Thermodynamics of DNA: heat capacity changes on duplex unfolding (original) (raw)
Related papers
The Role of Bound Water on the Energetics of DNA Duplex Melting
Journal of Thermal Analysis and Calorimetry - J THERM ANAL CALORIM, 2001
A combination of common and low-temperature differential scanning calorimetry (DSC) techniques was used to detect the thermodynamic parameters of heat denaturation and of ice-water phase transitions for native and denaturated DNA, at different low water contents. We suggest that the main contribution to the enthalpy of the process of the heat denaturation of DNA duplex (35±5 kJ/mol bp) is the enthalpy of disruption of the ordered water structure in the hydration shell of the double helix (26±1 kJ/mol bp). It is possible that this part of the energy composes the non-specific general contribution (70%) of the enthalpy of transition of all type of duplexes. For DNA in the condensed state the ratioα=ΔC p/ΔS ~2 is smaller than for DNA in diluted aqueous solutions (α≅2–4). This means that there are other sources for the large heat capacity change in diluted solutions of DNA – for example the hydrophobic effects and unstacking(unfolding) of single polynucleotide chains.
Heat Capacity Changes Associated with DNA Duplex Formation: Salt- and Sequence-Dependent Effects †
Biochemistry, 2006
Duplexes are the most fundamental elements of nucleic acid folding. Although it has become increasingly clear that duplex formation can be associated with a significant change in heat capacity (∆C p), this parameter is typically overlooked in thermodynamic studies of nucleic acid folding. Analogy to protein folding suggests that base stacking events coupled to duplex formation should give rise to a ∆C p due to the release of waters solvating aromatic surfaces of nucleotide bases. In previous work, we showed that the ∆C p observed by isothermal titration calorimetry (ITC) for RNA duplex formation depended on salt and sequence [
Journal of Biophysical Chemistry, 2012
Differential scanning calorimetry (DSC) melting analysis was performed on 27 short double stranded DNA duplexes containing 15 to 25 base pairs. Experimental duplexes were divided into two categories containing either two 5' danglingends or one 5' and one 3' dangling-end. Duplex regions were incrementally reduced from 25 to 15 base pairs with a concurrent increase in length of dangling-ends from 1 to 10 bases. Blunt-ended duplexes from 15 to 25 base pairs served as controls. An additional set of molecules containing 21 base pair duplexes and a single four base dangling-end were also examined. DSC melting curves were measured in varying concentrations of sodium ion (Na + ). From these measurements, thermodynamic parameters for 5' and 3' dangling-ends were evaluated as a function of dangling end length. 5' ends were found to be slightly stabilizing but essentially constant while the 3' ends were destabilizing with increasing length of the danglingend. 3' ends also display a stronger dependence on Na + concentration. In lower Na + environment, the 3' ends were more destabilizing than in higher salt environment suggesting a more significant electrostatic component of the destabilizing interactions. Analysis of thermodynamic parameters of dangling ended duplexes as a function of Na + concentration indicated the 3' dangling ends behave differently than 5' dangling ended and blunt-ended duplexes. Molecules with one 5' and one 3' dangling end showed variation in excess specific heat capacity (C p ) when compared to the blunt-ended molecule, while the molecules with two 5' ends had C p values that were essentially the same as bluntended duplexes. These observations suggested differences exist in duplexes with 3' and 5' dangling ends, which are interpreted in terms of composite differences in interactions with Na + , solvent, and terminal base pairs of the duplex.
Origin of heat capacity increment in DNA folding: The hydration effect
Biochimica Et Biophysica Acta - General Subjects, 2021
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Melting of polymeric DNA double helix at elevated temperature: a molecular dynamics approach
Journal of Molecular Modeling, 2017
Genomic DNA of higher organisms exists as extremely long polymers, while in bacteria and other lower organisms it is circular with no terminal base pairs. Temperature-induced melting of the DNA double helix by localized strand separation has been unattainable by molecular dynamic simulations due to more rapid fraying of the terminal base pairs in oligomeric DNA. However, local-sequencedependent unfolding of the DNA double helix is extremely important for understanding various biochemical phenomena, and can be addressed by simulating a model polymeric DNA duplex. Here, we present simulations of polymeric B-DNA of sequence d(CGCGCGCGAATTCGCGCGCG) 2 at elevated temperatures, along with its equivalent oligomeric constructs for comparison. Initiation of temperature-induced DNA melting was observed with higher fluctuations of the central d(AATT) region only in the model polymer. The polymeric construct shows a definite melting start site at the weaker A/T stretch, which propagates slowly through the CG rich regions. The melting is reflected in the hydrogen bond breaking, i.e. basepair opening, and by disruption of stacking interaction between successive basepairs. Melting at higher temperature of the oligomer, however, was only through terminal fraying, as also reported earlier.
