A critical evaluation of models for complex molecular dynamics: application of NMR studies of double- and single-stranded DNA

The nature of internal and overall motions in native (double-stranded) and denatured (single-stranded) DNA fragments 120–160 base pairs (bp) long is examined by molecular-dynamics modeling using ¹³C-nmr spin-relaxation data obtained over the frequency range of 37–125 MHz. The broad range of ¹³C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T₁ values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double-stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τ_x = ～10^?6 s;τ_Z = ～1.8 × 10^?8s), which is in good agreement with values calculated from hydrodynamic theory (τ_x = ～1.8 × 10^?6 s; τ_Z = ～2.7 × 10^?8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual C? H vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τ_w = ～4 × 10^?9 s, θ_cone = ～21°) or as a bistable jump (τ_A = τ_B = ～2 × 10^?9 s, θ = ～15°). We discuss the critical role in molecular-dynamics modeling played by the angle (β) that individual C? H vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τ_W = ～0.2 × 10^?9 s, θ_cone = ～50°), and overall motion is affected by becoming essentially isotropic (τ_x = τ_Z = ～5 × 10^?8 s) for the single-stranded molecules. Since ¹³C-nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.