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Comparative study of native and denatured Mg-DNA pure water solutions

After exploring Na-DNA [1], we studied Mg-DNA pure water solutions. For divalent Mg counterions it is conceivable that DNA may show different properties. We have prepared Mg-DNA samples by dialyzing Na-DNA (Sigma D1626) against MgCl2, and against water as a final step. The degree of polymerization of DNA samples is 2k-20k base pairs which corresponds to the contour length of . In order to determine the conformation of the Mg-DNA in pure water conditions (concentration range c=0.01-5 mg/mL ; semidilute regime) we have also prepared and tested the denatured MgDNA. The samples were heated for 20 minutes at 97°C and then quenched to 4°C. Subsequently, UV spectrophotometry (at 260 nm) and dielectric spectroscopy (DS) at 25°C were done and these results were compared with the results measured on the native samples. A quantitatively different behaviour between native and denatured Mg-DNA shows that Mg-DNA in pure water solutions is in the double-stranded conformation in the whole measured concentration range. DS results revealed two relaxation modes only for native Mg-DNA samples. The characteristic length scale of HF mode (f>105 Hz), scales with DNA concentration as c-0.5 in the whole measured range of concentrations. Thus, we associate it with de Gennes correlation length [2]. This is partly in contrast with behaviour previously found on Na-DNA [1] where that scaling changes to c-0.33 for samples with concentrations smaller than 0.6 g/L. The latter we ascribed to locally exposed hydrophobic cores due to conformational fluctuations. The next important result was that this characteristic length is 1.6 times larger than for denatured Mg-DNA. This is in accordance with the expression predicted by de Gennes theory , where b is monomer size. Characteristic length scale of LF mode (f<105 Hz) scales with DNA concentration as c-0.25 . This behaviour was also found previously for Na-DNA and it was associated with the single chain property, i.e. with the average end to end distance of a single chain modelled as a random walk of correlation blobs. Another important result was that for denatured Mg-DNA we did not detect LF mode probably since it shifted to higher frequencies and merged with the much larger HF mode. [1] S Tomić, et al., Phys. Rev. E 75, 021905 (2007) [2] P.G. de Gennes, P.Pincus, R.M. Velasco, F.Brochardi, J. Phys.(Paris) 37, 1461, (1976)

biomaterials; DNA; dielectric properties; dynamics and conformational changes; denaturation; divalent counterions

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