Accurate phase diagram of tetravalent DNA nanostars

Rovigatti, Lorenzo; Bomboi, Francesca; Sciortino, Francesco

doi:10.1063/1.4870467

Cited by 58 publications

(67 citation statements)

References 64 publications

(94 reference statements)

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“…This implies that the critical valence of our DNAns network is between 5 < fc ≤ 6, consistent with the prediction of fc = 6 for network chains that have vanishing bending stiffness and little rotational constraint at the junction (4,34,37). In the DNAns, we posit that these features are a consequence of the unpaired bases flanking the double-helical arms at the overhang and at the junction, consistent with flexibility seen in simulations of DNAns (18).…”

Section: Discussion An Isostatic Picture Explains Plateau Modulus Behsupporting

confidence: 83%

“…More recently, Sciortino and coworkers (13)(14)(15)(16)(17)(18)) engineered greater flexibility into the immobile junction design by incorporating unpaired bases at the vertex and sticky ends to create "DNA nanostars" (DNAns) ( Fig. 1).…”

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confidence: 99%

“…1). They found that tetravalent DNAns transition from a fluid to an equilibrium gel on cooling (16)(17)(18), with network dynamics controlled by the stickyend interaction strength (13,15,19). Equilibrium gel formation requires both limited valence (f < 12) (13,15,(20)(21)(22) and significant flexibility (16,23) as conferred by the unpaired bases in the DNAns design ( Fig.…”

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confidence: 99%

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Increasing valence pushes DNA nanostar networks to the isostatic point

Conrad

Kennedy

Fygenson

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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The classic picture of soft material mechanics is that of rubber elasticity, in which material modulus is related to the entropic elasticity of flexible polymeric linkers. The rubber model, however, largely ignores the role of valence (i.e., the number of network chains emanating from a junction). Recent work predicts that valence, and particularly the Maxwell isostatic point, plays a key role in determining the mechanics of semiflexible polymer networks. Here, we report a series of experiments confirming the prominent role of valence in determining the mechanics of a model system. The system is based on DNA nanostars (DNAns): multiarmed, self-assembled nanostructures that form thermoreversible equilibrium gels through base paircontrolled cross-linking. We measure the linear and nonlinear elastic properties of these gels as a function of DNAns arm number, f, and concentration [DNAns]. We find that, as f increases from three to six, the gel's high-frequency plateau modulus strongly increases, and its dependence on [DNAns] transitions from nonlinear to linear. Additionally, higher-valence gels exhibit less strain hardening, indicating that they have less configurational freedom. Minimal strain hardening and linear dependence of shear modulus on concentration at high f are consistent with predictions for isostatic systems. Evident strain hardening and nonlinear concentration dependence of shear modulus suggest that the low-f networks are subisostatic and have a transient, potentially fractal percolated structure. Overall, our observations indicate that network elasticity is sensitive both to entropic elasticity of network chains and to junction valence, with an apparent isostatic point 5 < fc ≤ 6 in agreement with the Maxwell prediction.DNA nanostars | equilibrium gels | network mechanics | network valence | isostatic network This article contains supporting information online at www.pnas.org/lookup/suppl/

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Section: Discussion An Isostatic Picture Explains Plateau Modulus Behsupporting

confidence: 83%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Increasing valence pushes DNA nanostar networks to the isostatic point

Conrad

Kennedy

Fygenson

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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“…Our choice of D =3 nm is based on the effective diameter estimates reported in refs 36, 37 using a salt concentration equal to 100 mM and a DNA concentration around 200 mg ml −1 , which amounts to an equivalent 800 mM salt concentration. The A sites account for hydrophobic interactions between the terminals of the duplexes38, and their geometry is the same as the one used in ref. 39.…”

Section: Resultsmentioning

confidence: 99%

Smectic phase in suspensions of gapped DNA duplexes

et al. 2016

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Smectic ordering in aqueous solutions of monodisperse stiff double-stranded DNA fragments is known not to occur, despite the fact that these systems exhibit both chiral nematic and columnar mesophases. Here, we show, unambiguously, that a smectic-A type of phase is formed by increasing the DNA's flexibility through the introduction of an unpaired single-stranded DNA spacer in the middle of each duplex. This is unusual for a lyotropic system, where flexibility typically destabilizes the smectic phase. We also report on simulations suggesting that the gapped duplexes (resembling chain-sticks) attain a folded conformation in the smectic layers, and argue that this layer structure, which we designate as smectic-fA phase, is thermodynamically stabilized by both entropic and energetic contributions to the system's free energy. Our results demonstrate that DNA as a building block offers an exquisitely tunable means to engineer a potentially rich assortment of lyotropic liquid crystals.

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“…oxDNA has also been used to study DNA in a range of other contexts, including large duplexes under applied stress 188 , and selfassembly driven phase transitions 189,190 . A modified version parameterised to describe RNA has recently been developed 191 .…”

Section: Discussionmentioning

confidence: 99%

DNA nanotechnology: understanding and optimisation through simulation

Ouldridge

2014

Molecular Physics

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DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended 'overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

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Accurate phase diagram of tetravalent DNA nanostars

Cited by 58 publications

References 64 publications

Increasing valence pushes DNA nanostar networks to the isostatic point

Increasing valence pushes DNA nanostar networks to the isostatic point

Smectic phase in suspensions of gapped DNA duplexes

DNA nanotechnology: understanding and optimisation through simulation

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