Literature DB >> 25136104

Direct measurement of the dielectric polarization properties of DNA.

Ana Cuervo1, Pablo D Dans2, José L Carrascosa3, Modesto Orozco4, Gabriel Gomila5, Laura Fumagalli6.   

Abstract

The electric polarizability of DNA, represented by the dielectric constant, is a key intrinsic property that modulates DNA interaction with effector proteins. Surprisingly, it has so far remained unknown owing to the lack of experimental tools able to access it. Here, we experimentally resolved it by detecting the ultraweak polarization forces of DNA inside single T7 bacteriophages particles using electrostatic force microscopy. In contrast to the common assumption of low-polarizable behavior like proteins (εr ∼ 2-4), we found that the DNA dielectric constant is ∼ 8, considerably higher than the value of ∼ 3 found for capsid proteins. State-of-the-art molecular dynamic simulations confirm the experimental findings, which result in sensibly decreased DNA interaction free energy than normally predicted by Poisson-Boltzmann methods. Our findings reveal a property at the basis of DNA structure and functions that is needed for realistic theoretical descriptions, and illustrate the synergetic power of scanning probe microscopy and theoretical computation techniques.

Keywords:  DNA packaging; DNA–ligand binding; Poisson–Boltzmann equation; atomic force microscopy; atomistic simulations

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Substances:

Year:  2014        PMID: 25136104      PMCID: PMC4156767          DOI: 10.1073/pnas.1405702111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  41 in total

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Journal:  Proteins       Date:  2001-09-01

Review 2.  Energies and pressures in viruses: contribution of nonspecific electrostatic interactions.

Authors:  Antonio Siber; Anže Lošdorfer Božič; Rudolf Podgornik
Journal:  Phys Chem Chem Phys       Date:  2011-12-06       Impact factor: 3.676

3.  Label-free identification of single dielectric nanoparticles and viruses with ultraweak polarization forces.

Authors:  Laura Fumagalli; Daniel Esteban-Ferrer; Ana Cuervo; Jose L Carrascosa; Gabriel Gomila
Journal:  Nat Mater       Date:  2012-07-08       Impact factor: 43.841

4.  Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.

Authors:  Alina Ionel; Javier A Velázquez-Muriel; Daniel Luque; Ana Cuervo; José R Castón; José M Valpuesta; Jaime Martín-Benito; José L Carrascosa
Journal:  J Biol Chem       Date:  2010-10-20       Impact factor: 5.157

Review 5.  Dielectric and dielectrophoretic properties of DNA.

Authors:  R Hölzel
Journal:  IET Nanobiotechnol       Date:  2009-06       Impact factor: 1.847

6.  Structure of DNA hydration shells studied by Raman spectroscopy.

Authors:  N J Tao; S M Lindsay; A Rupprecht
Journal:  Biopolymers       Date:  1989-05       Impact factor: 2.505

7.  Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)].poly[d(AT)]duplex.

Authors:  R Jin; K J Breslauer
Journal:  Proc Natl Acad Sci U S A       Date:  1988-12       Impact factor: 11.205

8.  The dielectric constant of a folded protein.

Authors:  M K Gilson; B H Honig
Journal:  Biopolymers       Date:  1986-11       Impact factor: 2.505

9.  Fluorescent d(CGCGAATTCGCG): characterization of major groove polarity and study of minor groove interactions through a major groove semantophore conjugate.

Authors:  D A Barawkar; K N Ganesh
Journal:  Nucleic Acids Res       Date:  1995-01-11       Impact factor: 16.971

10.  The role of DNA shape in protein-DNA recognition.

Authors:  Remo Rohs; Sean M West; Alona Sosinsky; Peng Liu; Richard S Mann; Barry Honig
Journal:  Nature       Date:  2009-10-29       Impact factor: 49.962

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  36 in total

1.  Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg(2+)-unsaturated solutions.

Authors:  Shu-ichi Nakano; Yuichi Kitagawa; Daisuke Miyoshi; Naoki Sugimoto
Journal:  J Biol Inorg Chem       Date:  2015-07-29       Impact factor: 3.358

2.  Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations.

Authors:  Samuel Bowerman; Jeff Wereszczynski
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

Review 3.  The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents.

Authors:  Shu-Ichi Nakano; Naoki Sugimoto
Journal:  Biophys Rev       Date:  2016-01-11

4.  Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions.

Authors:  Shu-Ichi Nakano; Yuichi Tanino; Hidenobu Hirayama; Naoki Sugimoto
Journal:  Biophys J       Date:  2016-10-04       Impact factor: 4.033

5.  Acceleration of DNA melting kinetics using alternating electric fields.

Authors:  Sebastian Sensale; Zhangli Peng; Hsueh-Chia Chang
Journal:  J Chem Phys       Date:  2018-08-28       Impact factor: 3.488

6.  Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR.

Authors:  Maxim A Voinov; Alex I Smirnov
Journal:  Methods Enzymol       Date:  2015-09-09       Impact factor: 1.600

7.  Bacteriochlorin Dyads as Solvent Polarity Dependent Near-Infrared Fluorophores and Reactive Oxygen Species Photosensitizers.

Authors:  Nopondo N Esemoto; Zhanqian Yu; Linda Wiratan; Andrius Satraitis; Marcin Ptaszek
Journal:  Org Lett       Date:  2016-09-07       Impact factor: 6.005

8.  Allosterism and signal transfer in DNA.

Authors:  Alexandra Balaceanu; Alberto Pérez; Pablo D Dans; Modesto Orozco
Journal:  Nucleic Acids Res       Date:  2018-09-06       Impact factor: 16.971

9.  BODIPY-Bacteriochlorin Energy Transfer Arrays: Toward Near-IR Emitters with Broadly Tunable, Multiple Absorption Bands.

Authors:  Adam Meares; Andrius Satraitis; Marcin Ptaszek
Journal:  J Org Chem       Date:  2017-11-22       Impact factor: 4.354

10.  What Makes Thienoguanosine an Outstanding Fluorescent DNA Probe?

Authors:  Jagannath Kuchlyan; Lara Martinez-Fernandez; Mattia Mori; Krishna Gavvala; Stefano Ciaco; Christian Boudier; Ludovic Richert; Pascal Didier; Yitzhak Tor; Roberto Improta; Yves Mély
Journal:  J Am Chem Soc       Date:  2020-09-23       Impact factor: 15.419

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