrevin, and synaptosome-associated protein of 25 kDa on deposited lipid bilayers. Surprisingly, we found a mixture of parallel as well as antiparallel configurations involving the SNARE motifs of syntaxin and synaptobrevin as well as those of syntaxin and synaptosome-associated protein of 25 kDa. The subpopulation with the parallel four-helix bundle configuration could be greatly enriched by an additional purification step in the presence of denaturant, indicating that the parallel configuration is the energetically most favorable state. Interconversion between the configurations was not observed. From this observation, we infer the conversion rate to be <1.5 h-1. The existence of antiparallel configurations suggests a regulatory role of chaperones, such as N-ethylmaleimide-sensitive factor, or the membrane environment during SNARE complex assembly in vivo, and it could be a partial explanation for the relatively slow rates of vesicle fusion observed by reconstituted fusion experiments in vitro.

The power and prospects of fluorescence microscopies and spectroscopies

Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.

Diversity in the rates of transcript elongation by single RNA polymerase molecules

Single-molecule measurements of the activities of a variety of enzymes show that rates of catalysis may vary markedly between different molecules in putatively homogeneous enzyme preparations. We measured the rate at which purified Escherichia coli RNA polymerase moves along a approximately 2650-bp DNA during transcript elongation in vitro at 0.5 mm nucleoside triphosphates. Individual molecules of a specifically biotinated RNA polymerase derivative were tagged with 199-nm diameter avidin-coated polystyrene beads; enzyme movement along a surface-linked DNA molecule was monitored by observing changes in bead Brownian motion by light microscopy. The DNA was derived from a naturally occurring transcription unit and was selected for the absence of regulatory sequences that induce lengthy pausing or termination of transcription. With rare exceptions, individual enzyme molecules moved at a constant velocity throughout the transcription reaction; the distribution of velocities across a population of 140 molecules was unimodal and was well fit by a Gaussian. However, the width of the Gaussian, sigma = 6.7 bp/s, was considerably larger than the precision of the velocity measurement (1 bp/s). The observations show that different transcription complexes have differences in catalytic rate (and thus differences in structure) that persist for thousands of catalytic turnovers. These differences may provide a parsimonious explanation for the complex transcription kinetics observed in bulk solution.

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

Single metallic nanoparticle imaging for protein detection in cells

We performed a visualization of membrane proteins labeled with 10-nm gold nanoparticles in cells, using an all-optical method based on photothermal interference contrast. The high sensitivity of the method and the stability of the signals allows 3D imaging of individual nanoparticles without the drawbacks of photobleaching and blinking inherent to fluorescent markers. A simple analytical model is derived to account for the measurements of the signal amplitude and the spatial resolution. The photothermal interference contrast method provides an efficient, reproducible, and promising way to visualize low amounts of proteins in cells by optical means.

Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models

The measurement of fluorescence from single protein molecules has become an important new tool in the study of dynamic processes, allowing for the direct visualization of the motions experienced by individual proteins and macromolecular complexes. The data from such single-molecule experiments are in the form of photon trajectories, consisting of arrival times and wavelength information on individual photons. The analysis of photon trajectories can be difficult, particularly if the motions are occurring at rates comparable to the photon arrival rate or in the presence of noise. In this paper, we introduce the use of hidden Markov models (HMMs) for the analysis of photon trajectory data that operate using the photon data directly, without the need for ensemble averaging of the data as implied by correlation function analysis. Using a simple kinetic model, we examine the relationship between the uncertainty in the estimates of the motional rate and the photon detection rate. Remarkably, we obtain relative uncertainties in the rate constants of as little as 3% even when the interconversion rate is equal to the photon detection rate, and the uncertainty increases to only 10% when the interconversion rate is 10 times the photon detection rate. This suggests that useful information can be obtained for much faster kinetic regimes than have typically been studied. We also examine the impact of background photons on the determination of the rate and demonstrate that the HMM-based approach is robust, displaying small uncertainties for background photon arrival rates approaching that of the signal. These results not only are relevant in establishing the theoretical limits on precision, but are also useful in the context of experimental design. Finally, to demonstrate how the methodology can be extended to more complex kinetic models and how it can allow one to make use of the full power of statistics for purposes of model evaluation and selection, we consider a four-state kinetic model for protein conformational transitions previously studied by Schenter et al. (J. Phys. Chem. A1999, 103, 10477). We show how an HMM can be used as an alternative to higher-order correlation function analysis for the detection of "conformational memory" and apparent non-Markovian dynamics arising from such temporally inhomogeneous kinetic schemes.

