2019/03/11 by Fosado, Yair Augusto Gutierrez, Xing, Zhongyang, Eiser, Erika +2
#Biological Physics (physics.bio-ph) #FOS: Physical sciences #Materials Science (cond-mat.mtrl-sci) #Soft Condensed Matter (cond-mat.soft)
paper · doi:10.48550/arxiv.1903.04186
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.