In silico self-assembly and complexation dynamics of cationic lipids with DNA nanocages to enhance lipofection

Sandip Mandal; Dhiraj Bhatia; Prabal K. Maiti

doi:10.1116/6.0004756

journal article Sep 01, 2025

In silico self-assembly and complexation dynamics of cationic lipids with DNA nanocages to enhance lipofection

Sandip Mandal

Dhiraj Bhatia

Prabal K. Maiti

Biointerphases Vol. 20 No. 5 · American Vacuum Society

View at Publisher Save 10.1116/6.0004756

Abstract

DNA nanostructures are promising materials for drug delivery due to their unique topology, shape, size control, biocompatibility, structural stability, and blood-brain-barrier penetration capability. However, their cellular permeability is hindered by strong electrostatic repulsion from negatively charged cellular membranes, posing a significant obstacle to the use of DNA nanostructures as a drug delivery vehicle. Recent experimental studies have shown enhanced cellular uptake for the conjugate binary mixtures of DNA Tetrahedron (TDN) with cationic lipid N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA) compared to TDN alone. However, the cationic DOTMA lipid binding mechanism with the TDN nucleotides is still elusive. Using fully atomistic MD simulations, we aim to understand the molecular interactions that drive the formation and stability of the TDN-DOTMA binary complexes in a physiological environment. Our results uncovered that lipid concentration plays a crucial role in the energetics of the TDN-DOTMA association. We also report that distinct time scales are associated with the self-assembly of cationic DOTMA lipids first, followed by the complexation of self-assembled DOTMA lipid clusters with the TDN nucleotides, where electrostatics, hydrophobicity, and hydrogen bonding are the key interactions that drive the formation and stability of these complexes. Our results provide molecular insights into TDN-DOTMA interactions, highlighting the lipid self-assembly dynamics, complex stability, and morphology, paving the way for the better rational design of cationic lipid-functionalized DNA nanostructures for efficient drug delivery and transfection.

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Details

Published: Sep 01, 2025
Vol/Issue: 20(5)

Authors

S

Sandip Mandal

Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science 1 , Bangalore 560012,

D

Dhiraj Bhatia

Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar 2 , Palaj, 382355 Gandhinagar, Gujarat,

P

Prabal K. Maiti

Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science 1 , Bangalore 560012,

Funding

Science and Engineering Research Board Award: CRG/2021/003659

Cite This Article

Sandip Mandal, Dhiraj Bhatia, Prabal K. Maiti (2025). In silico self-assembly and complexation dynamics of cationic lipids with DNA nanocages to enhance lipofection. Biointerphases, 20(5). https://doi.org/10.1116/6.0004756

In silico self-assembly and complexation dynamics of cationic lipids with DNA nanocages to enhance lipofection

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