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Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

ABSTRACT: The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety) of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine) to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.

SUBMITTER: Grasso G

PROVIDER: S-EPMC5663398 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

Grasso Gianvito G Deriu Marco Agostino MA Patrulea Viorica V Borchard Gerrit G Möller Michael M Danani Andrea A

PloS one 20171031 10

The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety) of these polymers is a challenge and in need of improvement. With the aim ...[more]

PMID: 29088239

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Project description:In this work the electrostatic complexation of two strong polyelectrolytes (PEs) was studied, the hydrophilic and positively charged poly (diallyldimethylammonium chloride) (PDADMAC) and the hydrophobic and negatively charged poly (styrene-co-sodium styrene sulfonate) (P(St-co-SSNa)), which was prepared at different sulfonation rates. The latter is known to adopt a pearl necklace conformation in solution for intermediate sulfonation rates, suggesting that a fraction of the P(St-co-SSNa) charges might be trapped in these hydrophobic domains; thus making them unavailable for complexation. The set of complementary techniques (DLS, zetametry, ITC, binding experiment with a cationic and metachromatic dye) used in this work highlighted that this was not the case and that all anionic charges of P(St-co-SSNa) were in fact available for complexation either with the polycationic PDADMAC or the monocationic o-toluidine blue dye. Only minor differences were observed between these techniques, consistently showing a complexation stoichiometry close to 1:1 at the charge equivalence for the different P(St-co-SSNa) compositions. A key result emphasizing that (i) the strength of the electrostatic interaction overcomes the hydrophobic effect responsible for pearl formation, and (ii) the efficiency of complexation does not depend significantly on differences in charge density between PDADMAC and P(St-co-SSNa), highlighting that PE chains can undergo conformational rearrangements favoring the juxtaposition of segments of opposite charge. Finally, these data have shown that the formation of colloidal PECs, such as PDADMAC and P(St-co-SSNa), occurs in two distinct steps with the formation of small primary complex particles (<50 nm) by pairing of opposite charges (exothermic step) followed by their aggregation within finite-size clusters (endothermic step). This observation is in agreement with the previously described mechanism of PEC particle formation from strongly interacting systems containing a hydrophobic PE.

Dataset Information

Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

Publications

Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

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