Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes

Arns, Loana; Knop, Jim‐Marcel; Patra, Satyajit; Anders, Christian; Winter, Roland

doi:10.1016/j.bpc.2019.106190

Cited by 15 publications

(9 citation statements)

References 75 publications

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“…Recently it was found that noncanonical nucleic acid structure, such as DNA hairpins (DNA-HP), i-motifs, and G-quadruplexes (G4Qs), are much more pressure sensitive, and their pressure sensitivity varies with their base sequence and the type and concentration of the counterions present in solution. − Guanine-rich nucleic acid molecules are able to fold into a G-quadruplex. Structurally, G4Qs are stabilized by stacked G-tetrads and centrally coordinated cations (Na + or K + ).…”

Section: Resultsmentioning

confidence: 99%

“…, the stability diagram is clearly distinct from that of a duplex B-DNA. Besides salts, cosolvents and crowding agents have a significant effect on the conformational dynamics and stability of noncanonical DNAs. ,− ,− The antiparallel G4Q-DNA is more pressure stable in the presence of 1 M TMAO, even up to pressures as high as ∼750 bar. At higher pressures, a partial conformational change from the antiparallel to the parallel conformation was observed but no unfolding.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View

et al. 2022

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Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View

et al. 2022

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“…The relative consistency and stability of inorganic ions’ contributions to the osmolality of cellular solutions reflects their strong effects on large molecular systems. High and variable concentrations of inorganic ions can be highly perturbing of macromolecular structure and function, for example by inhibiting enzyme activity (Bowlus and Somero 1979 ; Yancey et al 1982 ), by causing double-strand breaks in DNA (Dmitrieva et al 2006 ; Kültz and Chakravarty 2001 ), by affecting higher order structures of RNA (Arns et al 2019 ; Russell et al 2002 ), and by upsetting transmembrane ion gradients needed for neural transmission and uptake of small molecules into cells.…”

Section: Osmotic Adaptation: Basic Patterns Of Osmolyte Distributionmentioning

confidence: 99%

“…Overly labile RNA structures also can have negative effects on RNA function if this high lability switches the thermometer on at too low a temperature. Pressure effects on RNA and DNA also lead to a need for retention or restoration of the stability–flexibility balance in the face of this abiotic stressor (Arns et al 2019 ; Patra et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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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High-Pressure Single-Molecule Studies on Non-canonical Nucleic Acids and Their Interactions

Mukherjee¹,

Knop²,

Winter³

2022

Handbook of Chemical Biology of Nucleic Acids

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Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes

Cited by 15 publications

References 75 publications

Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View

Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View

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

High-Pressure Single-Molecule Studies on Non-canonical Nucleic Acids and Their Interactions

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