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Research Papers

Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic Acid Origami Nanoplates

[+] Author and Article Information
Bowen Liang, Anand Nagarajan, Ricardo Alvarez, Carlos E. Castro

Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210

Michael W. Hudoba

Department of Engineering,
Otterbein University,
Westerville, OH 43081

Soheil Soghrati

Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210;
Department of Materials
Science and Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: soghrati.1@osu.edu

1Corresponding author.

Manuscript received October 8, 2016; final manuscript received February 3, 2017; published online March 1, 2017. Assoc. Editor: Jeffrey Ruberti.

J Biomech Eng 139(4), 041003 (Mar 01, 2017) (8 pages) Paper No: BIO-16-1398; doi: 10.1115/1.4036022 History: Received October 08, 2016; Revised February 03, 2017

Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.

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Figures

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Fig. 1

Many staple strands bind piecewise to the scaffold strand to fold that into a compact structure for a small model of a DNA origami nanoplate

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Fig. 2

(a) Atomic-force microscopy image of DNA origami nanoplates, together with example DNA origami materials composed of an array of these nanoplates connected (b) along a complete edge and (c) at varying corner points

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Fig. 3

CISAMR transformation of a structured grid into a conforming mesh: (a) SAMR, (b) r-adaptivity, and (c) subtriangulation of background elements

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Fig. 4

(a) Cylinder and (b) realistic models of the nanoplate, (c) and (d) underlying molecular structure showing the helices and staple strand, and (e) small portion of the resulting CISAMR mesh using a 400 × 256 structured grid to discretize the domain

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Fig. 5

Boundary conditions for nanoplate subjected to (a) uniform and (b) asymmetric prescribed tensile displacements

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Fig. 6

Schematic of the process of identifying the background elements cut by DNA strands and performing the h-adaptivity phase during the construction of an FE model of the nanoplate using CISAMR

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Fig. 7

Different models analyzed to quantify the impact of defects on the DNA nanoplate mechanical behavior

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Fig. 8

Variations of (a) normalized effective stiffness and (b) normalized maximum normal tensile strain in the 42 DNA origami nanoplates shown in Fig. 7 subject to uniform tension

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Fig. 9

Deformed shape and normal strain in nanoplates #10 and #11 subject to uniform tension

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Fig. 10

Variations of (a) normalized reaction force and (b) normalized maximum normal tensile strain in the 42 DNA origami nanoplates shown in Fig. 7 subject to asymmetric tension

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Fig. 11

Deformed shape and normal strain in nanoplate #11 subject to asymmetric tension

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