DNA-Guided Assembly for Fibril Proteins

Iris Tuşa,Alfonso Rodriguez-Paton,Gefry Barad,Ana-Maria Prelipcean,Corina Iţcuş,Eugen Czeizler,Alexandru Amărioarei,Mihaela Păun,Frankie Spencer,Ana-Maria Gheorghe,Romică Trandafir,Andrei Păun

doi:10.3390/math9040404

Abstract

Current advances in computational modelling and simulation have led to the inclusion of computer scientists as partners in the process of engineering of new nanomaterials and nanodevices. This trend is now, more than ever, visible in the field of deoxyribonucleic acid (DNA)-based nanotechnology, as DNA’s intrinsic principle of self-assembly has been proven to be highly algorithmic and programmable. As a raw material, DNA is a rather unremarkable fabric. However, as a way to achieve patterns, dynamic behavior, or nano-shape reconstruction, DNA has been proven to be one of the most functional nanomaterials. It would thus be of great potential to pair up DNA’s highly functional assembly characteristics with the mechanic properties of other well-known bio-nanomaterials, such as graphene, cellulos, or fibroin. In the current study, we perform projections regarding the structural properties of a fibril mesh (or filter) for which assembly would be guided by the controlled aggregation of DNA scaffold subunits. The formation of such a 2D fibril mesh structure is ensured by the mechanistic assembly properties borrowed from the DNA assembly apparatus. For generating inexpensive pre-experimental assessments regarding the efficiency of various assembly strategies, we introduced in this study a computational model for the simulation of fibril mesh assembly dynamical systems. Our approach was based on providing solutions towards two main circumstances. First, we created a functional computational model that is restrictive enough to be able to numerically simulate the controlled aggregation of up to 1000s of elementary fibril elements yet rich enough to provide actionable insides on the structural characteristics for the generated assembly. Second, we used the provided numerical model in order to generate projections regarding effective ways of manipulating one of the the key structural properties of such generated filters, namely the average size of the openings (gaps) within these meshes, also known as the filter’s aperture. This work is a continuation of Amarioarei et al., 2018, where a preliminary version of this research was discussed.

Highlights

Nanoengineered materials have become a main object of focus for many industrial and academic communities alike
We briefly present first a rule-based modeling approach for capturing the assembly of the deoxyribonucleic acid (DNA)-fibril mesh
Lateral growth of the assembly is inhibited to some extent

Summary

Introduction

Nanoengineered materials have become a main object of focus for many industrial and academic communities alike. In most cases, it is the high-resolution arrangements of the material’s nanocomponents that give its exceptional characteristics, e.g., the highly aligned calcium silicate hydrate nanoplatelets with bending strength of nacre [9], the nanoengineered ultralight materials based on electroactive graphene aerogel with a high storage capacity of Li+/Na+ ions [10], etc In this framework, deoxyribonucleic acid (DNA)-based nanotechnology was able to demonstrate great engineering potential due to its versatility and addressability at the nanolevel; laboratory developments in the field include highly addressable scaffolds [11], precise pattering [12], 2- and 3D pattern and shape reconstruction [13,14], and even robotic-like constructs [15,16]. One can consider fibroin and vimentin (intermediate) filaments, both of these possessing significant mechanical properties as well as available DNA-aptamers (DNA-aptamers are 20–50 base long single-stranded DNA sequences with natural binding affinity towards a specific material or molecule) for selective binding [17,18]

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