The binding affinity and specificity of DNA to large biomolecules such as proteins, and the interactions between DNA and drugs such as anticancer drugs depend upon the local polarity of DNA. As a result of this dependence, much effort has been devoted recently to determining the dielectric constant along DNA molecules by both theoretical and experimental means. The dielectric constants obtained using theoretical and simulation methods vary significantly within DNA itself. Experimental measurements of the dielectric constant within the major and minor grooves have been reported, but its value between the stacked base pairs, where intercalators are usually found, apparently has not been experimentally determined. Furthermore, it is expected that the surrounding environment will have an effect on the dielectric constant within the DNA. Important factors in this regard include the ionic strength of the solution and the properties of any surface to which it adsorbs. These factors, and the dielectric constant experienced by intercalators will be explored in this presentation.<br/><br/>  In this report, Nile Red (NR), a solvatochromic fluorescent dye, is applied as the microenvironment-sensitive probe for both supercoiled and relaxed plasmid DNA. Different concentrations of phosphate buffered saline (PBS) are used for the preparation of NR DNA solutions. An aminosilane gradient, vapor deposited on a clean coverslip, is employed to adsorb NR doped DNA for spectroscopic imaging. The spectroscopic imaging results are used to determine the dielectric constant of DNA in solution and on the gradient surface. The results reveal that the dielectric constant of DNA is apparently independent of its conformation. However, the value in solution decreases with an increase in buffer concentration. When adsorbed to the amine gradient surface, the dependence on buffer concentration disappears when the DNA is adsorbed to the high amine surface but still appears at the low amine surface. The dielectric constant is found to be ~ 3-7 in solution and 2-3 when the DNA is adsorbed to the gradient surface. This work gives a better understanding of the dielectric properties of DNA and the significance of the surroundings in affecting its value. A better understanding of these properties will aid in the development of new drugs that exhibit improved binding affinity to DNA.

Probing the local dielectric properties of plasmid DNA in solution and adsorbed on chemically graded surfaces

255th National Meeting (2018)

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