Abstract
High concentrations of Na+ or [Co(NH3)6]3+ can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)4 and (dm5C-dG)4 as models can allow a thermodynamic characterization of the transition. Both form right handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na+ at 25 °C. However, at 2.0 M Na+ or 200 μM [Co(NH3)6]3+, (dm5C-dG)4 assumes a left handed double helical structure (Z-DNA) while the unmethylated (dC-dG)4 analogue remains right handed under those conditions. We have previously demonstrated that the enthalpy of the transition at 25 °C for either inducer can be determined using isothermal titration calorimetry (ITC). Here, ITC is used to investigate the linkages between temperature, water activity and DNA conformation. We found that the determined enthalpy for each titration varied linearly with temperature allowing determination of the heat capacity change (ΔCp) between the initial and final states. As expected, the ΔCp values were dependent upon the cation (i.e., Na+ vs. [Co(NH3)6]3+) as well as the sequence of the DNA oligomer (i.e., methylated vs. unmethylated). Osmotic stress experiments were carried out to determine the gain or loss of water by the oligomer induced by the titration. The results are discussed in terms of solvent accessible surface areas, electrostatic interactions and the role of water.
Highlights
The determination of the structure of B-DNA as a right-handed double helical structure in 1953 by Watson and Crick [1] was just the beginning of structural studies on DNA
To Z transition for Z8M but not for Z8A based on circular dichroism (CD) spectra
As demonstrated in our earlier report [14] and here, the transition enthalpy can be determined using Isothermal Titration Calorimetry (ITC) by assuming that the difference in total enthalpy between Z8A and Z8M upon addition of either Na+ or [Co(NH3 )6 ]3+ is due to the transition itself
Summary
The determination of the structure of B-DNA as a right-handed double helical structure in 1953 by Watson and Crick [1] was just the beginning of structural studies on DNA. The ability of DNA to adopt a left-handed double helical conformation was confirmed by X-ray crystallography in 1979 when Rich et al determined the structure of an alternating (GC). Z-DNA was first observed in chromosomes of the fruit fly Drosophila melanogaster by Rich et al and was shown to be present in fixed and unfixed tissue sections by immunohistochemical methods [10] These studies revealed that the B to Z transition in ds-DNA molecules is caused by the torsional stress build up related to the Z-DNA’s immunoreactivity. Using van’t Hoff analysis, Pohl and Jovin determined the enthalpy of the Na+ induced B to Z transition of poly(dC-dG) to be near zero (±1 kcal/mol bp) and temperature independent over the range of 30 to 50 ◦ C [2]. ITC measurements allow a direct and sensitive determination of the transition enthalpy, and provide a significant advantage over methods based on the indirect van’t Hoff analysis
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