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. 2006 May 26;91(4):1460–1470. doi: 10.1529/biophysj.105.074617

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Copyright © 2006, Biophysical Society

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Configurational entropy per atom of netropsin (A) and distamycin (B) free in solution (thin lines) and when bound to DNA (thick lines) calculated for nonhydrogen atoms. Configurational entropy was estimated for each ligand after removal of overall translation and rotation using all nonhydrogen atoms ( solid line) or using only four atoms of the central CO-NH peptide bond ( dashed line), and after a translational superposition of centers of mass and a rotational least-squares fit using the nonhydrogen atoms of the central GAAAAAC/GTTTTTC segment ( dot-dashed line) of the DNA duplex. The arrows point to the first and second rapid increases in entropy for distamycin.

Inline graphic — Configurational entropy per atom of netropsin (A) and distamycin (B) free in solution (thin lines) and when bound to DNA (thick lines) calculated for nonhydrogen atoms. Configurational entropy was estimated for each ligand after removal of overall translation and rotation using all nonhydrogen atoms ( solid line) or using only four atoms of the central CO-NH peptide bond ( dashed line), and after a translational superposition of centers of mass and a rotational least-squares fit using the nonhydrogen atoms of the central GAAAAAC/GTTTTTC segment ( dot-dashed line) of the DNA duplex. The arrows point to the first and second rapid increases in entropy for distamycin.