DOI: 10.1073/pnas.1405702111. Direct measurement of the dielectric polarization properties of DNA

Direct measurement of the dielectric polarization properties of DNA

10.1073/pnas.1405702111

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Significance The strength of DNA–DNA and DNA–ligand electrostatic interactions crucially depends on the electric polarizability of DNA, represented by its dielectric constant. This has remained unknown owing to the lack of experimental techniques able to measure it. Here, we experimentally determined the dielectric constant of double-stranded DNA in a native condensed state inside a single bacteriophage as well as the dielectric constants of the protein shell and tail that compose the viral capsid using scanning force microscopy. We supported the experimental data by theoretically determining the DNA dielectric constant using atomistic simulations. Both approaches yield a dielectric constant of DNA around 8, sensibly higher than commonly assumed, thus revealing a DNA intrinsic property essential for realistic computational description of DNA.

Bibliography

Cuervo, A., Dans, P. D., Carrascosa, J. L., Orozco, M., Gomila, G., & Fumagalli, L. (2014). Direct measurement of the dielectric polarization properties of DNA. Proceedings of the National Academy of Sciences, 111(35).

Authors 6

Ana Cuervo (first)
Pablo D. Dans (additional)
José L. Carrascosa (additional)
Modesto Orozco (additional)
Gabriel Gomila (additional)
Laura Fumagalli (additional)

References 52 Referenced 174

10.1126/science.7761829
10.1146/annurev.bb.19.060190.001505
10.1146/annurev.biophys.29.1.497
10.1039/c0cp02796k
10.1529/biophysj.108.131797
10.1103/PhysRevE.71.061928
10.1039/C1CP22756D
10.1093/nar/gkg922
10.1016/j.bpj.2010.04.066
10.1038/nature08473
10.1093/nar/gkq984
10.1021/cr00101a005
10.1002/bip.360280506
10.1002/(SICI)1097-0282(199812)46:7<503::AID-BIP8>3.0.CO;2-V
10.1007/s00214-009-0617-x
10.1016/S0006-3495(99)77419-9
10.1021/jp074166z
10.1016/0167-4781(95)00232-4
10.1103/PhysRevE.75.021905
10.1049/iet-nbt.2008.0014
10.1002/elps.200500928
10.1073/pnas.85.23.8939
10.1093/nar/23.1.159
10.1038/nmat3369
10.1088/0034-4885/66/5/202
10.1002/prot.1106
10.1021/jp1111873
10.1021/ja960884f
10.1002/bip.360251106
10.1021/j100665a011
10.1039/f19817701733
10.1038/sj.emboj.7600840
10.1074/jbc.M110.187211
10.1074/jbc.M113.491209
10.1073/pnas.0810095106
10.1021/ja01261a043
10.1002/bip.360280509
10.1016/S0006-3495(95)80022-6
10.1021/jp9823188
10.1529/biophysj.106.097782
10.1021/ja0753546
10.1093/nar/gks884
10.1002/bip.360250206
K Talley, P Kundrotas, E Alexov, Modeling salt dependent of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation. Commun Comput Phys 3, 1071–1086 (2008). / Commun Comput Phys / Modeling salt dependent of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation by Talley K (2008)
10.1021/bi982063o
10.1002/prot.1159
10.1002/jcc.540160303
10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
10.1093/nar/gkn082
10.1021/cr990052a
10.1016/0263-7855(96)00018-5

Dates

Type	When
Created	11 years ago (Aug. 19, 2014, 2:18 a.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 11:12 p.m.)
Indexed	3 weeks, 5 days ago (July 28, 2025, 5:58 p.m.)
Issued	11 years ago (Aug. 18, 2014)
Published	11 years ago (Aug. 18, 2014)
Published Online	11 years ago (Aug. 18, 2014)
Published Print	10 years, 11 months ago (Sept. 2, 2014)

Funders 0

None

BibTeX

@article{Cuervo_2014, title={Direct measurement of the dielectric polarization properties of DNA}, volume={111}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1405702111}, DOI={10.1073/pnas.1405702111}, number={35}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Cuervo, Ana and Dans, Pablo D. and Carrascosa, José L. and Orozco, Modesto and Gomila, Gabriel and Fumagalli, Laura}, year={2014}, month=aug }

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