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arXiv · 1903.04186

A Numerical Study of Three-Armed DNA Hydrogel Structures

Yair Augusto Gutierrez Fosado·Zhongyang Xing·Erika Eiser·Magdalena Hudek·Oliver Henrich
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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.

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Yair Augusto Gutierrez Fosado, Zhongyang Xing, Erika Eiser, Magdalena Hudek, Oliver Henrich. 2019-03-11. A Numerical Study of Three-Armed DNA Hydrogel Structures. https://arxiv.org/abs/1903.04186

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