title: Spontaneous ordering of DNA. Effects of intermolecular interactions on DNA motional dynamics monitored by 13C and 31P nuclear magnetic resonance spectroscopy.
abstract: Effects of intermolecular DNA interactions on the motional dynamics of defined length (147-, 234-, and 437-nucleotide pair (np)) double-stranded DNA were examined by 13C and 31P nuclear magnetic resonance spectroscopy. At a critical high concentration varying inversely with length, DNA undergoes a spontaneous transition to an ordered, liquid crystalline-like state. Ordering is accompanied by the appearance of distinct opalescence, and an increase in solution viscosity. An apparent standard heat of fusion of -38 kcal/mol of helix (-0.13 kcal/mol of DNA phosphate) and an entropy change of -0.13 entropy units (per mol of helix) were determined from the temperature dependence of the phase transition of 147-np DNA. The average phosphodiester configuration, monitored by Raman spectroscopy, was typical of B-form DNA above and below the phase transition. NMR spectra and relaxation data show that intermolecular interactions are strong at concentrations well below the phase transition and cause stepwise uncoupling of internal motions at specific sites. Motions of the exocyclic C5' carbon, but not other sugar carbons, are frozen in approximately 50% of 147-np DNA molecules at concentrations as low as 6.5 mg/ml. Motions of backbone ring carbons (C3', C4') are frozen in a progressively larger fraction of molecules at concentrations above 46 mg/ml. Rapid C2' motions are unaffected below the critical concentration (193 mg/ml at 32 degrees C), and still occur in the ordered phase. We conclude that rapid internal motions of DNA monitored by NMR consist mostly of coupled, periodic bending deformations and partially uncoupled local motions within the sugar ring. Rapid, extensive C2' motions can occur without strong coupling to other sugar carbon motions. From a comparison of 13C and 31P NMR data, we conclude that 31P NMR at best yields an incomplete representation of DNA dynamics.
mesh_terms: D000818:Animals; D002417:Cattle; D002843:Chromatin / Q000648:ultrastructure; D004247:DNA / Q000302:isolation & purification; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D013696:Temperature; D013816:Thermodynamics; D013950:Thymus Gland
chemical_list: D002843:Chromatin; D004247:DNA