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.

References

References
1.
Douglas
,
S.
,
Bachelet
,
I.
, and
Church
,
G.
,
2012
, “
A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads
,”
Science
,
335
(
6070
), pp.
831
834
.
2.
Linko
,
V.
,
Ora
,
A.
, and
Kostiainen
,
M. A.
,
2015
, “
DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices
,”
Trends Biotechnol.
,
33
(
10
), pp.
586
594
.
3.
Jiang
,
Q.
,
Song
,
C.
,
Nangreave
,
J.
,
Liu
,
X.
,
Lin
,
L.
,
Qiu
,
D.
,
Wang
,
Z.-G.
,
Zou
,
G.
,
Liang
,
X.
,
Yan
,
H.
, and
Ding
,
B.
,
2012
, “
DNA Origami as a Carrier for Circumvention of Drug Resistance
,”
J. Am. Chem. Soc.
,
134
(
32
), pp.
13396
13403
.
4.
Zhao
,
W.-W.
,
Xu
,
J.-J.
, and
Chen
,
H.-Y.
,
2014
, “
Photoelectrochemical DNA Biosensors
,”
Chem. Rev.
,
114
(
15
), pp.
7421
7441
.
5.
Wang
,
D.
,
Fu
,
Y.
,
Yan
,
J.
,
Zhao
,
B.
,
Dai
,
B.
,
Chao
,
J.
,
Liu
,
H.
,
He
,
D.
,
Zhang
,
Y.
,
Fan
,
C.
, and
Song
,
S.
,
2014
, “
Molecular Logic Gates on DNA Origami Nanostructures for MicroRNA Diagnostics
,”
Anal. Chem.
,
86
(
4
), pp.
1932
1936
.
6.
Pfitzner
,
E.
,
Wachauf
,
C.
,
Kilchherr
,
F.
,
Pelz
,
B.
,
Shih
,
W. M.
,
Rief
,
M.
, and
Dietz
,
H.
,
2013
, “
Rigid DNA Beams for High-Resolution Single-Molecule Mechanics
,”
Angew. Chem. Int. Ed.
,
52
(
30
), pp.
7766
7771
.
7.
Le
,
J. V.
,
Luo
,
Y.
,
Darcy
,
M. A.
,
Lucas
,
C. R.
,
Goodwin
,
M. F.
,
Poirier
,
M. G.
, and
Castro
,
C. E.
,
2016
, “
Probing Nucleosome Stability With a DNA Origami Nanocaliper
,”
ACS Nano
,
10
(
7
), pp.
7073
7084
.
8.
Seeman
,
N. C.
,
2010
, “
Nanomaterials Based on DNA
,”
Annu. Rev. Biochem.
,
79
(
1
), pp.
65
87
.
9.
Linko
,
V.
, and
Dietz
,
H.
,
2013
, “
The Enabled State of DNA Nanotechnology
,”
Curr. Opin. Biotechnol.
,
24
(
4
), pp.
555
561
.
10.
Funke
,
J. J.
, and
Dietz
,
H.
,
2016
, “
Placing Molecules With Bohr Radius Resolution Using DNA Origami
,”
Nat. Nanotechnol.
,
11
(
1
), pp.
47
52
.
11.
Woo
,
S.
, and
Rothemund
,
P. W. K.
,
2014
, “
Self-Assembly of Two-Dimensional DNA Origami Lattices Using Cation-Controlled Surface Diffusion
,”
Nat. Commun.
,
5
, p. 4889.
12.
Zheng
,
J.
,
Birktoft
,
J. J.
,
Chen
,
Y.
,
Wang
,
T.
,
Sha
,
R.
,
Constantinou
,
P. E.
,
Ginell
,
S. L.
,
Mao
,
C.
, and
Seeman
,
N. C.
,
2009
, “
From Molecular to Macroscopic Via the Rational Design of a Self-Assembled 3D DNA Crystal
,”
Nature
,
461
(
7260
), pp.
74
77
.
13.
Rothemund
,
P. W. K.
,
2006
, “
Folding DNA to Create Nanoscale Shapes and Patterns
,”
Nature
,
440
(
7082
), pp.
297
302
.
14.
Wei
,
B.
,
Dai
,
M.
, and
Yin
,
P.
,
2012
, “
Complex Shapes Self-Assembled From Single-Stranded DNA Tiles
,”
Nature
,
485
(
7400
), pp.
623
626
.
15.
Ke
,
Y.
,
Ong
,
L. L.
,
Shih
,
W. M.
, and
Yin
,
P.
