Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation

Abstract

The DNA origami technique has proven to have tremendous potential for therapeutic and diagnostic applications like drug delivery, but the relatively low concentrations of cations in physiological fluids cause destabilization and degradation of DNA origami constructs preventing in vivo applications. To reveal the mechanisms behind DNA origami stabilization by cations, we performed atomistic molecular dynamics simulations of a DNA origami rectangle in aqueous solvent with varying concentrations of magnesium and sodium as well as polyamines like oligolysine and spermine. We explored the binding of these ions to DNA origami in detail and found that the mechanism of stabilization differs between ion types considerably. While sodium binds weakly and quickly exchanges with the solvent, magnesium and spermine bind close to the origami with spermine also located in between helices, stabilizing the crossovers characteristic for DNA origami and reducing repulsion of parallel helices. In contrast, oligolysine of length ten prevents helix repulsion by binding to adjacent helices with its flexible side chains, spanning the gap between the helices. Shorter oligolysine molecules with four subunits are weak stabilizers as they lack both the ability to connect helices and to prevent helix repulsion. This work thus shows how the binding modes of ions influence the stabilization of DNA origami nanostructures on a molecular level.

Functionalizing DNA nanostructures with natural cationic amino acids

“…For cationic species other than metal ions, their interaction mechanisms with DNA are rarely reported. Markvoort et al simulated the interaction model between a series of small molecules and DNA nanostructures [ 38 ]. Larger molecules, such as peptides, mainly interacted with the phosphate backbone with one duplex or between two DNA duplexes.…”

Challenges and Perspectives of DNA Nanostructures in Biomedicine

“…[94,95] This is due to ion-specific differences in the type of interaction, binding site,a nd binding affinity between DNAa nd the individual ion species. [94,96] Recently,R oodhuizen et al performed atomistic molecular-dynamics simulations of DO stabilization by various cations. [96] They found that Mg 2+ ions bind strongly to minor-groove atoms and the backbone phosphates,whereas Na + binding is much weaker and barely involves the phosphates.T his strong binding of the Mg 2+ ions is responsible for the somewhat surprising observation that DO assembled in aM g 2+ -containing buffer can be gently transferred into Mg 2+ -free buffers and even pure water without al oss of integrity.…”

Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin

“…[94,95] Dies liegt an ionenspezifischen Unterschieden in der Art der Interaktion, der Bindungsstelle und der Bindungsaffinitätz wischen der DNAu nd der jeweiligen Ionenspezies. [94,96] Roodhuizen et al führten vor kurzem atomistische Moleküldynamiksimulationen der DO-Stabilisierung durch verschiedene Kationen durch. [96] Sie fanden, dass Mg 2+ -Ionen stark an Atome der kleinen Furche und die Phosphate des Rückgrats binden, wohingegen die Na + -Bindung viel schwächer ist und die Phosphate kaum involviert.…”

“…Roodhuizen et al. führten vor kurzem atomistische Moleküldynamiksimulationen der DO‐Stabilisierung durch verschiedene Kationen durch . Sie fanden, dass Mg 2+ ‐Ionen stark an Atome der kleinen Furche und die Phosphate des Rückgrats binden, wohingegen die Na + ‐Bindung viel schwächer ist und die Phosphate kaum involviert.…”