Single-molecule measurement of protein folding kinetics

In order to investigate the behavior of single molecules under conditions far from equilibrium, we have coupled a microfabricated laminar-flow mixer to a confocal optical system. This combination enables time-resolved measurement of Förster resonance energy transfer after an abrupt change in solution conditions. Observations of a small protein show the evolution of the intramolecular distance distribution as folding progresses. This technique can expose subpopulations, such as unfolded protein under conditions favoring the native structure, that would be obscured in equilibrium experiments.

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.

Fluorescence spectroscopy of single molecules under ambient conditions: methodology and technology

This review presents an overview of the fluorescence detection and spectroscopy of single molecules (SMS) in liquids and on surfaces under ambient conditions. The various techniques of SMS, such as confocal epifluorescence detection and wide-field imaging are presented and discussed, together with the different methods of data analysis such as fluorescence correlation spectroscopy and burst-by-burst analysis. Selected applications of the various techniques in physics, chemistry, and biology are described.

A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

The natural form of the hairpin ribozyme comprises two major structural elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction. The ribozyme folds into its active conformation by an intimate association between the loops, and the efficiency of this process is greatly enhanced by the presence of the junction. We have used single-molecule spectroscopy to show that the natural form fluctuates among three distinct states: the folded state and two additional, rapidly interconverting states (proximal and distal) that are inherited from the junction. The proximal state juxtaposes the two loop elements, thereby increasing the probability of their interaction and thus accelerating folding by nearly three orders of magnitude and allowing the ribozyme to fold rapidly in physiological conditions. Therefore, the hairpin ribozyme exploits the dynamics of the junction to facilitate the formation of the active site from its other elements. Dynamic interplay between structural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other functional RNA molecules.

Single-molecule transition-state analysis of RNA folding

How RNA molecules fold into functional structures is a problem of great significance given the expanding list of essential cellular RNA enzymes and the increasing number of applications of RNA in biotechnology and medicine. A critical step toward solving the RNA folding problem is the characterization of the associated transition states. This is a challenging task in part because the rugged energy landscape of RNA often leads to the coexistence of multiple distinct structural transitions. Here, we exploit single-molecule fluorescence spectroscopy to follow in real time the equilibrium transitions between conformational states of a model RNA enzyme, the hairpin ribozyme. We clearly distinguish structural transitions between effectively noninterchanging sets of unfolded and folded states and characterize key factors defining the transition state of an elementary folding reaction where the hairpin ribozyme's two helical domains dock to make several tertiary contacts. Our single-molecule experiments in conjunction with site-specific mutations and metal ion titrations show that the two RNA domains are in a contact or close-to-contact configuration in the transition state even though the native tertiary contacts are at most partially formed. Such a compact transition state without well formed tertiary contacts may be a general property of elementary RNA folding reactions.

Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction

Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (k(obs)) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg(2+) at physiological concentrations, with both showing an Mg(2+) Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min(-1) at 10 mM Mg(2+); neither slower kinetics nor obvious Mg(2+) inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.

Single-molecule detection of DNA hybridization

We demonstrate the detection of nanometer-scale conformational changes of single DNA oligomers through a micromechanical technique. The quantity monitored is the displacement of a micrometer-size bead tethered to a surface by the probe molecule undergoing the conformational change. This technique allows probing of conformational changes within distances beyond the range of fluorescence resonance energy transfer. We apply the method to detect single hybridization events of label-free target oligomers. Hybridization of the target is detected through the conformational change of the probe.

Single-molecule photon counting statistics via generalized optical Bloch equations

We derive the generating function for single molecule photon emission events within the context of the stochastically modulated optical Bloch equations. Statistical properties of single molecule photon counting experiments are deduced from a set of coupled differential equations only slightly more complicated than the Bloch equations themselves. This formulation allows for the study of photon bunching and antibunching within a single theoretical framework and provides a description of these behaviors that emphasizes the connection with single molecule experiments. Application is made to the spectroscopy of a chromophore coupled to a single two level system.

Unzipping kinetics of double-stranded DNA in a nanopore

We studied the unzipping of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. Polymerase chain reaction analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.

Photodestruction intermediates probed by an adjacent reporter molecule

We used a fluorescence resonance energy transfer donor molecule to probe the multiple intermediates in the photoinduced destruction of an acceptor molecule. These intermediates are nonemitting but are still able to quench the fluorescence of the donor at a distance scale shorter than conventional fluorescence resonance energy transfer, suggesting novel biophysical applications.

