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

Gao, Mimi; Arns, Loana; Winter, Roland

doi:10.1002/ange.201611843

Cited by 12 publications

(5 citation statements)

References 46 publications

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“…A study of pressure and osmolyte effects on RNA yielded results that essentially parallel those found in the studies of DNA mentioned above (Gao et al 2017a ). Pressure destabilized the hairpin structure of the RNA (a 4U RNA thermometer of Salmonella ), as did elevated temperature.…”

Section: Temperaturesupporting

confidence: 62%

“…An interesting example of osmolyte effects on stability of RNA secondary structure is given by a study of effects of TMAO and urea on a bacterial RNA thermometer, the Salmonella 4U RNA thermometer (Fig. 4 ; Gao et al 2017a ). This RNA thermometer consists of a 34 nucleotide hairpin loop located near the 5′ end of the RNA sequence.…”

Section: Temperaturementioning

confidence: 99%

“…TMAO and urea were separately added to solutions that contained either 25 mmol/L or 150 mmol/L KCl. (Figure redrawn after Gao et al 2017a ) …”

Section: Temperaturementioning

confidence: 99%

“…In the latter molecules, TMAO is strongly excluded from the protein surface due to effects mediated by water structure around TMAO and near the backbone peptide bonds between residues of a protein (Auton et al 2011 ). In RNA too, TMAO is strongly excluded from the nucleic acid surface, particularly in the case of the phosphate group, and it favors burial of the RNA backbone in tertiary structures (Gao et al 2017a ). However, there is some evidence from in silico analyses that the phosphate group of RNA can alter the pK a of TMAO and thereby change its ability to interact with RNA (Denning et al 2013 ); the biological implications of this finding remain to be determined.…”

Section: Temperaturementioning

confidence: 99%

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Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors

Somero

2022

Mar Life Sci Technol

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The seas confront organisms with a suite of abiotic stressors that pose challenges for physiological activity. Variations in temperature, hydrostatic pressure, and salinity have potential to disrupt structures, and functions of all molecular systems on which life depends. During evolution, sequences of nucleic acids and proteins are adaptively modified to “fit” these macromolecules for function under the particular abiotic conditions of the habitat. Complementing these macromolecular adaptations are alterations in compositions of solutions that bathe macromolecules and affect stabilities of their higher order structures. A primary result of these “micromolecular” adaptations is preservation of optimal balances between conformational rigidity and flexibility of macromolecules. Micromolecular adaptations involve several families of organic osmolytes, with varying effects on macromolecular stability. A given type of osmolyte generally has similar effects on DNA, RNA, proteins and membranes; thus, adaptive regulation of cellular osmolyte pools has a global effect on macromolecules. These effects are mediated largely through influences of osmolytes and macromolecules on water structure and activity. Acclimatory micromolecular responses are often critical in enabling organisms to cope with environmental changes during their lifetimes, for example, during vertical migration in the water column. A species’ breadth of environmental tolerance may depend on how effectively it can vary the osmolyte composition of its cellular fluids in the face of stress. Micromolecular adaptations remain an under-appreciated aspect of evolution and acclimatization. Further study can lead to a better understanding of determinants of environmental tolerance ranges and to biotechnological advances in designing improved stabilizers for biological materials.

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Section: Temperaturesupporting

confidence: 62%

Section: Temperaturementioning

confidence: 99%

“…TMAO and urea were separately added to solutions that contained either 25 mmol/L or 150 mmol/L KCl. (Figure redrawn after Gao et al 2017a ) …”

Section: Temperaturementioning

confidence: 99%

Section: Temperaturementioning

confidence: 99%

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Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors

Somero

2022

Mar Life Sci Technol

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“…; Gao et al . ), the optimal growth conditions for a given synthetic RNAT‐gene fusion will require careful consideration. As optimal SD sequences can vary from one organism to the next (Ma et al .…”

