A route to self-assemble suspended DNA nano-complexes

Lansac, Yves; Degrouard, Jéril; Renouard, Madalena; Toma, Adriana C.; Livolant, Françoise; Raspaud, Éric

doi:10.1038/srep21995

Cited by 18 publications

(31 citation statements)

References 59 publications

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“…To reduce noise, we take advantage of the large number and outer boundaries of the toroids (innermost and outermost layers, shadowed in grey in Fig. 2B) to eliminate the influence of the peripheral fluctuations due to the reduced number of neighboring filaments [38]. In giant toroids, we do not collect data from regions where the toroid is potentially perturbed by a contact with a neighbor ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Local structure of DNA toroids reveals curvature-dependent intermolecular forces

Barberi

Livolant

Leforestier

et al. 2020

Preprint

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In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.

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Section: Resultsmentioning

confidence: 99%

Local structure of DNA toroids reveals curvature-dependent intermolecular forces

Barberi

Livolant

Leforestier

et al. 2020

Preprint

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“…43 In fact, it is rather unlikely that positive-charged PEDOT fragments would stay together without anionic glues between them. The X anion can play the role of condensing agent (like positively charged condensing agents of negatively charged DNA), 44 which holds the p-doped PEDOT chains together, and the sustainability of p-doping of such PEDOT:X phase (i.e., PEDOT-to-X electron transfer or vice versa) would play a significant role in altering the conductivity (σ ∝ μ × n) of EMIM:X-treated PEDOT:PSS. Good X anions in EMIM:X IL would play the multiple roles of (1) disrupting the PEDOT− PSS attraction and bringing PEDOT together (to increase μ) and ( 2) increasing (or sustaining) the degree of p-doping in PEDOT (to increase n).…”

Section: Introductionmentioning

confidence: 99%

Ionic Liquid Designed for PEDOT:PSS Conductivity Enhancement

et al. 2018

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Poly-3,4-ethylenedioxythiophene:polystyrenesulfonate (PEDOT:PSS) is a water-processable conducting polymer with promise for use in transparent flexible electrodes and thermoelectric devices, but its conductivity is not satisfactory. Its low conductivity is attributed to the formation of hydrophilic/insulating PSS outer layers encapsulating the conducting/hydrophobic p-doped PEDOT cores. Recently a significant conductivity enhancement has been achieved by adding ionic liquid (IL). It is believed that ion exchange between PEDOT:PSS and IL components helps PEDOT to decouple from PSS and to grow into large-scale conducting domains, but the exact mechanism is still under debate. Here we show through free energy calculations using density functional theory on a minimal model that the most efficient IL pairs are the least tightly bound ones with the lowest binding energies, which would lead to the most efficient ion exchange with PEDOT:PSS. This spontaneous ion exchange followed by nanophase segregation between PEDOT and PSS, with formation of a π-stacked PEDOT aggregate decorated by IL anions, is also supported by molecular dynamics performed on larger PEDOT:PSS models in solution. We also show that the most efficient IL anions would sustain the highest amount of charge carriers uniformly distributed along the PEDOT backbone to further enhance the conductivity, providing that they remain in the PEDOT domain after the ion exchange. Hence, our design principle is that the high-performance IL should induce not only an efficient ion exchange with PEDOT:PSS to improve the PEDOT morphology (to increase mobility) but also a uniform high-level p-doping of PEDOT (to enhance intrinsic conductivity). Based on this principle, a promising (electron-withdrawing, but bulky, soft, and hydrophobic) new IL pair is proposed.

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“…Difference is also expected and indeed observed , between protamine and small multivalent cations because strongly charged long and flexible protamine can also induce attraction by bridging different parts of a long DNA or several short DNA fragments, resulting in specific aggregate morphology such as branched bundles and lamellar rafts. , The threshold concentration for DNA aggregation and the nature of the transition are also significantly different between protamine and small multivalent ions. Dilute solutions of short DNA fragments mixed with protamine at low salt concentration form a large DNA–protamine precipitate near the isoelectric point but turn into charged small soluble bundles upon varying protamine-to-DNA charge ratio. − Moreover, bundle formation is a reversible phenomenon and re-entrant condensation can be triggered by addition of a significant amount of protamine for both short fragments at low salt and long DNA at physiological salt concentration …”

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confidence: 99%

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue

et al. 2021

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Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 10 6 -fold compaction of DNA, corresponding to a 10−20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid−liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

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A route to self-assemble suspended DNA nano-complexes

Cited by 18 publications

References 59 publications

Local structure of DNA toroids reveals curvature-dependent intermolecular forces

Local structure of DNA toroids reveals curvature-dependent intermolecular forces

Ionic Liquid Designed for PEDOT:PSS Conductivity Enhancement

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue

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