Polygamous particles

Abstract

DNA is increasingly used as an important tool in programming the self-assembly of micrometer-and nanometer-scale particles. This is largely due to the highly specific thermoreversible interaction of cDNA strands, which, when placed on different particles, have been used to bind precise pairs in aggregates and crystals. However, DNA functionalized particles will only reach their true potential for particle assembly when each particle can address and bind to many different kinds of particles. Indeed, specifying all bonds can force a particular designed structure. In this paper, we present the design rules for multiflavored particles and show that a single particle, DNA functionalized with many different "flavors," can recognize and bind specifically to many different partners. We investigate the cost of increasing the number of flavors in terms of the reduction in binding energy and melting temperature. We find that a single 2-μm colloidal particle can bind to 40 different types of particles in an easily accessible time and temperature regime. The practical limit of ∼100 is set by entropic costs for particles to align complementary pairs and, surprisingly, by the limited number of distinct "useful" DNA sequences that prohibit subunits with nonspecific binding. For our 11 base "sticky ends," the limit is 73 distinct sequences with no unwanted overlaps of 5 bp or more. As an example of phenomena enabled by polygamous particles, we demonstrate a three-particle system that forms a fluid of isolated clusters when cooled slowly and an elastic gel network when quenched. multifunctional | thermodynamicsA defining feature of DNA nanotechnology is the ability of DNA single strands to bind selectively only with complementary strands (1-8). Identical particles coated with identical DNA strands can be joined together by adding to the suspension a linker strand that attaches to the two coatings (9, 10). Such structures have been used for immunoassays (11), particle aggregation, and formation of crystalline structures, typically Face Centered Cubic (FCC) (12). Use has also been made of different particles, A and B, functionalized with cDNA strands (13). This configuration, where A-A and B-B bonds do not occur but A-B bonds do (14-16), has been exploited to form more complex crystals, such as BCC or CsCl structures (12,17). Over the past several years, there has been a great deal of progress in modeling the DNA-mediated interparticle interaction and making quantitative comparisons with experiments (16,(18)(19)(20)(21)(22)(23). Although nanoscale particles are typically coated with tens to hundreds of DNA molecules, and micrometer-scale colloids can be coated with 10 4 -10 5 DNA strands, there has been little work on coating particles with more than one type of DNA sequence on the same particle. Allowing these particles to be "polygamous," to specifically bind to a particular set of other particles, enables not only the fabrication of more complex crystals but the design of more general programmed structures. For rigid structures,...

Size limits of self-assembled colloidal structures made using specific interactions

“…Although the practical limit of how many different types of strands per particle can be used is much higher than what we require (40), the density of strands is not high enough yet to avoid kinetic effects (40). Nonetheless, it is possible to implement the basic schemes outlined here with nonmaximal alphabets, in which the number of different strands on each particle is less than the number of contacts.…”

Colloidal matter: Packing, geometry, and entropy

“…DNA-functionalized colloidal particles have effective attractions that are both short-ranged and specific (101), and each particle can carry more than 40 different strands of DNA (102). It is therefore possible to explore systems in which the number of independent pair interactions is comparable to the number of particles.…”

Multistep kinetic self-assembly of DNA-coated colloids

“…Nature itself provides examples of amorphous, yet functional, materials assembled by controlling the kinetic arrest of out-of-equilibrium systems in their pathway towards the ground state [17][18][19][20][21] . This type of kinetic self-assembly is intrinsically more flexible and reliable than its equilibrium counterpart, allowing control over the morphology of the final phase by tuning both the interactions and the kinetic pathway leading to dynamic arrest [22][23][24] .…”