Dynamics of a bis-intercalator DNA complex by H-1-detected natural abundance C-13 NMR spectroscopy

The dynamics of the DNA oligomer d(CGCTAGCG)(2) (CTSYM) and its complex wit h the dye 1,1 -(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-bis-4-(3-meth yl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)-quinolinium tetraiodide (TOTO) (CTSYMTOTO) bis-intercalated at the 5'-CT-3' sequence steps have bee n determined from NMR relaxation parameters. Longitudinal and transverse C- 13 relaxation rates and heteronuclear NOE relaxation data were acquired and have been analyzed in the context of the Lipari and Szabo model-free forma lism. The overall rotational correlation time for the CTSYM is 3.44 ns and the CTSYMTOTO is 3.38 ns. The generalized order parameters (S-2) for methin e carbons in the CTSYM and CTSYMTOTO are relatively high but nonuniform for the molecules and show sequence context and conformation-dependent variati ons. Average values of S-2 = 0.79 +/- 0.02 for the CTSYM, S-2 = 0.80 +/- 0. 04 for the CTSYMTOTO aromatic spins, S-2 = 0.76 +/- 0.02 for the CTSYM, and S-2 = 0.83 +/- 0.05 for the CTSYMTOTO deoxyribose spins were found. The S- 2 values for the 5' terminal deoxyribose are lower than for the other resid ues. The DNA backbone in CTSYMTOTO is distorted and elongated at the site o f intercalation, and the C3' atom of the C3 deoxyribose residue has a very low S-2 = 0.57 +/- 0.06. The low order for this spin is interpreted in term s of exchange between the C2'-endo and O1'-endo conformations of the C3 deo xyribose. Significant chemical exchange processes were found for most of th e aromatic spins in CTSYM that are interpreted in terms of microsecond to m illisecond time scale dynamics. The microsecond to millisecond dynamics of the bases in CTSYM are quenched upon TOTO complex formation due to unwindin g of the helix and an increase in the surface area of the bases in mutual c ontact and the large surface area in contact with the intercalated dye. The derived order parameters combined with the solution structure provide moti onal models for conformational changes induced in the backbone in response to the ligand binding.