An official website of the United States government
Abstract RNA folds cotranscriptionally to traverse out-of-equilibrium intermediate structures that are important for RNA function in the context of gene regulation. To investigate this process, here we study the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional riboswitch that downregulates a nucleoside transporter in response to binding guanine. Although the aptamer and expression platform domain sequences of the yxjA riboswitch do not completely overlap, we hypothesized that a strand exchange process triggers its structural switching in response to ligand binding. In vivo fluorescence assays, structural chemical probing data and experimentally informed secondary structure modeling suggest the presence of a nascent intermediate central helix. The formation of this central helix in the absence of ligand appears to compete with both the aptamer’s P1 helix and the expression platform’s transcriptional terminator. All-atom molecular dynamics simulations support the hypothesis that ligand binding stabilizes the aptamer P1 helix against central helix strand invasion, thus allowing the terminator to form. These results present a potential model mechanism to explain how ligand binding can induce downstream conformational changes by influencing local strand displacement processes of intermediate folds that could be at play in multiple riboswitch classes.
more »
« less
Solvation and Stabilization of Single-Strand RNA at the Air/Ice Interface Support a Primordial RNA World on Ice
Outstanding questions about the RNA world hypothesis for the emergence of life on Earth concern the stability and self-replication of prebiotic aqueous RNA. Recent experimental work has suggested that solid substrates and low temperatures could help resolve these issues. Herein, we use classical molecular dynamics simulations to explore the possibility that the substrate is ice itself. Simulations at −20 °C show that an eight-nucleotide single strand of RNA, initially situated in the quasiliquid layer at the air/ice interface, exhibits a robust propensity to reorient itself -- its bases turn toward the (hydrophobic) air/ice interface, while its anionic phosphodiester oxygens align with the underlying ice lattice. Kinetic analysis of hydrogen bonding indicates resistance to hydrolysis that is greater than that of an aqueous single-strand RNA at the same temperature. This enhanced resistance, in turn, could increase the opportunities for polymerization and self-copying. These findings thus offer the possibility of a role for an ancient RNA world on ice distinct from that considered in extant elaborations of the RNA world hypothesis. This work is, to the best of our knowledge, the first molecular dynamics study of RNA on ice.
more »
« less
- Award ID(s):
- 1807898
- PAR ID:
- 10282751
- Date Published:
- Journal Name:
- Journal of physical chemistry
- Volume:
- 124
- ISSN:
- 1932-7455
- Page Range / eLocation ID:
- 18587-18594
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Atmospheric freezing of water droplets suspended in air followed by cloud formation and precipitation represent fundamental steps of the terrestrial water cycle. These aqueous droplets exhibit distinct freezing mechanisms and thermodynamic requirements compared to bulk water often forming metastable supercooled water at subzero temperatures on the Celsius scale (<273 K) prior to crystallization. Here, we report on a real-time spectroscopic investigation combined with simultaneous visualizations of single aqueous droplet freezing events inside a cryogenically cooled ultrasonic levitation chamber with the ultimate goal of probing the molecular structure evolution and stages of ice formation. The observed droplet freezing follows a pseudoheterogeneous ice nucleation mechanism mimicking the process that occurs for atmospherically supercooled water droplets at the air–water interface. This proof-of-concept experimental setup allows future crystallization studies of homo- and heterogeneously doped aqueous droplets under simulated atmospheric environments—also in the presence of reactive trace gases, thus untangling dynamic molecular interactions and chemical reactions, which are of fundamental interest to low-temperature atmospheric chemistry delineating with ice nucleation mechanisms.more » « less
-
