Quantitative study of the association thermodynamics and kinetics of DNA-coated particles for different functionalization schemes.

Surface functionalization with complementary single-stranded DNA sticky ends is increasingly used for guiding the self-assembly of nano- and micrometer-sized particles into larger scale ordered structures. Here we present measurements, formulas, and graphs that allow one to quantitatively predict the association behavior of DNA-coated particles from readily available Web-based data. From experiments it appears that the suspension behavior is very sensitive to the grafting details, such as the length and flexibility of the tether constructs and the particles' surface coverage. Thus, if one wants to control the interactions and assembly processes, insight is needed into the structural and dynamical features of the DNA coatings. We demonstrate how a straightforward measurement of the particles' association-dissociation kinetics during selected temperature cycles, combined with a simple quantitative model, can reveal the relevant properties. We used this method in a systematic study where we varied the temperature cycle, the bead concentration, the particles' surface coverage, and the DNA construct. Among other things, we find that the backbone that tethers the sticky ends to the surface can have a significant impact on the particles' dissociation properties, as it affects the total number of interparticle bonds and the configurational entropy cost associated with these bonds. We further find that, independent of the tether backbone, self-complementary "palindromic" sticky ends readily form intraparticle hairpins and loops, which greatly affect the particles' association behavior. Such secondary structure formation is increasingly important in faster temperature quenches, at lower particle concentration, and at lower surface coverage. The latter observations are especially useful for the design of so-called self-protected DNA-mediated interactions, which we pioneered recently and for which we expect to find an increasing use, as they enable more versatile assembly schemes.

Switchable self-protected attractions in DNA-functionalized colloids.

Surface functionalization with DNA is a powerful tool for guiding the self-assembly of nanometre- and micrometre-sized particles. 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. 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.

Templated synthesis of nylon nucleic acids and characterization by nuclease digestion.

Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.

Aggregation-disaggregation transition of DNA-coated colloids: experiments and theory.

Colloids coated with complementary single-stranded DNA "sticky ends" associate and dissociate upon heating. Recently, microscopy experiments have been carried out where this association-dissociation transition has been investigated for different types of DNA and different DNA coverages [R. Dreyfus, M. E. Leunissen, R. Sha, A. V. Tkachenko, N. C. Seeman, D. J. Pine, and P. M. Chaikin, Phys. Rev. Lett. 102, 048301 (2009)]. It has been shown that this transition can be described by a simple quantitative model which takes into account the features of the tethered DNA on the particles and unravels the importance of an entropy cost due to DNA confinement between the surfaces. In this paper, we first present an extensive description of the experiments that were carried out. A step-by-step model is then developed starting from the level of statistical mechanics of tethered DNA to that of colloidal aggregates. This model is shown to describe the experiments with excellent agreement for the temperature and width of the transition, which are both essential properties for complex self-assembly processes.

Simple quantitative model for the reversible association of DNA coated colloids.

We investigate the reversible association of micrometer-sized colloids coated with complementary single-stranded DNA "sticky ends" as a function of the temperature and the sticky end coverage. We find that even a qualitative description of the dissociation transition curves requires the inclusion of an entropic cost. We develop a simple general model for this cost in terms of the configurational entropy loss due to binding and confinement of the tethered DNA between neighboring particles. With this easy-to-use model, we demonstrate for different kinds of DNA constructs quantitative control over the dissociation temperature and the sharpness of the dissociation curve, both essential properties for complex self-assembly processes.