Computer Simulation Study of the Structural Stability and Materials Properties of DNA-Intercalated Layered Double Hydroxides

Abstract

The intercalation of DNA into layered double hydroxides (LDHs) has various applications, including drug delivery for gene therapy and origins of life studies. The nanoscale dimensions of the interlayer region make the exact conformation of the intercalated DNA difficult to elucidate experimentally. We use molecular dynamics techniques, performed on high performance supercomputing grids, to carry out large-scale simulations of double stranded, linear and plasmid DNA up to 480 base pairs in length intercalated within a magnesium-aluminum LDH. Currently only limited experimental data have been reported for these systems. Our models are found to be in agreement with experimental observations, according to which hydration is a crucial factor in determining the structural stability of DNA. Phosphate backbone groups are found to align with aluminum lattice positions. At elevated temperatures and pressures, relevant to origins of life studies which maintain that the earliest life forms originated around deep ocean hydrothermal vents, the structural stability of LDH-intercalated DNA is substantially enhanced as compared to DNA in bulk water. We also discuss how the materials properties of the LDH are modified due to DNA intercalation.

Biomedical Applications of Layered Double Hydroxides

“…Recently, the structural stability and material properties of DNA-intercalated LDH were examined by a computer simulation study based on molecular dynamics. [78] The structural models thus suggested were in good agreement with the experimental observations that anionic phosphate backbones aligned with aluminium hydroxide lattice, resulting in structural stability of DNA due to the hydration. The binding behaviour of DNA was also studied with flow cytometry, [79] and it was concluded that the anionic exchange capability of LDH could offer strong electrostatic interaction with DNA.…”

Bio-Layered Double Hydroxides Nanohybrids for Theranostics Applications

“…3C) [54,55]. As a result of molecular dynamic modeling, it was found that the LDH layers are flexible enough to deform around bulky DNA molecules.…”

Two‐Dimensional Hybrid Materials: Transferring Technology from Biology to Society

“…[34] To explain such structural compatibility, the conformation of DNA was found to match the interlayer topology with the phosphate backbone groups aligned with aluminum lattice positions. [35] Once again, the enhanced stability supplied by the organoceramic material is surmised to have played a key role in prebiotic evolution when the earliest life forms were exposed to harsh thermal conditions.…”