Abstract. Photochemical reactions of contaminants in snow and ice can be importantsinks for organic and inorganic compounds deposited onto snow from theatmosphere and sources for photoproducts released from snowpacks into theatmosphere. Snow contaminants can be found in the bulk ice matrix, ininternal liquid-like regions (LLRs), or in quasi-liquid layers (QLLs) at theair–ice interface, where they can readily exchange with the firn air. Somestudies have reported that direct photochemical reactions occur faster inLLRs and QLLs than in aqueous solution, while others have found similarrates. Here, we measure the photodegradation rate constants for loss of thethree dimethoxybenzene isomers under varying experimental conditions,including in aqueous solution, in LLRs, and at the air–ice interface ofnature-identical snow. Relative to aqueous solution, we find modestphotodegradation enhancements (3- and 6-fold) in LLRs for two of theisomers and larger enhancements (15- to 30-fold) at the air–ice interfacefor all three isomers. We use computational modeling to assess the impact oflight absorbance changes on photodegradation rate enhancements at theinterface. We find small (2–5 nm) bathochromic (red) absorbance shifts atthe interface relative to in solution, which increases light absorption, butthis factor only accounts for less than 50 % of the measured rate constantenhancements. The major factor responsible for photodegradation rateenhancements at the air–ice interface appears to be more efficientphotodecay: estimated dimethoxybenzene quantum yields are 6- to 24-foldlarger at the interface compared to in aqueous solution and account for themajority (51 %–96 %) of the observed enhancements. Using a hypotheticalmodel compound with an assumed Gaussian-shaped absorbance peak, we find thata shift in the peak to higher or lower wavelengths can have a minor tosubstantial impact on photodecay rate constants, depending on the originallocation of the peak and the magnitude of the shift. Changes in other peakproperties at the air–ice interface, such as peak width and height (i.e.,molar absorption coefficient), can also impact rates of light absorption anddirect photodecay. Our results suggest our current understanding ofphotodegradation processes underestimates the rate at which some compoundsare broken down, as well as the release of photoproducts into theatmosphere.more » « less
-
null (Ed.)Snowpacks contain a wide variety of inorganic and organic compounds, including some that absorb sunlight and undergo direct photoreactions. How the rates of these reactions in, and on, ice compare to rates in water is unclear: some studies report similar rates, while others find faster rates in/on ice. Further complicating our understanding, there is conflicting evidence whether chemicals react more quickly at the air–ice interface compared to in liquid-like regions (LLRs) within the ice. To address these questions, we measured the photodegradation rate of guaiacol (2-methoxyphenol) in various sample types, including in solution, in ice, and at the air–ice interface of nature-identical snow. Compared to aqueous solution, we find modest rate constant enhancements (increases of 3- to 6-fold) in ice LLRs, and much larger enhancements (of 17- to 77-fold) at the air–ice interface of nature-identical snow. Our computational modeling suggests the absorption spectrum for guaiacol red-shifts and increases on ice surfaces, leading to more light absorption, but these changes explain only a small portion (roughly 2 to 9%) of the observed rate constant enhancements in/on ice. This indicates that increases in the quantum yield are primarily responsible for the increased photoreactivity of guaiacol on ice; relative to solution, our results suggest that the quantum yield is larger by a factor of roughly 3–6 in liquid-like regions and 12–40 at the air–ice interface.more » « less
-
The collapse of ice shelves could expose tall ice cliffs at ice sheet margins. The marine ice cliff instability (MICI) is a hypothesis that predicts that, if these cliffs are tall enough, ice may fail structurally leading to self-sustained retreat. To date, projections that include MICI have been performed with a single model based on a simple parameterization. Here, we implement a physically motivated parameterization in three ice sheet models and simulate the response of the Amundsen Sea Embayment after a hypothetical collapse of floating ice. All models show that Thwaites Glacier would not retreat further in the 21st century. In another set of simulations, we force the grounding line to retreat into Thwaites’ deeper basin to expose a taller cliff. In these simulations, rapid thinning and velocity increase reduce the calving rate, stabilizing the cliff. These experiments show that Thwaites may be less vulnerable to MICI than previously thought, and model projections that include this process should be re-evaluated.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- The DOI is not currently available.
