Microrheology of DNA hydrogels

Xing, Zhongyang; Caciagli, Alessio; Cao, Tianyang; Stoev, Iliya D.; Zupkauskas, Mykolas; O’Neill, Thomas; Wenzel, Tobias; Lamboll, Robin; Eiser, Erika

doi:10.1073/pnas.1722206115

Cited by 105 publications

(140 citation statements)

References 49 publications

(105 reference statements)

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“…In agreement with our previous measurements on hydrogels made only of Y-shapes with the appropriate sticky overhangs, 29,30 we observe a liquid-to-gel transition in the Y-L0 system signalling that most sticky ends are hybridised below Tm,YL  52°C, as demonstrated in Figure 2a.…”

Section: Discussionsupporting

confidence: 92%

On the role of flexibility in linker-mediated DNA hydrogels

et al. 2020

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Three-dimensional DNA networks, composed of tri-or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexiblity provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters.

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Section: Discussionsupporting

confidence: 92%

On the role of flexibility in linker-mediated DNA hydrogels

et al. 2020

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“…The typical Sshaped curves show for both nanostars an almost identical melting temperature Tm ≈ 64-65°C, which is the temperature, at which half of all possible hydrogen bonds between the SS DNA strands have formed. 12 We further see that all nanostars have fully formed below about 55°C.…”

Section: Sample Characterizationmentioning

confidence: 57%

“…The curves indeed reflect the theoretically predicted curves based on the SantaLucia model. 12 They also confirm that when we melt the system to about 30°C, it is a completely fluid suspension of Y-shaped building blocks, but then starts to form a viscoelastic network as we cool the system down to 10°C. This gelation behavior is fully thermally reversible.…”

Section: Sample Characterizationmentioning

confidence: 58%

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Using single-beam optical tweezers for the passive microrheology of complex fluids

Stoev¹,

Caciagli²,

Xing³

et al. 2018

Optical Trapping and Optical Micromanipulation XV

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One important aspect of the complete physical characterization of novel viscoelastic materials is the assessment of their response on short timescales. Optical tweezers, equipped with a fast quadrant photodiode, aid in fulfilling this task by providing high-frequency viscoelastic information about the sample. In passive microrheology, this is normally achieved by extracting rheological information from the thermal motion of an optically trapped bead embedded in a test fluid. Here we present the calibration and use of optical tweezers to study the formation of thermally reversible DNA hydrogels. We complement our results with rheological data from dynamic light scattering, video microscopy and conventional bulk rheology. Merging experimental data from different techniques allows us to study the viscoelastic behavior of these DNA networks over a wide frequency-band and the scaling of the complex viscoelastic modulus at the two frequency extremes. By analyzing the high-frequency behavior of our transient network, we prove the semi-flexible polymer nature of DNA and provide an estimate of its persistence length.

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“…The exquisite control over structure and interactions enabled the realization of equilibrium gels with Arrhenius temperature-dependence of viscosity over five orders of magnitude [21] and is at the basis of the design of a DNA vitrimer [22]. DNA nanostars phase behaviour, connectivity, and the conditions for the formation of an elastic, stress-bearing network have been widely investigated [23,24]. Through an active microrheology technique (conceptually as simple as dragging a bead through the sample with a calibrated force and measuring its velocity), the whole temperature- A high degree of programmability and control over mechanical properties could also be obtained through single strands, 36-72 bases in length, with different self-complementary domains.…”

Section: Dna-based Dynamic Materialsmentioning

confidence: 99%

Control and optical mapping of mechanical transitions in polymer networks and DNA-based soft materials

Zanchetta

2019

Current Opinion in Colloid & Interface Science

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Complex mechanical changes in response to an external trigger are pervasive in natural soft materials and often sought for applications. Be it the reversible stiffening of sea cucumber, the failure of a polymeric or colloidal gel under load, or the dissolution of a biosensing hydrogel upon target binding, mechanical transitions are typically enabled, and critically affected, by heterogeneous structures and reversible bonds. New possibilities to monitor evolving properties and to gain access to stress propagation with temporal and spatial resolution are being disclosed by mechanochromic molecules and molecular complexes, which transduce a mechanical stress into a light signal and act as built-in stress reporters. I will review recent strategies and identify future directions for the design of mechanically responsive soft networks and for their optical mapping, focusing particular attention on the emerging class of hydrogels based on DNA self-assembly.

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Microrheology of DNA hydrogels

Cited by 105 publications

References 49 publications

On the role of flexibility in linker-mediated DNA hydrogels

On the role of flexibility in linker-mediated DNA hydrogels

Using single-beam optical tweezers for the passive microrheology of complex fluids

Control and optical mapping of mechanical transitions in polymer networks and DNA-based soft materials

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