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High flexibility of DNA on short length scales probed by atomic force microscopy

Wiggins, Paul A. and van der Heijden, Thijn and Moreno-Herrero, Fernando and Spakowitz, Andrew and Phillips, Rob and Widom, Jonathan and Dekker, Cees and Nelson, Philip C. (2006) High flexibility of DNA on short length scales probed by atomic force microscopy. Nature Nanotechnology, 1 (2). pp. 137-141. ISSN 1748-3387.

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The mechanics of DNA bending on intermediate length scales (5–100 nm) plays a key role in many cellular processes, and is also important in the fabrication of artificial DNA structures, but previous experimental studies of DNA mechanics have focused on longer length scales than these. We use high-resolution atomic force microscopy on individual DNA molecules to obtain a direct measurement of the bending energy function appropriate for scales down to 5 nm. Our measurements imply that the elastic energy of highly bent DNA conformations is lower than predicted by classical elasticity models such as the worm-like chain (WLC) model. For example, we found that on short length scales, spontaneous large-angle bends are many times more prevalent than predicted by the WLC model. We test our data and model with an interlocking set of consistency checks. Our analysis also shows how our model is compatible with previous experiments, which have sometimes been viewed as confirming the WLC.

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Phillips, Rob0000-0003-3082-2809
Dekker, Cees0000-0001-6273-071X
Additional Information:© 2006 Nature Publishing Group. Received 23 June 2006; accepted 31 August 2006; published online: 3 November 2006. We thank N. R. Dan, N. H. Dekker, M. Inamdar, R. James, R. D. Kamien, I. Kulic, T. Laurence, R. Lavery, J. Maddocks J. Marko, A. Onufriev, P. Purohit, I. Rouzina, J. M. Schurr, R. Seidel, V. Soghomonian, Z.-G. Wang and Y. Zhang for helpful discussions and correspondence. P.A.W. acknowledges grant support from an NSF graduate fellowship. F.M.-H. acknowledges support from La Fundacien Ramon Areces as a postdoctoral fellow. A.J.S. acknowledges funding from the National Institutes of Health (NIH-GM071552). R.P. and P.A.W. acknowledge the Keck Foundation and NSF Grant CMS-0301657 as well as the NSF-funded Center for Integrative Multiscale Modeling and Simulation. J.W. acknowledges support from NIH grants R01 GM054692 and R01 GM058617. C.D. acknowledges the Stichting voor Fundamenteel Onderzoek der Materie (FOM), which is financially supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). P.N. acknowledges NSF Grant DMR04-04674 and the NSF-funded NSEC on Molecular Function at the Nano/Bio Interface DMR04-25780. J.W., R.P. and P.C.N. acknowledge the hospitality of the Kavli Institute for Theoretical Physics, supported in part by the National Science Foundation under Grant PHY99-07949.
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NSF Graduate FellowshipUNSPECIFIED
La Fundacien Ramon ArecesUNSPECIFIED
Keck FoundationUNSPECIFIED
NSF Center for Integrative Multiscale Modeling and SimulationUNSPECIFIED
NIHR01 GM054692
NIHR01 GM058617
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)UNSPECIFIED
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Record Number:CaltechAUTHORS:20150409-090719819
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Official Citation:High flexibility of DNA on short length scales probed by atomic force microscopy - pp137 - 141 Paul A. Wiggins, Thijn van der Heijden, Fernando Moreno-Herrero, Andrew Spakowitz, Rob Phillips, Jonathan Widom, Cees Dekker & Philip C. Nelson doi:10.1038/nnano.2006.63
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:56510
Deposited By: Ruth Sustaita
Deposited On:09 Apr 2015 18:21
Last Modified:09 Mar 2020 13:19

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