Direct Simulation of the Self-Assembly of a Small DNA Origami

Autor(en)

Benedict E. K. Snodin, Flavio Romano, Lorenzo Rovigatti, Thomas E. Ouldridge, Ard A. Louis, Jonathan P. K. Doye

Abstrakt

By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature-window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.

Organisation(en)

Computergestützte Physik und Physik der Weichen Materie

Externe Organisation(en)

University of Oxford, Imperial College London

Journal

ACS Nano

Band

10

Seiten

1724-1737

Anzahl der Seiten

14

ISSN

1936-0851

DOI

https://doi.org/10.1021/acsnano.5b05865

Publikationsdatum

02-2016

Peer-reviewed

Ja

ÖFOS 2012

104010 Makromolekulare Chemie, 210006 Nanotechnologie

Schlagwörter

ASJC Scopus Sachgebiete

Allgemeiner Maschinenbau, Allgemeine Physik und Astronomie, Allgemeine Materialwissenschaften

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/e2e1a433-d862-48f8-8ace-a1c5ba477daf