,
2012
, “
Three-Dimensional Structures Self-Assembled From DNA Bricks
,”
Science
,
338
(
6111
), pp.
1177
1183
.
16.
Benson
,
E.
,
Mohammed
,
A.
,
Gardell
,
J.
,
Masich
,
S.
,
Czeizler
,
E.
,
Orponen
,
P.
, and
Högberg
,
B.
,
2015
, “
DNA Rendering of Polyhedral Meshes at the Nanoscale
,”
Nature
,
523
(
7561
), pp.
441
444
.
17.
Veneziano
,
R.
,
Ratanalert
,
S.
,
Zhang
,
K.
,
Zhang
,
F.
,
Yan
,
H.
,
Chiu
,
W.
, and
Bathe
,
M.
,
2016
, “
Designer Nanoscale DNA Assemblies Programmed From the Top Down
,”
Science
,
352
(
6293
), p.
1534
.
18.
Castro
,
C. E.
,
Su
,
H.-J.
,
Marras
,
A. E.
,
Zhou
,
L.
, and
Johnson
,
J.
,
2015
, “
Mechanical Design of DNA Nanostructures
,”
Nanoscale
,
7
(
14
), pp.
5913
5921
.
19.
Sedeh
,
R. S.
,
Pan
,
K.
,
Adendorff
,
M. R.
,
Hallatschek
,
O.
,
Bathe
,
K.-J.
, and
Bathe
,
M.
,
2016
, “
Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies
,”
J. Chem. Theory Comput.
,
12
(
1
), pp.
261
273
.
20.
Kauert
,
D. J.
,
Kurth
,
T.
,
Liedl
,
T.
, and
Seidel
,
R.
,
2011
, “
Direct Mechanical Measurements Reveal the Material Properties of Three-Dimensional DNA Origami
,”
Nano Lett.
,
11
(
12
), pp.
5558
5563
.
21.
Shrestha
,
P.
,
Emura
,
T.
,
Koirala
,
D.
,
Cui
,
Y.
,
Hidaka
,
K.
,
Maximuck
,
W. J.
,
Endo
,
M.
,
Sugiyama
,
H.
, and
Mao
,
H.
,
2016
, “
Mechanical Properties of DNA Origami Nanoassemblies Are Determined by Holliday Junction Mechanophores
,”
Nucleic Acids Res.
,
44
(
14
), pp.
6574
6582
.
22.
Schiffels
,
D.
,
Liedl
,
T.
, and
Fygenson
,
D. K.
,
2013
, “
Nanoscale Structure and Microscale Stiffness of DNA Nanotubes
,”
ACS Nano
,
7
(
8
), pp.
6700
6710
.
23.
Dietz
,
H.
,
Douglas
,
S. M.
, and
Shih
,
W. M.
,
2009
, “
Folding DNA Into Twisted and Curved Nanoscale Shapes
,”
Science
,
325
(
5941
), pp.
725
730
.
24.
Pan
,
K.
,
Kim
,
D.-N.
,
Zhang
,
F.
,
Adendorff
,
M. R.
,
Yan
,
H.
, and
Bathe
,
M.
,
2014
, “
Lattice-Free Prediction of Three-Dimensional Structure of Programmed DNA Assemblies
,”
Nat. Commun.
,
5
, p.
5578
.
25.
Kim
,
D.-N.
,
Kilchherr
,
F.
,
Dietz
,
H.
, and
Bathe
,
M.
,
2012
, “
Quantitative Prediction of 3D Solution Shape and Flexibility of Nucleic Acid Nanostructures
,”
Nucleic Acids Res.
,
40
(
7
), pp.
2862
2868
.
26.
Yoo
,
J.
, and
Aksimentiev
,
A.
,
2013
, “
In Situ Structure and Dynamics of DNA Origami Determined Through Molecular Dynamics Simulations
,”
Proc. Natl. Acad. Sci. USA
,
110
(
50
), pp.
20099
20104
.
27.
Castro
,
C. E.
,
Kilchherr
,
F.
,
Kim
,
D.-N.
,
Shiao
,
E. L.
,
Wauer
,
T.
,
Wortmann
,
P.
,
Bathe
,
M.
, and
Dietz
,
H.
,
2011
, “
A Primer to Scaffolded DNA Origami
,”
Nat. Methods
,
8
(
3
), pp.
221
229
.
28.
Wagenbauer
,
K. F.
,
Wachauf
,
C. H.
, and
Dietz
,
H.
,
2014
, “
Quantifying Quality in DNA Self-Assembly
,”
Nat. Commun.
