binding of surfactants to double stranded oligonucleotides. effect of nucleotide sequence

Buckin V. A., Morrissey S. and Cragg E.

Biophysical Journal, 78, pp. 47(2000)

In, this work we studied the binding of surfactant to two double stranded oligonucleotides, each containing a high percentage (76%) of GC or AT base-pairs. A combination of isothermal titration calorimetry, UV spectroscopy, fluorescence, and a high-resolution ultrasonic spectroscopy was employed to gain both a structural and thermodynamic insight into the complex formation. We found that the binding of surfactant to the oligonucleotides occurs in two distinct stages, Small ‘micelle-like’ surfactant aggregates on the surface of the oligonucleotides are formed at the first stage of binding. These aggregates have a highly compressible core, which are large enough to accommodate our fluorescence probe. On the second stage, we observed the formation of large aggregates accompanied by light scattering in the visible region of the spectrum. The beat and compressibility effects at both stages were found to differ for the two duplexes indicating that the overall structure and thermodynamics of the surfactant aggregates are sequence dependent.

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