The Dynamics of the B−A Transition of Natural DNA Double Helices

• Published in: Journal of the American Chemical Society 2005-11, Vol.127 (46), p.16120-16128
• Main Authors: Jose, Davis, Porschke, Dietmar
• Format: Article
• Language: English
• Subjects: Animals; Bacteriophage lambda - genetics; Base Composition; Biological and medical sciences; Conformational dynamics in molecular biology; DNA - chemistry; DNA - genetics; DNA, A-Form - chemistry; DNA, A-Form - genetics; DNA, Viral - chemistry; DNA, Viral - genetics; Electrons; Fundamental and applied biological sciences. Psychology; Male; Molecular biophysics; Nucleic Acid Conformation; Plasmids - chemistry; Plasmids - genetics; Poly dA-dT - chemistry; Poly dA-dT - genetics; Salmon - genetics; Spectrum Analysis; Testis
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja053691d

The dynamics of the B−A transition of DNA double helices with different GC contents and various chain lengths has been characterized by an electric field pulse technique. The field-induced B−A reaction is separated from orientation effects using the magic angle technique. Amplitudes reflecting the B−A reaction are observed selectively in the limited range of ethanol contents, where CD spectra demonstrate the B−A transition. The maximum amplitude appears at 1−2% higher ethanol content than the center of the B−A transition observed by CD because electric field pulses induce a relatively large perturbation from the A- toward the B-form. The relaxation curves measured after pulse termination reflect a spectrum of up to three relaxation processes. For DNA's with ∼50% GC, the main part of the amplitude (∼75%) is associated with time constants of ∼2 μs, and another major component appears with time constants of 50−100 μs. These relaxation effects have been observed for DNA samples with 859, 2629, 7160, and 48501 bp. The time constant associated with the main amplitude increases with decreasing GC content from ∼2 μs at 50% GC to ∼3 μs at 41% GC and ∼10 μs at 0% GC at the center of the B−A transition. Model calculations on the kinetics of cooperative linear Ising lattices predict the appearance of a distinct maximum of the mean relaxation time at the center of the transition. The absence of such maximum in our experimental data indicates a low cooperativity of the B−A transition with a nucleation parameter of ∼0.1. The rate of the B−A transition is lower by ∼3 orders of magnitude than that predicted by molecular dynamics simulations.