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  The dynamics of the B-A transition of natural DNA double helices.

Jose, D., & Porschke, D. (2005). The dynamics of the B-A transition of natural DNA double helices. Journal of American Chemical Society, 127(46), 16120-16128. Retrieved from http://pubs.acs.org/cgi-bin/article.cgi/jacsat/2005/127/i46/html/ja053691d.html.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-E786-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0002-0346-C
Genre: Journal Article

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Jose, D.1, Author              
Porschke, D.1, Author              
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1Research Group of Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578610              

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 Abstract: 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 approximately 50% GC, the main part of the amplitude (approximately 75%) is associated with time constants of approximately 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 approximately 2 µs at 50% GC to approximately 3 µs at 41% GC and approximately 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 approximately 0.1. The rate of the B-A transition is lower by approximately 3 orders of magnitude than that predicted by molecular dynamics simulations.

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 Dates: 2005-11-23
 Publication Status: Published in print
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Title: Journal of American Chemical Society
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Pages: - Volume / Issue: 127 (46) Sequence Number: - Start / End Page: 16120 - 16128 Identifier: -