Binding branched and linear DNA structures: From isolated clusters to fully bonded gels

Abstract

The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of selfassembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well defined valence, namely tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T . We report dynamic light scattering experiments in a window of T s ranging from 10°C to 55°C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T , when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel and as a cluster fluid depending on the selected r.

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

“…The formation of clusters during DNAns gel formation was studied by Fernandez-Castanon et al using DLS and variable ratios of tetravalent DNAns to linker. They found that at low temperatures a percolating network was formed regardless of the ratio; however, the ratio affected the formation of clusters at higher temperatures and thus could be used as a factor to program the formation of the gel [120]. As previously mentioned, Conrad et al studied the effect of DNAns valency on DNA hydrogels at different concentrations ranging from 200-800 µM of DNAns.…”

DNA-GEL, Novel Nanomaterial for Biomedical Applications and Delivery of Bioactive Molecules

“…In recent years, DNA self-assembly has been exploited to produce bulk quantities of nanometric particles of predefined shape and size. The possibility to take control at design time of the particle-particle interactions and built-in functionalities has led to several applications in the assembly of biodegradable and biocompatible DNA-gels with tailored properties (Um et al, 2006;Biffi et al, 2013;Bomboi et al, 2016;Nguyen and Saleh, 2017;Fernandez-Castanon et al, 2018). One important class of DNA constructs is represented by limited-valence DNA nanostars (NSs), that is, DNA nanoparticles with a finite number f of arms departing from a common central junction.…”

Smoluchowski equations for linker-mediated irreversible aggregation

“…The self-assembly of micro-and nano-size particles mediated by linkers has been the focus of extensive experimental, 1-9 theoretical [10][11][12] and simulation 4,10,11,[13][14][15][16][17] studies in recent years, since the addition of a second species provides extra control of the aggregation process. Indeed the linkers to particles ratio, 1,4,6,8,9 the strength of the linker-particle interactions, 5,7 and the maximum number of linkers that can bond to one particle, 7,8 may be used to tune the stability of the mixture, the extent and topology of the assembled structures, the equilibrium phase behavior and the rheological properties of the system. 3,18 The linker-particle interactions are most often engineered using complementary biological macromolecules, such as complementary DNA strands 3,8 or streptavidin and biotin.…”

“…Indeed the linkers to particles ratio, 1,4,6,8,9 the strength of the linker-particle interactions, 5,7 and the maximum number of linkers that can bond to one particle, 7,8 may be used to tune the stability of the mixture, the extent and topology of the assembled structures, the equilibrium phase behavior and the rheological properties of the system. 3,18 The linker-particle interactions are most often engineered using complementary biological macromolecules, such as complementary DNA strands 3,8 or streptavidin and biotin. 1,2,4 As a consequence, the bonds formed between particles mediated by linkers are extremely strong.…”

“…These systems form several types of disordered and more or less open clusters, even at extremely low volume fractions. 3,4,8 Theoretical studies have focused mostly on equilibrium properties. 12,14 Some simulations have addressed the dynamics of these systems, either to get information about the early stages of aggregation 4 or to try to predict the type of assembled structures at long times.…”