A molecular mechanics study of spermine complexation to DNA: a new model for spermine-poly(dG-dC) binding.
Molecular mechanics calculations of the binding of spermine to a number of solvated DNA helices have led to the development of a new model for spermine complexation. The structural details of the complexes formed with d(GCGCGCGCGC)2 and d(ATATATATAT)2 decamers allowed a rationalization of the observed experimental differences for binding to these two helices. For d(ATATATATAT)2 it was concluded that spermine remains in a cross-major groove binding site. Conversely, for d(GCGCGCGCGC)2 spermine reorientation via specific ligand-base-pair hydrogen-bond formation allows complexation along the major groove. The solvent plays an important role in differentiating the two binding modes. A mechanism of spermine complexation to natural DNA is postulated from these results. Past experimental data are also considered in the context of the new model.
Haworth
I S
IS
Physical Chemistry Laboratory, Oxford, U.K.
Rodger
A
A
Richards
W G
WG
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D008956:Models, Chemical; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D013096:Spermine / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
D011089:Polydeoxyribonucleotides; C019530:poly(dC-dG); D013096:Spermine; D004247:DNA