Direct measurement of the dielectric polarization properties of DNA

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 (e r ∼ 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.DNA-ligand binding | DNA packaging | atomic force microscopy | atomistic simulations | Poisson-Boltzmann equation E lectrostatic forces have long been recognized to inherently influence the DNA structure and interactions (1, 2) including DNA bending and folding (3, 4), DNA packaging (5-7), and DNA-ligand recognition (8-10), owing to the high charge density of the DNA molecule. In particular, the crucial role of coulombic forces in the binding affinity of molecules to a specific DNA sequence, such as clinically important drugs into minor grooves (9) and protein complexes into major grooves (11), has been well established (12). However, although detailed knowledge of DNA-DNA and DNA-ligand interactions can nowadays be obtained by high-resolution structural techniques, energetic analysis remains experimentally challenging because it requires quantification of the different contributions to such interactions, in particular the electrostatic energy term.To study the DNA electrostatics, theoretical methods are normally used. All of them require to precisely know the DNA polarization properties in addition to the detailed molecular structure and charge distribution (13-15). In the commonly used mean-field approximation, such as the Poisson-Boltzmann theory, this means including explicitly or implicitly the dielectric constant of DNA, « DNA , a measure of the screening of coulombic forces between charges due to the presence of the DNA molecule. However, despite its crucial impact, the dielectric constant of DNA has remained unknown so far. In the absence of a precise knowledge of « DNA , theoretical models typically assume DNA to be a low-polarizable medium with « DNA ∼ 2-4 like dry proteins surrounded by a highly screening solvent with the dielectric constant of the bulk water ∼80 (13-17). However, this is a simplified picture that lacks experimental validation and introduces a major source of uncertainty, which can give completely biased results in theoretical met...

Catalytic Activities of Ribozymes and DNAzymes in Water and Mixed Aqueous Media

“…This mechanism is consistent with the dielectric constant effect that facilitates electrostatic Mg 2+ binding and allows greater enhancement of the turnover activity observed at the low Mg 2+ concentration of 1 mM. In the cellular environment, the dielectric constant is relatively low [50,51] and the concentration of Mg 2+ is as low as 1 mM or less [52]. Thus, it is speculated that the hammerhead ribozyme is suitable for use in living cells, for example to achieve intracellular mRNA cleavage and in vivo sensing.…”

Nanoscale dielectric microscopy of non-planar samples by lift-mode electrostatic force microscopy

“…The use of lift mode imaging ensures the maximum sensitivity in all positions of the sample, and our analysis ensures the results are free from topographic crosstalk artefacts. We would like to highlight, however, that for planar samples or low dimensional non-planar samples (like nanoparticles, nanotubes, etc,) the use of constant height imaging mode can be preferred since the accuracy required (very often in the sub-1zF/nm) [26,27,29] cannot be offered by the reconstruction procedure presented here.…”

“…Among them, we can cite nanoscale capacitance microscopy [1][2][3], electrostatic force microscopy (EFM) [4][5][6][7][8][9][10], nanoscale impedance microscopy [11,12], scanning polarization force microscopy [13][14][15][16], scanning microwave microscopy (SMM) [17,18] and nanoscale non-linear dielectric microscopy [19]. These techniques have allowed measuring the electric permittivity with nanoscale spatial resolution on planar samples, such as thin oxides, polymer films and supported biomembranes [2][3][4]8,10], and on non-planar ones, such as, single carbon nanotubes, nanowires, nanoparticles, viruses and bacterial cells [20][21][22][23][24][25][26][27][28][29][30].…”

Internal Hydration Properties of Single Bacterial Endospores Probed by Electrostatic Force Microscopy

“…EFM is a scanning probe microscopy technique sensitive to the local dielectric properties of the samples. 33,34 Examples showing this ability include numerous applications to samples of non-biological origin (thin and thick oxides, 35 polymer films, [36][37][38] nanowires, 39 nanotubes 40,41 or nanoparticles [42][43][44][45] ), and of biological origin (single bacterial cells, 46,47 single virus particles, 45 solid supported biomembranes, 48 protein complexes 49 or DNA molecules). 50 EFM has two important properties relevant for the present application, namely, (i)…”

“…45,49 This fact makes its presence easily detectable in the EFM images even when small amounts of moisture are present. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 We addressed next the question whether the overall hydration properties, as well as the internal water distribution, of endospores and vegetative cells is the same or whether they offer distinct properties.…”