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DNA-Guided Assembly of Nanocellulose Meshes

Alexandru Amărioarei, Gefry Barad, Eugen Czeizler, Ana-Maria Dobre, Corina Iţcuş, Victor Mitrana, Andrei Păun, Mihaela Păun, Frankie Spencer, Romică Trandafir, Iris Tuşa, DNA-Guided Assembly of Nanocellulose Meshes. In: David Fagan, Carlos Martin-Vide, Michael O'Neill, Miguel A. Vega-Rodriguez (Eds.), Theory and Practice of Natural Computing, Lecture Notes in Computer Science 11324, 253 – 265, Springer International Publishing, 2018.

http://dx.doi.org/10.1007/978-3-030-04070-3_20

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.

BibTeX entry:

@INPROCEEDINGS{inpAmBaCzDoIxMiPxPxSpTrTu18a,
  title = {DNA-Guided Assembly of Nanocellulose Meshes},
  booktitle = {Theory and Practice of Natural Computing},
  author = {Amărioarei, Alexandru and Barad, Gefry and Czeizler, Eugen and Dobre, Ana-Maria and Iţcuş, Corina and Mitrana, Victor and Păun, Andrei and Păun, Mihaela and Spencer, Frankie and Trandafir, Romică and Tuşa, Iris},
  volume = {11324},
  series = {Lecture Notes in Computer Science},
  editor = {Fagan, David and Martin-Vide, Carlos and O'Neill, Michael and Vega-Rodriguez, Miguel A.},
  publisher = {Springer International Publishing},
  pages = {253 – 265},
  year = {2018},
  keywords = {DNA nanotechnology, DNA-guided assembly, Self-assembly system, Rule-based modelling },
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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