The effect of hydrostatic pressure on the thermal stability of DNA hairpins

Amiri, Amir Reza; Macgregor, Robert B.

doi:10.1016/j.bpc.2011.02.001

Cited by 27 publications

(14 citation statements)

References 48 publications

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“…Different studies looked at the effect of hydrostatic pressure, e.g., the stability of hairpins, B-DNA, the stalling of transcription elongation complexes [56][57][58][59][60][61]. The melting temperature T c seems to depend on the hydrostatic pressure, P , only at a very high P .…”

Section: Resultsmentioning

confidence: 99%

“…Besides the conjugate pairs (T, S), and (g, x), there could be other types of external forces, e.g., isotropic hydrostatic or osmotic pressure affecting the volume of the polymer, and a stretching force (f ) that distorts and elongates the chain. Although there are evidences of hydrostatic or osmotic pressure affecting protein-DNA interaction [56][57][58][59][60][61], there is only a very weak effect on the melting of DNA. In contrast, a stretching force may lead to an "overstretching" transition where the length of the DNA increases by a factor of 1.7 [8,17,25,26].…”

Section: Introductionmentioning

confidence: 99%

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Thermodynamic relations for DNA phase transitions

Sadhukhan

Bhattacharjee

2014

Indian J Phys

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The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The thermodynamic approach is based on the hypothesis of impenetrability of the force in the zipped state. The melting and the unzipping transitions are considered in the same framework and compared with the existing statistical model results. The analysis is then extended to a possible continuous unzipping transition.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Thermodynamic relations for DNA phase transitions

Sadhukhan

Bhattacharjee

2014

Indian J Phys

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“…Such effects lead to an increase in hydration and the thermal volume of the unfolded state,r esulting in an increased expansibility and volume change for the hairpin-to-coil transition. [15] Next, we studied the effect of TMAOa nd urea on the thermal stability of the 4U RNAa tv arious KCl concentrations.T he most pronounced effect of these two common osmolytes is that TMAOc auses elevated melting temperatures,w hereas urea induces as hift of the melting temperature to lower values ( Figure S2). Accordingly,T MAO increases the excess standard free energy of unfolding, ÀÁ ,t he so-called m-value,v aries markedly with the ionic strength.…”

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confidence: 99%

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

2017

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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.

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“…Similar observations were reported for RNA . Studied nucleic acid forms included RNA and DNA hairpins, and tRNA . Some effects were modeled by molecular dynamics (MD) .…”

Section: Introductionmentioning

confidence: 58%

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

Plamitzer

Bouř

2020

Chirality

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Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques. K E Y W O R D S density functional theory, high pressure, molecular dynamics, spectra simulations, vibrational optical activity

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The effect of hydrostatic pressure on the thermal stability of DNA hairpins

Cited by 27 publications

References 48 publications

Thermodynamic relations for DNA phase transitions

Thermodynamic relations for DNA phase transitions

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

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

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