,
5
.
29.
Kalidindi
,
S. R.
, and
De Graef
,
M.
,
2015
, “
Materials Data Science: Current Status and Future Outlook
,”
Annu. Rev. Mater. Res.
,
45
(
1
), pp.
171
193
.
30.
Geers
,
M. G.
,
Kouznetsova
,
V. G.
, and
Brekelmans
,
W.
,
2010
, “
Multi-Scale Computational Homogenization: Trends and Challenges
,”
J. Comput. Appl. Math.
,
234
(
7
), pp.
2175
2182
.
31.
Rozavany
,
G. I. N.
,
2009
, “
A Critical Review of Established Methods of Structural Topology Optimization
,”
Struct. Multidiscip. Optim.
,
37
(
3
), pp.
217
237
.
32.
Geuzaine
,
C.
, and
Remacle
,
J. F.
,
2009
, “
GMSH: A 3D Finite Element Mesh Generator With Built-In Pre-and Post-Processing Facilities
,”
Int. J. Numer. Methods Eng.
,
79
(
11
), pp.
1309
1331
.
33.
Shewchuk
,
J. R.
,
2002
, “
Delaunay Refinement Algorithms for Triangular Mesh Generation
,”
Comput. Geom.
,
22
(
1
), pp.
21
74
.
34.
Schöberl
,
J.
,
1997
, “
NETGEN: An Advancing Front 2D/3D-Mesh Generator Based on Abstract Rules
,”
Comput. Visualization Sci.
,
1
(
1
), pp.
41
52
.
35.
Yerry
,
M. A.
, and
Shephard
,
M. S.
,
1984
, “
Automatic Three-Dimensional Mesh Generation by the Modified-Octree Technique
,”
Int. J. Numer. Methods Eng.
,
20
(
11
), pp.
1965
1990
.
36.
Soghrati
,
S.
,
Nagarajan
,
A.
, and
Liang
,
B.
,
2017
, “
Conforming to Interface Structured Adaptive Mesh Refinement: New Technique for the Automated Modeling of Materials With Complex Microstructures
,”
J. Fin. Elements in Anal. and Design.
,
125
(C), pp.
24
40
.
37.
Godonoga
,
M.
,
Lin
,
T.-Y.
,
Oshima
,
A.
,
Sumitomo
,
K.
,
Tang
,
M. S. L.
,
Cheung
,
Y.-W.
,
Kinghorn
,
A. B.
,
Dirkzwager
,
R. M.
,
Zhou
,
C.
,
Kuzuya
,
A.
,
Tanner
,
J. A.
, and
Heddle
,
J. G.
,
2016
, “
A DNA Aptamer Recognising a Malaria Protein Biomarker Can Function as Part of a DNA Origami Assembly
,”
Sci. Rep.
,
6
(
2
), p.
21266
.
38.
Koirala
,
D.
,
Shrestha
,
P.
,
Emura
,
T.
,
Hidaka
,
K.
,
Mandal
,
S.
,
Endo
,
M.
,
Sugiyama
,
H.
, and
Mao
,
H.
,
2014
, “
Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures
,”
Angew. Chem.
,
126
(
31
), pp.
8275
8279
.
39.
Jungmann
,
R.
,
Scheible
,
M.
,
Kuzyk
,
A.
,
Pardatscher
,
G.
,
Castro
,
C. E.
, and
Simmel
,
F. C.
,
2011
, “
DNA Origami-Based Nanoribbons: Assembly, Length Distribution, and Twist
,”
Nanotechnology
,
22
(
27
), p.
275301
.
40.
Tang
,
Y.
,
Lin
,
G.
,
Han
,
L.
,
Qiu
,
S.
,
Yang
,
S.
, and
Yin
,
J.
,
2015
, “
Design of Hierarchically Cut Hinges for Highly Stretchable and Reconfigurable Metamaterials With Enhanced Strength
,”
Adv. Mater.
,
27
(
44
), pp.
7181
7190
.
41.
Bai
,
X. C.
,
Martin
,
T. G.
,
Scheres
,
S. H. W.
, and
Dietz
,
H.
,
2012
, “
Cryo-EM Structure of a 3D DNA-Origami Object
,”
Proc. Natl. Acad. Sci. USA
,
109
(
49
), pp.
20012
20017
.
42.
Kim
,
Y. J.
, and
Kim
,
D. N.
,
2016
, “
Structural Basis for Elastic Mechanical Properties of the DNA Double Helix
,”
PLoS One
,
11
(
4
), p.
e0153228
.
You do not currently have access to this content.