Comparison of theoretical and thermodynamic values of interconstituent interactions in DNA

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Abstract
Experimental base stacking and hydrogen bonding enthalpies, as determined from double stranded DNA melting studies, are compared with theoretical calculations of interactions between the respective DNA interconstituent components. Comparisons are made in relation to the differences in magnitudes, sequence dependent spreads, and trends. It is shown that the use of an effective dielectric constant reconciles the differences between the experimental and theoretical values. Suggestions are made for calibration of potential functions suitable for nucleic acid conformational analysis.