Exploring the effect of the number of arms and junction bases on DNA nanostar conformation using molecular dynamics simulations

Immobile branched junctions in DNA, a.k.a. nanostars, are crosslinking nanostructures that, under the right conditions of concentration and temperature, condense to form a liquid or gel phase in water. Programmability of DNA base pairing offers unprecedented control over the number and strength of the weak bonds that drive condensation. To better understand how nanostar design affects the accessibility of those bonds, we used oxDNA2, a coarse-grained, molecular dynamics model of DNA, to simulate nanostars with different numbers of arms (3-6) and unpaired bases per arm in the junction (0-10).