Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine experiments and simulations to examine the folding/unfolding pathways of the VPK pseudoknot, a variant of the Mouse Mammary Tumor Virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) placed at different stem/loop positions in the PK, and laser temperature-jump approaches serve as local probes allowing us to monitor the order of assembly of VPK with two helices with different intrinsic stabilities. The experiments and molecular simulations show that at 50 mM KCl the dominant folding pathway populates only the more stable partially folded hairpin. As the salt concentration is increased a parallel folding pathway emerges, involving the less stable hairpin structure as an alternate intermediate. Notably, the flux between the pathways is modulated by the ionic strength. The findings support the principle that the order of PK structure formation is determined by the relative stabilities of the hairpins, which can be altered by sequence variations or salt concentrations. Our study not only unambiguously demonstrates that PK folds by parallel pathways, but also establishes that quantitative description of RNA self-assembly requires a synergistic combination of experiments and simulations.Comment: Supporting Information include

Folding Mechanisms of RNA Pseudoknots Unveiled with Laser Temperature-Jump and Global Modeling Approaches

The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the free energy landscape underlying their thermodynamics/folding mechanisms. Although computational studies have revealed folding pathways and energy landscapes for pseudoknots, experimental measurements to validate them are lacking. This study examines the folding/unfolding of VPK -a variant of the Mouse Mammary Tumor Virus PK involved in ribosomal frameshifting- using fluorescent nucleotide analogs placed at different stem/loop positions as local probes of the RNA folded conformations. We measure the folding kinetics using laser temperature-jump approaches and use global analysis based on a master equation to analyze in a self-consistent way the thermodynamics and kinetics over a broad (20-90 °C) temperature range. These measurements provide the first experimental observation of parallel folding pathways of a pseudoknot and an important benchmark for validating coarse-grained simulations of RNA. Our results, in remarkable agreement with simulations from the Thirumalai group (U. of Texas Austin), demonstrate how the flux between alternative folding pathways of VPK are modulated by ionic strength, with one dominant folding pathway observed at 50 mM KCl, and a parallel pathway emerging at higher ionic strength. These studies highlight a connection between salt-dependent stability of partially folded, intermediate states and folding heterogeneity of pseudoknots. Additionally, in collaboration with the Liang group (UIC Bioengineering), we investigated the thermodynamics of the individual hairpins that make up VPK. The Liang group performed simulations that enumerated all possible folded and misfolded states of these hairpins on a lattice; predictions from the simulations were tested experimentally by designing appropriate mutational studies. We find that even these simple hairpin structures require a minimum of three states to describe their thermodynamics, providing evidence for “off-pathway” traps in the folding energy landscape of VPK. Altogether, this study establishes that quantitative description of RNA self-assembly requires a synergistic combination of experiments and simulations. Such studies are potentially useful in the design of functional RNA molecules

Exploring the energy landscape of nucleic acid hairpins using laser temperature-jump and microfluidic mixing

We have investigated the multidimensionality of the free energy landscape accessible to a nucleic acid hairpin by measuring the relaxation kinetics in response to two very different perturbations of the folding/unfolding equilibrium, either a laser temperature-jump or ion-jump (from rapid mixing with counterions). The two sets of measurements carried out on DNA hairpins (4 or 5 base pairs in the stem and 21-nucleotide polythymine loop), using FRET between end labels or fluorescence of 2-aminopurine in the stem as conformational probes, yield distinctly different relaxation kinetics in the temperature range 10–30 °C and salt range 100–500 mM NaCl, with rapid mixing exhibiting slower relaxation kinetics after an initial collapse of the chain within 8 μs of the counterion mixing time. The discrepancy in the relaxation times increases with increasing temperatures, with rapid mixing times nearly 10-fold slower than T-jump times at 30 °C. These results rule out a simple two-state scenario with the folded and unfolded ensemble separated by a significant free energy barrier, even at temperatures close to the thermal melting temperature Tm. Instead, our results point to the scenario in which the conformational ensemble accessed after counterion condensation and collapse of the chain is distinctly different from the unfolded ensemble accessed with T-jump perturbation. Our data suggest that, even at temperatures in the vicinity of Tm or higher, the relaxation kinetics obtained from the ion-jump measurements are dominated by the escape from the collapsed state accessed after counterion condensation

Exploring the Energy Landscape of Nucleic Acid Hairpins Using Laser Temperature-Jump and Microfluidic Mixing

We have investigated the multidimensionality of the free energy landscape accessible to a nucleic acid hairpin by measuring the relaxation kinetics in response to two very different perturbations of the folding/unfolding equilibrium, either a laser temperature-jump or ion-jump (from rapid mixing with counterions). The two sets of measurements carried out on DNA hairpins (4 or 5 base pairs in the stem and 21-nucleotide polythymine loop), using FRET between end labels or fluorescence of 2-aminopurine in the stem as conformational probes, yield distinctly different relaxation kinetics in the temperature range 10–30 °C and salt range 100–500 mM NaCl, with rapid mixing exhibiting slower relaxation kinetics after an initial collapse of the chain within 8 μs of the counterion mixing time. The discrepancy in the relaxation times increases with increasing temperatures, with rapid mixing times nearly 10-fold slower than T-jump times at 30 °C. These results rule out a simple two-state scenario with the folded and unfolded ensemble separated by a significant free energy barrier, even at temperatures close to the thermal melting temperature <i>T</i>_m. Instead, our results point to the scenario in which the conformational ensemble accessed after counterion condensation and collapse of the chain is distinctly different from the unfolded ensemble accessed with T-jump perturbation. Our data suggest that, even at temperatures in the vicinity of <i>T</i>_m or higher, the relaxation kinetics obtained from the ion-jump measurements are dominated by the escape from the collapsed state accessed after counterion condensation