Single molecule detection of DNA looping by NgoMIV restriction endonuclease

Single molecule fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy were used to investigate DNA looping by NgoMIV restriction endonuclease. Using a linear double-stranded DNA (dsDNA) molecule labeled with a fluorescence donor molecule, Cy3, and fluorescence acceptor molecule, Cy5, and by varying the concentration of NgoMIV endonuclease from 0 to 3 x 10(-6) M, it was possible to detect and determine diffusion properties of looped DNA/protein complexes. FRET efficiency distributions revealed a subpopulation of complexes with an energy transfer efficiency of 30%, which appeared upon addition of enzyme in the picomolar to nanomolar concentration range (using 10(-11) M dsDNA). The concentration dependence, fluorescence burst size analysis, and fluorescence correlation analysis were all consistent with this subpopulation arising from a sequence specific interaction between an individual enzyme and a DNA molecule. A 30% FRET efficiency corresponds to a distance of approximately 65 A, which correlates well with the distance between the ends of the dsDNA molecule when bound to NgoMIV according to the crystal structure of this complex. Formation of the looped complexes was also evident in measurements of the diffusion times of freely diffusing DNA molecules with and without NgoMIV. At very high protein concentrations compared to the DNA concentration, FRET and fluorescence correlation spectroscopy results revealed the formation of larger DNA/protein complexes.

RNA labeling and immobilization for nano-displacement measurement: probing three-dimensional RNA structure

RNA molecules play essential roles in many biological processes, including the storage and transfer of information in the cell. These events are mediated via RNA-protein interactions or by catalytic RNA molecules. It is now recognized that unique RNA folds are associated with biological functions. Therefore, to study the intrinsic structural changes and dynamics which regulate the various functions of RNA, it is necessary to probe its three-dimensional structure in solution. In this respect, using single-molecule methodologies may allow study of native RNA molecules independent of their size and in real time. However, this may require the immobilization of RNA on a surface. Here, we report a novel approach to immobilize RNA on a glass. The procedures involve both chemical and enzymatic modifications of long RNA molecules. In addition, we demonstrate the application of an optical tweezers apparatus to measure the length and, hence, the dynamics of immobilized intact ribosomal RNA molecules as a function of different solution conditions.

RNA folding: models and perspectives

Intrinsic events during RNA folding include conformational search and metal ion binding. Several experimentally testable models have been proposed to explain how large ribozymes accomplish folding. Future challenges include the validation of these models, and the correlation of experimental results and theoretical simulations.

Effect of transcription on folding of the Tetrahymena ribozyme

Sequential formation of RNA interactions during transcription can bias the folding pathway and ultimately determine the functional state of a transcript. The kinetics of cotranscriptional folding of the Tetrahymena L-21 ribozyme was compared with refolding of full-length transcripts under the same conditions. Sequential folding after transcription by phage T7 or Escherichia coli polymerase is only twice as fast as refolding, and the yield of native RNA is the same. By contrast, a greater fraction of circularly permuted variants folded correctly at early times during transcription than during refolding. Hybridization of complementary oligonucleotides suggests that cotranscriptional folding enables a permuted RNA beginning at G303 to escape non-native interactions in P3 and P9. We propose that base pairing of upstream sequences during transcription elongation favors branched secondary structures that increase the probability of forming the native ribozyme structure.

Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Gō-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T(opt). The optimal folding temperature T(opt) is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T(opt) and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T(opt) and start to diverge when the temperature is lower than T(opt). The distribution of FPT is close to a log-normal-like distribution at T > or = T(opt). At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA

Docking of the P1 duplex into the pre-folded core of the Tetrahymena group I ribozyme exemplifies the formation of tertiary interactions in the context of a complex, structured RNA. We have applied Phi-analysis to P1 docking, which compares the effects of modifications on the rate constant for docking (k(dock)) with the effects on the docking equilibrium (K(dock)). To accomplish this we used a single molecule fluorescence resonance energy transfer assay that allows direct determination of the rate constants for formation of thermodynamically favorable, as well as unfavorable, states. Modification of the eight groups of the P1 duplex that make tertiary interactions with the core and changes in solution conditions decrease K(dock) up to 500-fold, whereas k(dock) changes by </=2-fold. The absence of effects on k(dock), both from atomic modifications and global perturbations, strongly suggests that the transition state for docking is early and does not closely resemble the docked state. These results, the slow rate of docking of 3s(-1), and the observation that a modification that is expected to increase the degrees of freedom between the P1 duplex and the ribozyme core accelerates docking, suggest a model in which a kinetic trap(s) slows docking substantially. Nonetheless, urea does not increase k(dock), suggesting that there is little change in the exposed surface area between the trapped, undocked state and the transition state. The findings highlight that urea and temperature dependencies can be inadequate to diagnose the presence of kinetic traps in a folding process. The results described here, combined with previous work, provide an in-depth view of an RNA tertiary structure formation event and suggest that large, highly structured RNAs may have local regions that are misordered.

