A Numerical Study of Three-Armed DNA Hydrogel Structures

TL;DR

This paper presents a numerical analysis of three-armed Y-shaped DNA hydrogel structures, comparing simulation results with experiments and exploring how design modifications affect their geometry and hybridization behavior.

Contribution

It introduces a detailed numerical study of three-armed DNA hydrogels, highlighting the effects of sequence modifications on their structural properties.

Findings

Simulation and experimental melting curves show excellent agreement.

Adding inert nucleotides has minimal impact on overall geometry.

Palindromic sequences significantly influence twisting and bending angles.

Abstract

We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both simulations with the oxDNA2 model and experiments and find excellent agreement. The morphology of the Y-DNA molecules is investigated when several alterations in the design are made. Adding inert nucleotides to the central core region of the Y-DNA molecules has a very minor effect on their overall geometry, whereas palindromic sequences in the sticky ends via which the individual Y-DNA molecules hybridize, have a profound influence on their relative twisting and bending angles.