Hydration differences between the major and minor grooves of DNA revealed from heat capacity measurements

Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation

Sequence-specific recognition of transcription factor (TF) binding motifs in the target site of DNA over the vast amount of non-target DNA is of primary importance for the transcriptional regulation of gene expression by the TFs. Binding of TFs to the target site of DNA relies not only on the direct contact formation but also on the structural and conformational features of DNA. Recognition of DNA structural features or shape readout by proteins is an important factor in the context of TF-DNA interaction. Based on the atomistic molecular simulation, here we report the sequence-dependent unique structural features, solvation, and ion-binding properties of biologically relevant AT- and GC-rich human TF binding motifs in DNA. Counterion and water distribution around the motif is found to be sensitive to the motif sequence, which is accompanied with the DNA shape features. The motif sequence affects the electrostatic potential along the grooves, and cytosine methylation alters the DNA shape features. Characteristic solvation properties of TF binding motif DNA fragments infer that an ionic environment and hydration influences are essential to describe TF-DNA interactions.

Role of Water in Defining the Structure and Properties of B-Form DNA

DNA in the cell is rarely naked but normally protein-bound in nucleosomes. Of special interest is the DNA bound to other factors that control its key functions of transcription, replication, and repair. For these several transactions of DNA, the state of hydration plays an important role in its function, and therefore needs to be defined in as much detail as possible. High-resolution crystallography of short B-form duplexes shows that the mixed polar and apolar surface of the major groove binds water molecules over the broad polar floor of the groove in a sequence-dependent varied manner. In contrast, the narrower minor groove, particularly at AT-rich segments, binds water molecules to the polar groups of the bases in a regular double layer reminiscent of the structure of ice. This review is largely devoted to measurements made in solution, principally calorimetric, that are fully consistent with the location of water molecules seen in crystals, thereby emphasizing the substantial difference between the hydration patterns of the two grooves.

Analysis of Protein-DNA Interactions Using Isothermal Titration Calorimetry: Successes and Failures

Isothermal titration calorimetry (ITC) is a golden standard for the characterization of protein-DNA binding affinities and allows direct assessment of the accompanying thermodynamic driving forces. Their interpretation can give insight into role of electrostatics, specificity of the DNA recognition, contribution of protein folding upon DNA binding and help to distinguish between minor and major groove binders. The main advantages of ITC are that the binding is measured in solution, and it requires no labeling of the samples, however, the method is not well suited for high-performance studies. Here we describe the sample preparation, a procedure to perform a typical ITC experiment, data analysis, and lastly discuss how to interpret the obtained thermodynamic parameters. In conclusion, we show examples of several unsuccessful ITC experiments and identify the underlying reasons for failed experiments. In most cases with a proper adjustment of the experimental setup, it was possible to obtain data appropriate for further analysis.

Origin of heat capacity increment in DNA folding: The hydration effect

BACKGROUND

Understanding DNA folding thermodynamics is crucial for prediction of DNA thermal stability. It is now well established that DNA folding is accompanied by a decrease of the heat capacity ∆c_{p, F}, however its molecular origin is not understood. In analogy to protein folding it has been assumed that this is due to dehydration of DNA constituents, however no evidence exists to support this conclusion.

METHODS

Here we analyze partial molar heat capacity of nucleic bases and nucleosides in aqueous solutions obtained from calorimetric experiments and calculate the hydration heat capacity contribution ∆c_p^hyd.

RESULTS

We present hydration heat capacity contributions of DNA constituents and show that they correlate with the solvent accessible surface area. The average contribution for nucleic base dehydration is +0.56 J mol^-1 K^-1 Å^-2 and can be used to estimate the ∆c_{p, F} contribution for DNA folding.

CONCLUSIONS

We show that dehydration is one of the major sources contributing to the observed ∆c_{p, F} increment in DNA folding. Other possible sources contributing to the overall ∆c_{p, F} should be significant but appear to compensate each other to high degree. The calculated ∆c_p^hyd for duplexes and noncanonical DNA structures agree excellently with the overall experimental ∆c_{p, F} values. By contrast, empirical parametrizations developed for proteins result in poor ∆c_p^hyd predictions and should not be applied to DNA folding.

GENERAL SIGNIFICANCE

Heat capacity is one of the main thermodynamic quantities that strongly affects thermal stability of macromolecules. At the molecular level the heat capacity in DNA folding stems from removal of water from nucleobases.

Thermodynamics of DNA: heat capacity changes on duplex unfolding

The heat capacity change, ΔCp, accompanying the folding/unfolding of macromolecules reflects their changing state of hydration. Thermal denaturation of the DNA duplex is characterized by an increase in ΔCp but of much lower magnitude than observed for proteins. To understand this difference, the changes in solvent accessible surface area (ΔASA) have been determined for unfolding the B-form DNA duplex into disordered single strands. These showed that the polar component represents ~ 55% of the total increase in ASA, in contrast to globular proteins of similar molecular weight for which the polar component is only about 1/3rd of the total. As the exposure of polar surface results in a decrease of ΔCp, this explains the much reduced heat capacity increase observed for DNA and emphasizes the enhanced role of polar interactions in maintaining duplex structure. Appreciation of a non-zero ΔCp for DNA has important consequences for the calculation of duplex melting temperatures (T_m). A modified approach to T_m prediction is required and comparison is made of current methods with an alternative protocol.