Polyethylenimine–DNA Ratio Strongly Affects Their Nanoparticle Formation: A Large-Scale Coarse-Grained Molecular Dynamics Study

Abstract

Polyethylenimine (PEI)–DNA nanoparticles (NPs) have shown a lot of potential in gene delivery. The N/P ratio, the ratio between the total number of amines in PEIs and total number of phosphates in DNAs, is an essential factor determining the efficacy of delivery. In this work, the aggregation of PEIs and DNAs under different N/P ratios is studied using large-scale coarse-grained simulations under the Martini framework. At very low N/P ratio, the aggregation of DNAs is limited, and as the N/P ratio increases, the NPs change from a loose linear structure to a compact branched structure. Such a transition in the mode of aggregation is caused by the different alignments of PEIs with DNA backbones prior to aggregation, which dictates their ability to serve as polycation bridges. Except for very large NPs at high N/P ratios, the charge of a NP is proportional to the number of DNAs in it. Their ratio allows for the definition of an intrinsic property called specific repulsion, which controls the characteristics of the steady-state size distribution of NPs: unimodal for strong specific repulsion, bimodal for moderate specific repulsion, and more or less uniform for weak specific repulsion. Understanding the mechanism behind DNA–PEI NP formation helped us propose a two-step process to generate NPs that are more compact and closer to being spherical.

Meeting experiments at the diffraction barrier: anin-silicowidefield fluorescence microscopy

“… In-silico microscopy images generated with different parameters. MS on PEI-DNA aggregation [14] (see Methods) is used as the specimen. Unless otherwise specified, the PSF is modeled with β = 59.4°, n = z, n O = 12 nm, Δ l ′ = Δ m ′ = 0.1 nm, Δ n ′ = 0.05 nm, P l ′ = P m ′ = P n ′ = 25 nm, f s = 800, ( λ, I 0 ) = (670 nm, 0.13) for DNA and (518 nm, 0.27) for PEI; DNA and PEI particles are assigned indigo and yellow hues respectively (colocalization color bar below (a) and (d)); and no time-averaging is performed.…”

“…In-silico microscopy images generated with different parameters. MS on PEI-DNA aggregation [14] (see Methods) is used as the specimen. Unless otherwise specified, the PSF is modeled with β = 59.4°, n = z, nO = 12 nm,…”

“…On the other hand, molecular simulations (MS) can probe biochemical systems with molecular [13] , sub-molecular [14,15] , or atomic [16] resolutions. It is not surprising that such MS have been referred to as the computational microscope.…”

“…In this work, PSF is calculated for 461 (not shown), 518 and 670 nm (corresponding to emission peaks of DAPI, Cy5, and FITC), at different n ′ (black arrow). b) A polyethylenimine (PEI)-DNA aggregation simulation [14] (see Methods) is used as an MS specimen. The box represents the initial configuration of the MS, in the xyz coordinate system shown.…”

A dendritic, redox-responsive, supramolecular (Dr.S) system for lysis-triggered delivery for drug-resistant renal cancer

“…2a), because the nucleic acid and cationic materials tend to form looser nanogels at a relatively low N : P ratio. 18,19 Once the N : P ratio at which the nucleotides were completely condensed (N : P ratio ¼ 5) was reached, the size of nanoparticles remained stably ranging from 169 nm to 186 nm (N : P ratio over 5), which facilitated its delivery in circulation along with the spherical shape ( Fig. 2a).…”