Developments in understanding and controlling self assembly of DNA-functionalized colloids

Michele, Lorenzo Di; Eiser, Erika

doi:10.1039/c3cp43841d

Cited by 89 publications

(123 citation statements)

References 96 publications

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“…[31][32][33][34] On the other hand, the use of micron-sized particles can facilitate visualization of the dynamics of the colloidal polymers. The DNA linkers can be easily synthesized and their sizes precisely controlled using standard molecular biology techniques.…”

Section: Introductionmentioning

confidence: 99%

Directing Assembly of DNA-Coated Colloids with Magnetic Fields To Generate Rigid, Semiflexible, and Flexible Chains

et al. 2014

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We report the formation of colloidal macromolecules consisting of chains of micron-sized paramagnetic particles assembled using a magnetic field and linked with DNA. The interparticle spacing and chain flexibility was controlled by varying the magnetic field strength and the linker spring constant. Variations in the DNA lengths allowed for the generation of chains with an improved range of flexibility, as compared to previous studies. These chains adopted the rigid-rod, semi-flexible, and flexible conformations that are characteristic of linear polymer systems. These assembly techniques were investigated to determine the effects of the nanoscale DNA linker properties on the properties of the microscale colloidal chains. With stiff DNA linkers (564 base pairs) the chains were only stable at moderate to high field strengths and produced rigid chains. For flexible DNA linkers (8000 base pairs), high magnetic field strengths caused the linkers to be excluded from the gap between the particles, leading to a transition from very flexible chains at low field strengths to semi-flexible chains at high field strengths. In the intermediate range of linker sizes, the chains exhibited predictable behavior, demonstrating increased flexibility with longer DNA linker length or smaller linking field strengths. This study provides insight into the process of directed assembly using magnetic fields and DNA by precisely tuning the components to generate colloidal analogues of linear macromolecular chains.

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Section: Introductionmentioning

confidence: 99%

Directing Assembly of DNA-Coated Colloids with Magnetic Fields To Generate Rigid, Semiflexible, and Flexible Chains

et al. 2014

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“…DNA can also be used to functionalise colloids by grafting single-stranded DNA (ss-DNA) molecules on the surface of the particles [16][17][18]. By choosing strands terminating with complementary sequences, the particles can bind to each other via DNA hybridisation and self-assemble into disordered or ordered structures [17,[19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Accurate phase diagram of tetravalent DNA nanostars

Rovigatti

Bomboi

Sciortino

2014

The Journal of Chemical Physics

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We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarsegrained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA. We find that, as the system is cooled down, tetramers undergo a gas-liquid phase separation in a region of concentrations which, if the difference in salt concentration is taken into account, is comparable with the recently measured experimental phase diagram [S. Biffi et al, Proc. Natl. Acad. Sci, 110, 15633 (2013)]. We also present a meanfield free energy for modelling the phase diagram based on the bonding contribution derived by Wertheim in his studies of associating liquids. Combined with mass-action law expressions appropriate for DNA binding and a numerically evaluated reference free energy, the resulting free energy qualitatively reproduces the numerical data. Finally, we report information on the nanostar structure, e.g. geometry and flexibility of the single tetramer and of the collective behaviour, providing a useful reference for future small angle scattering experiments, for all investigated temperatures and concentrations.

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“…Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level. They also ignore any entropic effects relevant to this self-assembly process (9)(10)(11)(12)(17)(18)(19)(20)(21). Molecular dynamics simulations avoid these difficulties and extend this analysis to superlattice self-assembly so as to provide a detailed understanding of the effects of kinetics (13), DNA sequence (14), and electrostatics (15,16,22) on lattice stability.…”

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confidence: 99%

“…A large number of theories and simulations have been developed to delineate the hybridization interactions between two interacting DNA-NPs (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level.…”

mentioning

confidence: 99%

Stoichiometric control of DNA-grafted colloid self-assembly

Venkatasubramanian

Kumar

et al. 2015

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

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There has been considerable interest in understanding the selfassembly of DNA-grafted nanoparticles into different crystal structures, e.g., CsCl, AlB 2 , and Cr 3 Si. Although there are important exceptions, a generally accepted view is that the right stoichiometry of the two building block colloids needs to be mixed to form the desired crystal structure. To incisively probe this issue, we combine experiments and theory on a series of DNA-grafted nanoparticles at varying stoichiometries, including noninteger values. We show that stoichiometry can couple with the geometries of the building blocks to tune the resulting equilibrium crystal morphology. As a concrete example, a stoichiometric ratio of 3:1 typically results in the Cr 3 Si structure. However, AlB 2 can form when appropriate building blocks are used so that the AlB 2 standard-state free energy is low enough to overcome the entropic preference for Cr 3 Si. These situations can also lead to an undesirable phase coexistence between crystal polymorphs. Thus, whereas stoichiometry can be a powerful handle for direct control of lattice formation, care must be taken in its design and selection to avoid polymorph coexistence. colloidal interactions | functional particle | superlattice engineering | molecular design | modeling O ver the past several decades, there has been increasing interest in programmable self-assembly for materials fabrication. Rather than using traditional methods of shaping bulk materials, the emerging concept is to focus on the design of nanoscale building blocks that self-organize into desired structures. This "design" philosophy has led to the development of novel techniques such as DNA origami, where specific interactions are used to direct the folding of oligonucleotides into a variety of assemblies (1-6). Another vein of research is to focus on the directed assembly of DNA-grafted nanoparticles (DNA-NPs) into superlattices with well-defined crystal morphologies. These systems have unusual photonic and plasmonic properties with applications in spectroscopy, surface imaging, and optical sensors (7,8).A large number of theories and simulations have been developed to delineate the hybridization interactions between two interacting DNA-NPs (9-20). Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level. They also ignore any entropic effects relevant to this self-assembly process (9-12, 17-21). Molecular dynamics simulations avoid these difficulties and extend this analysis to superlattice self-assembly so as to provide a detailed understanding of the effects of kinetics (13), DNA sequence (14), and electrostatics (15, 16, 22) on lattice stability. We particularly highlight the work of Li et al. (16), who explicitly considered the role of stoichiometry on the crystal morphology formed. They selected several stoichiometries, i.e., 1:1, 2:1, and 3:1. We focus here on one specific case, 2:1. As the size and linker ratios of ...

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Developments in understanding and controlling self assembly of DNA-functionalized colloids

Cited by 89 publications

References 96 publications

Directing Assembly of DNA-Coated Colloids with Magnetic Fields To Generate Rigid, Semiflexible, and Flexible Chains

Directing Assembly of DNA-Coated Colloids with Magnetic Fields To Generate Rigid, Semiflexible, and Flexible Chains

Accurate phase diagram of tetravalent DNA nanostars

Stoichiometric control of DNA-grafted colloid self-assembly

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