Attractions between Hard Colloidal Spheres in Semiflexible Polymer Solutions (original) (raw)
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Entropic Colloidal Interactions in Concentrated DNA Solutions
Physical Review Letters, 1998
We explore the entropic interactions between a pair of micron-sized colloidal spheres in DNA solutions. By confining the particles in a line-scanned optical tweezer, we directly measured the functional form of the interaction potential with sub-k B T resolution in samples where the spheres and the polymer coils were of comparable size. The potential is well described by the Asakura-Oosawa depletion model even in the semidilute regime where DNA coils overlap strongly. Its range and depth increase with increasing concentration in a manner consistent with a crossover from a dilute solution of Gaussian coils to the weakly fluctuating semidilute regime dominated by two-point collisions which is unique to semiflexible polymers. [S0031-9007(98)07491-2]
Switchable self-protected attractions in DNA-functionalized colloids
Nature Materials, 2009
Surface functionalization with DNA is a powerful tool for guiding the self-assembly of nanometre-and micrometresized particles 1-11. Complementary 'sticky ends' form specific inter-particle links and reproducibly bind at low temperature and unbind at high temperature. Surprisingly, the ability of single-stranded DNA to form folded secondary structures has not been explored for controlling (nano) colloidal assembly processes, despite its frequent use in DNA nanotechnology 12-14. Here, we show how loop and hairpin formation in the DNA coatings of micrometre-sized particles gives us in situ control over the inter-particle binding strength and association kinetics. We can finely tune and even switch off the attractions between particles, rendering them inert unless they are heated or held together-like a nano-contact glue. The novel kinetic control offered by the switchable self-protected attractions is explained with a simple quantitative model that emphasizes the competition between intra-and inter-particle hybridization, and the practical utility is demonstrated by the assembly of designer clusters in concentrated suspensions. With self-protection, both the suspension and assembly product are stable, whereas conventional attractive colloids would quickly aggregate. This remarkable functionality makes our self-protected colloids a novel material that greatly extends the utility of DNA-functionalized systems, enabling more versatile, multi-stage assembly approaches. In many DNA-functionalized systems, the particle association and structural organization are equilibrium processes that depend solely on the system temperature, relative to the particles' DNA-dependent dissociation temperature. This is, for instance, demonstrated by our observations on mixtures of beads that form normal Watson-Crick pairs of complementary C N /C N sticky ends (interaction scheme Ia, Fig. 1). Figure 2a shows the fraction of nonassociated particles, or singlet fraction, as a function of time in an experiment where we first lowered the temperature from 52 to 20 • C (t < 810 s) and then ramped it back up (t > 810 s). Clearly, as soon as we go below the particles' dissociation temperature (T dis ≈ 40 • C), the singlet fraction quickly drops to zero, and the particles come together in extensive structures; conversely, when we increase the temperature above T dis the aggregates quickly dissociate. The rate of temperature change determines how fast T dis is reached, but it does not change the qualitative shape of the curves. Much more flexibility is gained if the sticky ends possess secondary conformations, such as hairpins and loops due to intra-particle complementarity (for example, interaction scheme II, Fig. 1). Such secondary structures form in fractions of a microsecond, as estimated from the rotational diffusion time of singlestranded DNA with an end-to-end distance of ∼14 nm. This should
The Journal of chemical physics, 2015
Although the scaling theory of polymer solutions has had many successes, this type of argument is deficient when applied to hydrodynamic solution properties. Since the foundation of polymer science, it has been appreciated that measurements of polymer size from diffusivity, sedimentation, and solution viscosity reflect a convolution of effects relating to polymer geometry and the strength of the hydrodynamic interactions within the polymer coil, i.e., "draining." Specifically, when polymers are expanded either by self-excluded volume interactions or inherent chain stiffness, the hydrodynamic interactions within the coil become weaker. This means there is no general relationship between static and hydrodynamic size measurements, e.g., the radius of gyration and the hydrodynamic radius. We study this problem by examining the hydrodynamic properties of duplex DNA in solution over a wide range of molecular masses both by hydrodynamic modeling using a numerical path-integration...
Predicting DNA-mediated colloidal pair interactions
PNAS, 2012
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Statics and Dynamics of Single DNA Molecules Confined in Nanochannels
Physical Review Letters, 2005
The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics.
A general theory of DNA-mediated and other valence-limited colloidal interactions
2012
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the configurational and combinatorial entropic factors that play a key role in valence-limited interactions. By rigorously enforcing self-consistency, it achieves near-quantitative accuracy with respect to detailed Monte Carlo calculations.
Comprehensive view of microscopic interactions between DNA-coated colloids
Nature Communications
The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy to measure in situ the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We present a first-principles model that screens and combines existing theories into one coherent framework and quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our theory identifies a subtle competition between DNA binding and steric repulsion and accurately predicts a...
Effect of electrostatic interactions on the dynamics of semiflexible monodisperse DNA fragments
The Journal of Chemical Physics, 2000
The dynamics of three monodisperse linear duplex DNA fragments-a 2311 base pair restriction fragment and 1500 and 1100 base pair polymerase chain reaction fragments-in dilute solution are studied as functions of added salt ͑NaCl͒ concentration by dynamic light scattering-photon correlation spectroscopy. Translational diffusion coefficients and intramolecular relaxation times are extracted from the measured light scattering intensity time autocorrelation functions as the added salt concentration is reduced from 100 mM to approximately 0.1 mM. The relaxation times of the first intramolecular mode increase as the added salt concentration is lowered. The dependence of the translational diffusion coefficient D on the added salt concentration is not very large, although it exhibits a maximum for all three fragments. The maximum is interpreted as the consequence of two opposing effects-the stiffening of the molecule that produces an increase of the size ͑decrease of D͒ as the added salt concentration is lowered, and the coupling of the diffusion of the DNA through the electrostatic forces to the motion of the small and other polyions in the solution that results in an increase of its mobility ͑increase of D͒. The increase of the slowest intramolecular relaxation times as the salt concentration is lowered is interpreted in terms of a theory relating this time to the mean-squared radius of gyration of the molecule.
Kinetics and non-exponential binding of DNA-coated colloids
Soft Matter, 2013
Transient bridges of DNA have been used to direct the self-assembly of colloidal particles into interesting soft materials, but the particle binding kinetics are often slow or anomalous. Using line optical tweezers, we quantify the dynamics of two DNA-coated microspheres as a function of DNA density and strength of the DNA-induced pair interaction potential. At high DNA density, the binding kinetics is limited by the rate of microsphere diffusion and displays the expected dependence on the interaction potential energy. At low DNA density, the particle binding kinetics is set by single molecular binding events and exhibits bound times having a non-exponential distribution, suggesting that individual DNA bridges may also have intrinsic non-exponential kinetics. A dynamic model that includes such dispersion in the lifetimes of molecular bridges reproduces our observations, while an alternative model based on fluctuations in DNA density does not.
Microscopics of Complexation between Long DNA Molecules and Positively Charged Colloids
Physical Review Letters, 2002
Extensive atomic force and electron microscopy reveal a new, generic DNA-colloid complex with a fixed number of DNA bases per colloid. The fiber shaped complex is stable in the presence of excess colloids in the solution. As more DNA is added to the solution and the ratio between colloids and DNA approaches the fiber's stoichiometry, the system undergoes a sharp coagulation transition. The system is restabilized at even higher DNA concentrations through localization of small colloid clusters on extensive DNA networks.