Mechanically probing the folding pathway of single RNA molecules

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating the experimentally determined free energy rules for RNA secondary structure, whereas exterior single-stranded regions are modeled as freely jointed chains. For exemplary RNA sequences (hairpins and the Tetrahymena thermophila group I intron), we compute the quasiequilibrium fluctuations in the end-to-end distance as the molecule is unfolded by pulling on opposite ends. Unlike the average quasiequilibrium force-extension curves, these fluctuations reveal clear signatures from the unfolding of individual structural elements. We find that the resolution of these signatures depends on the spring constant of the force-measuring device, with an optimal value intermediate between very rigid and very soft. We compare and relate our results to recent experiments by Liphardt et al. (2001).

Perturbed folding kinetics of circularly permuted RNAs with altered topology

The folding pathway of the Tetrahymena ribozyme correlates inversely with the sequence distance between native interactions, or contact order. The rapidly folding P4-P6 domain has a low contact order, while the slowly folding P3-P7 region has a high contact order. To examine the role of topology and contact order in RNA folding, we screened for circular permutants of the ribozyme that retain catalytic activity. Permutants beginning in the P4-P6 domain fold 5 to 20 times more slowly than the wild-type ribozyme. By contrast, 50% of a permuted RNA that disjoins a non-native interaction in P3 folds tenfold faster than the wild-type ribozyme. Hence, the probability of rapidly folding to the native state depends on the topology of tertiary domains.

Biology and polymer physics at the single-molecule level

The ability to look at individual molecules has given us new insights into molecular processes. Examples of our recent work are given to illustrate how behaviour that may otherwise be hidden from view can be clearly seen in single-molecule experiments.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.

Single-molecule fluorescence lifetime and anisotropy measurements of the red fluorescent protein, DsRed, in solution

Fluorescence lifetime and anisotropy measurements were made on the red fluorescent protein (DsRed) from tropical coral of the Discosoma genus, both at single-molecule and bulk concentrations. As expected from previous work, the fluorescence lifetime of DsRed in solution is dependent on laser power, decreasing from an average fluorescence lifetime in the beam of about 3.3 ns at low power (3.5 ns if one extrapolates to zero power) to about 2.1 ns at 28 kW/cm2. At the single-molecule level, exciting with 532 nm, 10 ps laser pulses at 80 MHz repetition rate, DsRed particles entering the laser beam initially have a lifetime of about 3.6 ns and convert to a form having a lifetime of about 3.0 ns with a quantum yield of photoconversion on the order of 10(-3) (calculated in terms of photons per DsRed tetramer). The particles then undergo additional photoconversion with a quantum yield of roughly 10(-5), generating a form with an average lifetime of 1.6 ns. These results may be explained by rapid photoconversion of one DsRed monomer in a tetramer, which acts as an energy transfer sink, resulting in a lower quantum yield for photoconversion of subsequent monomers. Multiparameter correlation and selective averaging can be used to identify DsRed in a mixture of fluorophores, in part exploiting the fact that fluorescent lifetime of DsRed changes as a function of excitation intensity.

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

Mechanical unfolding trajectories for single molecules of the Tetrahymena thermophila ribozyme display eight intermediates corresponding to discrete kinetic barriers that oppose mechanical unfolding with lifetimes of seconds and rupture forces between 10 and 30 piconewtons. Barriers are magnesium dependent and correspond to known intra- and interdomain interactions. Several barrier structures are "brittle," breakage requiring high forces but small (1 to 3 nanometers) deformations. Barrier crossing is stochastic, leading to variable unfolding paths. The response of complex RNA structures to locally applied mechanical forces may be analogous to the responses of RNA during translation, messenger RNA export from the nucleus, and viral replication.

Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function

The Tetrahymena ribozyme derived from the self-splicing group I intron binds a 5'-splice site analog (S) and guanosine (G), catalyzing their conversion to a 5'-exon analog (P) and GA. Herein, we show that binding of guanosine is exceptionally slow, limiting the reaction at near neutral pH. Our results implicate a conformational rearrangement on guanosine binding, likely because the binding site is not prearranged in the absence of ligand. The fast accommodation of guanosine (10(2) to 10(3) x s(-1)) and prior structural data suggest local rather than global rearrangements, raising the possibility that folding of this and perhaps other large RNAs is not fully cooperative. Guanosine binding is accelerated by addition of residues that form helices, referred to as P9.0 and P10, immediately 5' and 3' to the guanosine. These rate enhancements provide evidence for binding intermediates that have the adjacent helices formed before accommodation of guanosine into its binding site. Because the ability to form the P9.0 and P10 helices distinguishes the guanosine at the correct 3'-splice site from other guanosine residues, the faster binding of the correct guanosine can enhance specificity of 3'-splice site selection. Thus, paradoxically, the absence of a preformed binding site and the resulting slow guanosine binding can contribute to splicing specificity by providing an opportunity for the adjacent helices to increase the rate of binding of the guanosine specifying the 3'-splice site.

Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes

By using single-molecule multiparameter fluorescence detection, fluorescence resonance energy transfer experiments, and newly developed data analysis methods, this study demonstrates directly the existence of three structurally distinct forms of reverse transcriptase (RT):nucleic acid complexes in solution. Single-molecule multiparameter fluorescence detection also provides first information on the structure of a complex not observed by x-ray crystallography. This species did not incorporate nucleotides and is structurally distinct from the other two observed species. We determined that the nucleic acid substrate is bound at a site far removed from the nucleic acid-binding tract observed by crystallography. In contrast, the other two states are identified as being similar to the x-ray crystal structure and represent distinct enzymatically productive stages in DNA polymerization. These species differ by only a 5-A shift in the position of the nucleic acid. Addition of nucleoside triphosphate or of inorganic pyrophosphate allowed us to assign them as the educt and product state in the polymerization reaction cycle; i.e., the educt state is a complex in which the nucleic acid is positioned to allow nucleotide incorporation. The second RT:nucleic acid complex is the product state, which is formed immediately after nucleotide incorporation, but before RT translates to the next nucleotide.

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA(ile). Base pairing of the ribozyme core requires 10-fold less Mg(2+) than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37 degrees C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.

Single-molecule folding

Recent developments in fluorescence and force spectroscopy enable us to go beyond the ensemble average and measure the behavior of individual biomacromolecules. These single-molecule approaches can directly resolve transient intermediate states and multiple reaction pathways, and thus are uniquely powerful in characterizing the complex dynamics of biological processes. Recent applications of these two techniques to the protein and RNA folding problems have led to exciting new results.

Single-molecule kinetics with time-dependent rates: a generating function approach

A theoretical strategy for calculating the statistical properties of time series generated by single molecule measurements is presented. Emphasis is placed on the case where observable states interconvert via rate "constants" exhibiting stochastic time dependence. Such is the case for measurements of single fluorophores coupled to biomolecules undergoing conformational fluctuations [H. P. Lu, L. Xun, and X. S. Xie, Science 282, 1877 (1998)]]. In contrast to previous studies, we focus on the number of fluorophore blinking events occurring within a given amount of time as our stochastic variable. This formulation allows for an elementary analysis within the generating function framework.

Early steps of supported bilayer formation probed by single vesicle fluorescence assays

We have developed a single vesicle assay to study the mechanisms of supported bilayer formation. Fluorescently labeled, unilamellar vesicles (30-100 nm diameter) were first adsorbed to a quartz surface at low enough surface concentrations to visualize single vesicles. Fusion and rupture events during the bilayer formation, induced by the subsequent addition of unlabeled vesicles, were detected by measuring two-color fluorescence signals simultaneously. Lipid-conjugated dyes monitored the membrane fusion while encapsulated dyes reported on the vesicle rupture. Four dominant pathways were observed, each exhibiting characteristic two-color fluorescence signatures: 1) primary fusion, in which an unlabeled vesicle fuses with a labeled vesicle on the surface, is signified by the dequenching of the lipid-conjugated dyes followed by rupture and final merging into the bilayer; 2) simultaneous fusion and rupture, in which a labeled vesicle on the surface ruptures simultaneously upon fusion with an unlabeled vesicle; 3) no dequenching, in which loss of fluorescence signal from both dyes occur simultaneously with the final merger into the bilayer; and 4) isolated rupture (pre-ruptured vesicles), in which a labeled vesicle on the surface spontaneously undergoes content loss, a process that occurs with high efficiency in the presence of a high concentration of Texas Red-labeled lipids. Vesicles that have undergone content loss appear to be more fusogenic than intact vesicles.

Single-molecule fluorescence of nucleic acids

Less than a decade old, single-molecule fluorescence of nucleic acids has rapidly become an important tool in the arsenal of biological probes. A variety of novel approaches to investigate conformational dynamics, catalytic mechanisms, folding pathways and protein-nucleic-acid interactions have recently been devised for nucleic acids using this technique. Combined with biomechanical tools and ensemble measurements, single-molecule fluorescence methods extend our ability to observe and understand biomolecules and complex biological processes.