Journal of Physical Chemistry B, 2009
Systematical differential calorimetry experiments on DNA oligomers with different lengths and placed in water solutions with various added salt concentrations may, in principle, unravel important information about the structure and dynamics of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated that the application of the latter could enable direct estimation of thermodynamic parameters of the microphase transitions connected to the changes in DNA dynamical regimes versus the length of the biopolymers and the ionic strengths of their water solutions, and this calls for much more systematical experimental and theoretical studies in this field.
Entropy and Heat Capacity of DNA Melting from Temperature Dependence of Single Molecule Stretching
Biophysical Journal, 2001
When a single molecule of double-stranded DNA is stretched beyond its B-form contour length, the measured force shows a highly cooperative overstretching transition. We have measured the force at which this transition occurs as a function of temperature. To do this, single molecules of DNA were captured between two polystyrene beads in an optical tweezers apparatus. As the temperature of the solution surrounding a captured molecule was increased from 11°C to 52°C in 500 mM NaCl, the overstretching transition force decreased from 69 pN to 50 pN. This reduction is attributed to a decrease in the stability of the DNA double helix with increasing temperature. These results quantitatively agree with a model that asserts that DNA melting occurs during the overstretching transition. With this model, the data may be analyzed to obtain the change in the melting entropy ⌬S of DNA with temperature. The observed nonlinear temperature dependence of ⌬S is a result of the positive change in heat capacity of DNA upon melting, which we determine from our stretching measurements to be ⌬C p ϭ 60 Ϯ 10 cal/mol K bp, in agreement with calorimetric measurements.
Thermodynamic Studies on Interaction of Glucose and Alkali Metal Ions with DNA Duplex
Here we report the thermodynamic analysis of glucose interaction on conformational transitions on DNA duplex with different base compositions and lengths by using Circular Dichroism, UV thermal melting and native gel electrophoresis. CD results revealed that three duplexes Duplex 1 ―D1‖ and Duplex 2 ―D2‖ folded into B-form while Duplex 3 ―D3‖ folded into mixed A and B like forms in the presence of different cations and glucose. We monitor the interaction between DNA duplex and glucose over a range of temperatures. Thermal melting data revealed that these duplexes are more stable without glucose under all cationic (Na+, K+, Na+ + Mg++ and K+ + Mg++) conditions tested and calculated the enthalpy ―ΔH‖, entropy ―ΔS‖ and free energy ―ΔG‖. Moreover, these duplexes are marginally destabilized at high concentration of glucose. In this study, glucose was considered as an essential model for understanding interactions between interfacial water molecules at hydrophilic surfaces of DNA duplexes.
Thermal equivalence of DNA duplexes without calculation of melting temperature
Nature Physics, 2005
The common key to nearly all processes involving DNA is the hybridisation and melting of the double helix: from transmission of genetic information and RNA transcription, to PCR and DNA microarray analysis, DNA mechanical nanodevices and DNA computing. Selecting DNA sequences with similar melting temperatures is essential for many applications in biotechnology. We show that instead of calculating these temperatures, a single parameter can be derived from a statistical mechanics model which conveniently represents the thermodynamic equivalence of DNA sequences. This parameter is shown to order correctly experimental melting temperatures, is much more readily obtained than the melting temperature, and easier to handle than the numerous parameters of empirical regression models.
Biochemistry, 1998
The abasic site in DNA may arise spontaneously, as a result of nucleotide base damage, or as an intermediate in glycosylase-mediated DNA-repair pathways. It is the most common damage found in DNA. We have examined the consequences of this lesion and its sequence context on DNA duplex structure, as well as the thermal and thermodynamic stability of the duplex, including the energetic origins of that stability. To this end, we incorporated a tetrahydrofuran abasic site analogue into a family of 13-mer DNA duplexes, wherein the base opposite the lesion (A, C, G, or T) and the base pairs neighboring the lesion (C‚G or G‚C) were systematically varied and characterized by a combination of spectroscopic and calorimetric techniques. The resulting data allowed us to reach the following conclusions: (i) the presence of the lesion in all sequence contexts studied does not alter the global B-form conformation characteristic of the parent undamaged duplex; (ii) the presence of the lesion induces a significant enthalpic destabilization of the duplex, with the magnitude of this effect being dependent on the sequence context; (iii) the thermodynamic impact of the lesion is dominated by the identity of the neighboring base pairs, with the cross strand partner base exerting only a secondary thermodynamic effect on duplex properties. In the aggregate, our data reveal that even in the absence of lesion-induced alterations in global structure, the abasic lesion can significantly alter the thermodynamic properties of the host duplex, with the magntiude of this impact being strongly dependent on sequence context.