Enthalpies of DNA melting in the presence of osmolytes

Spink, Charles H.; Garbett, Nichola C.; Chaires, Jonathan B.

doi:10.1016/j.bpc.2006.07.013

Cited by 64 publications

(75 citation statements)

References 37 publications

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“…The unfolding enthalpies in Table S1 increase with GB molality with the greatest increases in

normalΔ H_{obs}^{o}

occurring for the higher GC content dodecamers. A similar trend for

normalΔ H_{obs}^{o}

was found by Spink and coworkers with poly(dAdT) and poly(dGdC) (13). As a test of two-state transitions in the RNA dodecamer duplexes, absorbance unfolding profiles were fit to the nonlinear two-state transition equation (23, 33).…”

Section: Resultssupporting

confidence: 87%

Quantifying the Temperature Dependence of Glycine—Betaine RNA Duplex Destabilization

et al. 2013

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Glycine betaine stabilizes folded protein structure due to its unfavorable thermodynamic interactions with amide oxygen and aliphatic carbon surface area exposed during protein unfolding. However, glycine betaine can attenuate nucleic acid secondary structure stability, although its mechanism of destabilization is not currently understood. In this work we quantify glycine betaine interactions with the surface area exposed during thermal denaturation of nine RNA dodecamer duplexes with guanine-cytosine (GC) contents of 17–100%. Hyperchromicity values indicate increasing glycine betaine molality attenuates stacking. Glycine betaine destabilizes higher GC content RNA duplexes to a greater extent than low GC content duplexes due to greater accumulation at the surface area exposed during unfolding. The accumulation is very sensitive to temperature and displays characteristic entropy-enthalpy compensation. Since the entropic contribution to the m-value (used to quantify GB interaction with the RNA solvent accessible surface area exposed during denaturation) is more dependent on temperature than the enthalpic contribution, higher GC content duplexes with their larger transition temperatures are destabilized to a greater extent than low GC content duplexes. The concentration of glycine betaine at the RNA surface area exposed during unfolding relative to bulk was quantified using the solute partitioning model. Temperature correction predicts a glycine betaine concentration at 25 °C to be nearly independent of GC content, indicating that glycine betaine destabilizes all sequences equally at this temperature.

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“…The unfolding enthalpies in Table S1 increase with GB molality with the greatest increases in

normalΔ H_{obs}^{o}

occurring for the higher GC content dodecamers. A similar trend for

normalΔ H_{obs}^{o}

Section: Resultssupporting

confidence: 87%

Quantifying the Temperature Dependence of Glycine—Betaine RNA Duplex Destabilization

et al. 2013

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“…These species also affect RNA folding. They promote ribozyme cleavage (Nakano et al 2009;Strulson et al 2012Strulson et al , 2013, drive compaction of large RNAs (Kilburn et al 2010), and affect folding free energy (Spink and Chaires 1998;Lambert and Draper 2007;Spink et al 2007;Feng et al 2010;Denesyuk and Thirumalai 2011;Kilburn et al 2013). While these studies provide insight into ways in which biological conditions affect RNA folding and function, there has been little focus on how they affect RNA folding cooperativity.…”

Section: Introductionmentioning

confidence: 99%

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

Strulson

Boyer

Whitman

et al. 2014

RNA

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Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg 2+ ion concentrations are low, K + concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg 2+ (0.5-2 mM) and K + (140 mM) if the solution is supplemented with physiological amounts (∼20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperaturedependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.

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“…Glycerol modestly stabilizes globular proteins 14–17 , beta-hairpins 18, 19 , protein assemblies 20–23 and protein-DNA complexes 24 , but modestly destabilizes nucleic acid duplexes 25–27 , and can stabilize or destabilize RNA tertiary structure 27 . Tetraethylene glycol (tetraEG) is a weak destabilizer of nucleic acid duplexes 26, 28 , and larger PEGs destabilize proteins 29–32 . Oligo ethylene glycols and polymeric PEGs are common protein crystallization agents 1 , stabilize protein-DNA complexes 24, 33, 34 and perturb their kinetics 24, 35 .…”

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confidence: 99%

Chemical Interactions of Polyethylene Glycols (PEGs) and Glycerol with Protein Functional Groups: Applications to Effects of PEG and Glycerol on Protein Processes

et al. 2015

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Here we obtain the data needed to predict chemical interactions of polyethylene glycols (PEGs) and glycerol with proteins and related organic compounds, and thereby interpret or predict chemical effects of PEGs on protein processes. To accomplish this we determine interactions of glycerol and tetraEG with >30 model compounds displaying the major C, N, and O functional groups of proteins. Analysis of these data yields coefficients (α-values) quantifying interactions of glycerol, tetraEG and PEG end (-CH2OH) and interior (-CH2OCH2-) groups with these groups, relative to interactions with water. TetraEG (strongly) and glycerol (weakly) interact favorably with aromatic C, amide N, and cationic N, but unfavorably with amide O, carboxylate O and salt ions. Strongly unfavorable O and salt anion interactions help make both small and large PEGs effective protein precipitants. Interactions of tetraEG and PEG interior groups with aliphatic C are quite favorable, while interactions of glycerol and PEG end groups with aliphatic C are not. Hence tetraEG and PEG 300 favor unfolding of the DNA-binding domain of lac repressor (lacDBD) while glycerol, di- and mono-ethylene glycol are stabilizers. Favorable interactions with aromatic and aliphatic C explain why PEG400 greatly increases the solubility of aromatic hydrocarbons and steroids. PEG400-steroid interactions are unusually favorable, presumably because of simultaneous interactions of multiple PEG interior groups with the fused ring system of the steroid. Using α-values reported here, chemical contributions to PEG m-values can be predicted or interpreted in terms of changes in water-accessible surface area (ΔASA), and separated from excluded volume effects.

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Enthalpies of DNA melting in the presence of osmolytes

Cited by 64 publications

References 37 publications

Quantifying the Temperature Dependence of Glycine—Betaine RNA Duplex Destabilization

Quantifying the Temperature Dependence of Glycine—Betaine RNA Duplex Destabilization

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

Chemical Interactions of Polyethylene Glycols (PEGs) and Glycerol with Protein Functional Groups: Applications to Effects of PEG and Glycerol on Protein Processes

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