Section: Rna Thermometersmentioning

confidence: 99%

Applications and limitations of regulatoryRNAelements in synthetic biology and biotechnology

et al. 2019

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Summary Synthetic biology requires the design and implementation of novel enzymes, genetic circuits or even entire cells, which can be controlled by the user. RNA‐based regulatory elements have many important functional properties in this regard, such as their modular nature and their ability to respond to specific external stimuli. These properties have led to the widespread exploration of their use as gene regulation devices in synthetic biology. In this review, we focus on two major types of RNA elements: riboswitches and RNA thermometers (RNATs). We describe their general structure and function, before discussing their potential uses in synthetic biology (e.g. in the production of biofuels and biodegradable plastics). We also discuss their limitations, and novel strategies to implement RNA‐based regulatory devices in biotechnological applications. We close with a description of some common model organisms used in synthetic biology, with a focus on the current applications and limitations of RNA‐based regulation.

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

et al. 2017

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The structural dynamics of aDNA hairpin (Hp) are studied in the absence and presence of the two natural osmolytes trimethylamine-N-oxide (TMAO) and urea at ambient and extreme environmental conditions,i ncluding high pressures and high temperatures,byusing single-molecule Fçrster resonance energy transfer and fluorescence correlation spectroscopy. The effect of pressure on the conformational dynamics of the DNAHpisinvestigated on asingle-molecule level, providing novel mechanistic insights into its conformational conversions.D ifferent from canonical DNAd uplex structures of similar melting points,the DNAHpisfound to be rather pressure sensitive.T he combined temperature and pressure dependent data allow dissection of the folding free energy into its enthalpic,e ntropic,a nd volumetric contributions.T he folded conformation is effectively stabilized by the compatible osmolyte TMAOnot only at high temperatures,but also at high pressures and in the presence of the destabilizing co-solute urea.Even though DNAh airpins (Hps) play ap rominent role in many biological processes, [1] as biosensors and in DNA nanotechnology, [2] results on their conformational and free energy landscape remain still controversial. [3][4][5][6][7][8] Here,w e report on the effect of the important natural osmolytes TMAOa nd urea on the conformational dynamics of aw ellknown DNAH p [4] at both ambient and extreme environmental (i.e., high pressure and temperature) conditions by using diffusion-based single-molecule Fçrster resonance energy transfer (smFRET) and fluorescence correlation spectroscopy (FCS). What is still unknown is the combined effect of temperature,p ressure and osmolytes on the conformational dynamics of the nucleic acid on the singlemolecule level. We combined the pressure perturbation approach-to our knowledge for the first time-with smFRET in order to obtain additional mechanistic and volumetric information on the Hp.S uch studies are also of high biological relevance as in the deep sea and sub-seafloor crust, high pressures up to the 1kbar (100 MPa) range are encountered, and living organisms have to cope with such harsh conditions. [9] According to Le Châteliersp rinciple, pressurization shifts chemical equilibria towards conformations occupying smaller partial volumes,t hereby facilitating the experimental characterization of important high-energy conformers,w hich are sparsely populated at ambient condition. [10] First, smFRET measurements (for details see the Supporting Information, SI) were performed on the DNAHpin buffer solution (20 mm Tris-HCl, 50 mm NaCl, pH 8.0) in the absence and presence of TMAOand urea at ambient pressure (1 bar) and temperature (25 8 8C). To this end, donor and acceptor fluorophore labeled oligonucleotide strands were annealed to generate ad ually labeled DNAH p ( Figure 1a). Thedonor-acceptor intensity time trace and the correspond-[*] Dr.Figure 1. a) DNA hairpin including the position of the fluorophores T-Atto 550 (donor) and T-Atto 647 N( acceptor) serving as FRET pair. b) Plots of the...

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

Cited by 12 publications

References 46 publications

Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors

Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors

Applications and limitations of regulatoryRNAelements in synthetic biology and biotechnology

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

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