Thermal fluctuations of partially extended DNA single molecules

Rajalakshmi Nambiar; Jens-Christian Meiners

doi:10.1117/12.609502

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23 May 2005 Thermal fluctuations of partially extended DNA single molecules

Rajalakshmi Nambiar, Jens-Christian Meiners

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Proceedings Volume 5841, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems III; (2005) https://doi.org/10.1117/12.609502
Event: SPIE Third International Symposium on Fluctuations and Noise, 2005, Austin, Texas, United States

Abstract

Studying the thermal fluctuations of DNA molecules reveals not only a wealth of interesting equilibrium and non-equilibrium statistical mechanics, but is also of importance for understanding the dynamics of DNA in vivo. An instance of the latter is in the context of regulatory functions that require collaborative interactions of distant operator sites on the DNA molecule. These thermal fluctuations are extremely sensitive to mechanical constraints, such as supercoiling or mechanical tension in the DNA. The natural force scale f_c on which these fluctuations are sensitive to tension is related to the persistence length l_p by f_c = k_BT/l_p = 80 fN, which is generally considered small for a crowded cellular environment. We are studying the dynamics of single DNA molecules under tension under equilibrium conditions using a modified scanning-line laser trap. This technique allows us to apply a constant force between 20 fN and 3 pN to a λ-DNA molecule while we measure fluctuations of its extension with sub-millisecond time resolution. We compute the time-correlation functions of these fluctuations to determine their time constants, and model them with a simple bead-and-spring model. We observe a decrease of the fundamental time constant with increasing extension of the molecule. This suggests that the change in spring constant dominates changes in the intra-chain hydrodynamic coupling between segments as the Gaussian coil unravels into an extended conformation.

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Rajalakshmi Nambiar and Jens-Christian Meiners "Thermal fluctuations of partially extended DNA single molecules", Proc. SPIE 5841, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems III, (23 May 2005); https://doi.org/10.1117/12.609502

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