DNA-Guided Assembly of Nanocellulose Meshes

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Publication Details

List of Authors: Alexandru Amărioarei, Gefry Barad, Eugen Czeizler, Ana-Maria Dobre, Corina Iţcuş, Victor Mitrana, Andrei Păun, Mihaela Păun, Frankie Spencer, Romică Trandafir, Iris Tuşa
Editors: Fagan David, Martin-Vide Carlos, O'Neill Michael, Vega-Rodriguez Miguel
Publication year: 2018
Journal: Lecture Notes in Computer Science
Publisher: Springer
Book title: Theory and Practice of Natural Computing. TPNC 2018
Title of series: Lecture Notes in Computer Science (LNCS)
Volume number: 11324
Start page: 253
End page: 265
ISBN: 978-3-030-04069-7
eISBN: 978-3-030-04070-3
ISSN: 0302-9743


Abstract

Nanoengineered materials are a product of joint collaboration of
theoreticians and experimentalists, of physicists, (bio-)chemists, and
recently, of computer scientists. In the field of Nanotechnology and
Nanoengineering, DNA (algorithmic) self-assembly has an acknowledged
leading position. As a fabric, DNA is a rather inferior material; as a
medium for shape, pattern, and dynamic behavior reconstruction, it is
one of the most versatile nanomaterials. This is why the prospect of
combining the physical properties of known high performance
nanomaterials, such as cellulose, graphene, or fibroin, with the
assembly functionality of DNA scaffolds is a very promising prospect. In
this work we analyze the dynamical and structural properties of a
would-be DNA-guided assembly of nanocellulose meshes. The aim is to
generate pre-experimental insights on possible ways of manipulating
structural properties of such meshes. The mechanistic principles of
these systems, implemented through the DNA assembly apparatus, ensure
the formation of 2D nanocellulose mesh structures. A key desired feature
for such an engineered synthetic material, e.g. with applications in
bio-medicine and nano-engineering, would be to control the size of the
openings (gaps) within these meshes, a.k.a. its aperture. However, in
the case of this composite material, this is not a direct engineered
feature. Rather, we assert it could be indirectly achieved through
varying several key parameters of the system. We consider here several
experimentally tunable parameters, such as the ratio between
nanocellulose fibrils and the DNA guiding elements, i.e.,
aptamer-functionalized DNA origamis, as well as the assumed length of
the nanocellulose fibrils. To this aim, we propose a computational model
of the mesh-assembly dynamical system, which we subject to numerical
parameter scan and analysis.


Keywords

Computational Biomodeling, DNA origami, self-assembly


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