Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts

Abstract

Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state. Further, we find a strong interplay between water, salt, and osmolyte in driving the thermodynamics and defining the temperature and pressure stability limit of the RNA. Our results support a universal working mechanism of TMAO and urea to (de)stabilize proteins and the RNA.

Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions

“…Studies have shown that tertiary interactions lead to as ubstantial decrease in the phosphatesS ASA, thereby stabilizing the folded state of the RNAi nt he presence of TMAO. [17] In agreement with these data, we found that TMAOp redominantly assists population of the folded state of the DNAH p ( Figure 1a nd Figure S2), because also for such DNAH ps tructure the unfolded conformation has al arger SASA of exposed phosphate and nucleobase groups than the folded conformation. [13] The interaction between TMAOand nucleobases is also energetically unfavorable and therefore provides anet stabilization of the DNAd uplex structure based on nucleobase SASA.…”

“…[13] TMAOi nteracts unfavorably with the phosphate backbone and nucleobases of the nucleic acids structure,and therefore exclusion of TMAOfrom these surfaces is exothermic and entropically costly. [17] Forc anonical double-stranded DNAs tructures,p ressure has been shown to have either astabilizing,destabilizing or no effect on the structure of the DNA, depending on the temperature and salt concentration. Urea interacts strongly with nucleobases.…”

“…Our data show that urea also populates anew conformational state next to the fully closed and open state.A ss een in Figure S3, the maximum of the high-FRET peak shifts to lower values with increasing urea concentration. [17] Thev olume decrease for DNAHpunfolding possibly arises from packing defects and void volume present in the loop area. Increasing urea concentration and temperature weaken base stacking interaction and H-bonding,l eading to partially unfolded or quasi-open conformations.T hese intermediate states are most likely formed by weakening of base stacking and H-bonding interaction in the stem region of the DNAHp owing to its lower G-C content compared to the adjacent double helix linker ( Figure S17).…”

Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

“…However, the exact values depend the change in SASA of the protein upon unfolding. Slightly lower values have been found for RNA secondary and tertiary structures . Both, the transfer model and the preferential interaction coefficient can be related to the m ‐value, that is, .…”

The Deep Sea Osmolyte TrimethylamineN‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex from Urea and Pressure Stress

“…Living cells respond to physical and chemical stresses like temperature, pressure, pH, salinity, and desiccation with changes in the pattern of gene expression . As a response to such stressors, the structure and dynamics of biomolecules may also be altered . Recently, it has been found that noncanonical DNA structures, such as G‐quadruplexes (G4‐DNAs) formed by guanine‐rich nucleic acid sequences, are markedly responsive to such stimuli .…”