Structural and dynamical properties of two DNA oligomers with the same base composition and different sequence

We compared the structural and dynamical properties of two DNA fragments, 27 bp long, having the same base composition but a different sequence. This work aims to understand how the base sequence on a purine rich strand in a double helix, which is important for many biological functions, is related to structural features and to measurable physical quantities. Structural characterization of the two samples was performed both by conventional spectroscopic methods (circular dichroism and UV denaturation experiments) and by means of a γ-ray footprinting technique which gives information on fine conformational differences. Dynamical features of the samples were studied by fluorescence polarization anisotropy (FPA) measurements which allow the evaluation of some hydrodynamic parameters, such as the hydrodynamic radius and the elastic torsion constant of DNA. Using a γ-ray footprinting technique, we observed that the interruption of the long homopurine–homopyrimidine run in the control sample, due to the `scrambling' operation, alters the DNA three-dimensional structure, also at nucleotide level. Besides, an increase in thermal stability and in the torsional rigidity of the `scrambled' sample was observed. A possible association between base-stacking interaction and torsional rigidity was inferred from the comparison of the two samples.