Effect of Inert Tails on the Thermodynamics of DNA Hybridization

Michele, Lorenzo Di; Mognetti, Bortolo Matteo; Yanagishima, Taiki; Varilly, Patrick; Ruff, Zachary; Frenkel, Daan; Eiser, Erika

doi:10.1021/ja500027v

Cited by 45 publications

(87 citation statements)

References 25 publications

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“…However this modelling choice is far from being univocal. On the one hand, it has been demonstrated that the presence of inert DNA tails emanating from the duplexes, like the dsDNA spacers in the present system, can have substantial destabilising effect 18,[75][76][77]. On the other hand, Cy3 and Cy5 fluorophores have a stabilising effect, decreasing the hybridisation free energy by ≈ 2 kJ mol −1 .…”

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confidence: 73%

Melting transition in lipid vesicles functionalised by mobile DNA linkers

et al. 2016

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We study phase behaviour of lipid-bilayer vesicles functionalised by ligand-receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand-receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand-receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion.

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confidence: 73%

Melting transition in lipid vesicles functionalised by mobile DNA linkers

et al. 2016

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“…12, ∆G 0 AB is the complexation free energy of the linkers free in solution, which depends on their chemical details and is usually determined experimentally or via atomistic simulations. When considering DNA oligomers ∆G 0 AB is calculated using the nearest-neighbour thermodynamic model [23,24,[147][148][149], possibly corrected for the presence of dangling DNA tails [44,149]. ∆G conf AB (h) describes the additional constraints that surface-tethered linkers experience whenever they form a complex, as compared to the same complex formed by untethered linkers [144,145].…”

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confidence: 99%

Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces

2019

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At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes where, among other functions, they control cell adhesion, motility and tissue formation. Besides being central to several biological processes, multivalent interactions mediated by reactive linkers confined to deformable substrates underpin the design of syntheticbiological platforms and advanced biomimetic materials. Here we review recent advances on the experimental study and theoretical modelling of a heterogeneous class of biomimetic systems in which synthetic linkers mediate multivalent interactions between fluid and deformable colloidal units, including lipid vesicles and emulsion droplets. Linkers are often prepared from synthetic DNA nanostructures, enabling full programmability of the thermodynamic and kinetic properties of their mutual interactions. The coupling of the statistical effects of multivalent interactions with substrate fluidity and deformability gives rise to a rich emerging phenomenology that, in the context of self-assembled soft materials, has been shown to produce exotic phase behaviour, stimuli-responsiveness, and kinetic programmability of the self-assembly process. Applications to (synthetic) biology will also be reviewed.

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“…The three types of modifications accordingly provide the following interactions: a mixed attraction and repulsion between all particles types ('blending') instead of repulsion-only and attraction-only as in the mother phase; predominant interparticle attraction ('stapling'); and predominant repulsion between neighbouring particles ('repelling'). Although the interaction-shifting does not depend on specific sequences, as long as input DNA strands fulfil their designated roles, the magnitude of the interaction shift may depend on the DNA length 29,30 , melting temperature, and the inert DNA tails 31 .…”

Section: Selective Lattice Transformations By Modifying Dna Shellmentioning

confidence: 99%

Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

et al. 2015

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The rapid development of self-assembly approaches has enabled the creation of materials with desired organization of nanoscale components. However, achieving dynamic control, wherein the system can be transformed on demand into multiple entirely different states, is typically absent in atomic and molecular systems and has remained elusive in designed nanoparticle systems. Here, we demonstrate with in situ small-angle X-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensional lattice of DNA-coated nanoparticles can be switched from an initial 'mother' phase into one of multiple 'daughter' phases. The introduction of different types of reprogramming DNA strands modifies the DNA shells of the nanoparticles within the superlattice, thereby shifting interparticle interactions to drive the transformation into a particular daughter phase. Moreover, we mapped quantitatively with free-energy calculations the selective reprogramming of interactions onto the observed daughter phases.

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Effect of Inert Tails on the Thermodynamics of DNA Hybridization

Cited by 45 publications

References 25 publications

Melting transition in lipid vesicles functionalised by mobile DNA linkers

Melting transition in lipid vesicles functionalised by mobile DNA linkers

Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces

Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

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