CBES Investigators

Chad Mirkin

Haixin Lin

Postdoctoral Fellow

Research Overview

The Mirkin group will utilize its world-class expertise in the synthesis of DNA programmable materials to generate a new class of adaptive materials that, like biological entities, respond and undergo transformations in the presence of applied stimuli. Specifically, we will examine systems that exist in kinetically trapped states, and how the chemical pathway taken towards a thermodynamic equilibrated minima can dictate the materials ultimate path-dependent assembly behavior. This work differs from previous explorations into smart-materials in that its goal is to develop design rules governing assembly along a thermodynamic gradient, as opposed to the design of a thermodynamic minima. The exploration and development of such principles are critical in understanding how “living” biological systems function. In a living system, the assemblies generated are rarely the result of reaching a thermodynamic minima – rather, they are the result of thermodynamic gradients created by the continual flux of both matter and energy.

Schematic illustration of the preparation and assembly of kinetically-stabilized colloids. (A) Particles functionalized with recognition elements (depicted here as hairpin motifs) that act to bury sticky end sequences are kinetically trapped until the introduction of a target element (depicted here as oligonucleotides that open the hairpin). (B) The order and type of target element introduced to a collection of kinetically-trapped colloids dictates the particular superlattice that self-assembles, here from state 0 to state 4 via path 0,1,2,4 or path 0,1,3,4. (C) Energy diagram representing the various states (0 to 4) depicted in (B) where the color contour represents the thermodynamic gradient. A traditional crystallization path is depicted by a dashed line, while the proposed kinetically controlled pathways are depicted by solid arrows between the energetic wells. (D) Two dimensional representation of (C) along specific pathways. The red pathway represents a traditional crystallization path in which design rules dictate the location of the final state (0,4). The blue and green pathways (0,1,2,4 and 0,1,3,4) represent proposed design paths with kinetically stabilized crystalline states in which the crystalline nature of each state is programmed by the stick-end sequences, and the depth of each energetic well is programmed through the design of the hairpin motif.

In the first system we intend to study, we will develop a series of hairpin DNA programmable-atom-equivalents (PAEs) in which the “sticky-ends” of the DNA, responsible for governing assembly behavior, can be activated through the addition of complementary oligomer sequences in a serial manner. In this system we intend to show that, despite sharing a common thermodynamic minima, two separate thermodynamic pathways can be explored to selectively generate a differing sequence of assemblies. In our second system, we will continue our efforts with the above mentioned hairpin DNA PAEs – but instead of the sticky-ends being activated by oligomer complements we intend for them to be thermally activated. While the sticky-ends will be responsible for the nature of the assembly motif of the PAEs, the properties of the DNA hairpin will govern the temperature at which the sticky-ends are activated. Our goal will be to control the assembly behavior through a series of thermal fluctuations, effectively shuttling our PAEs through a chain of kinetically trapped states in programmable manner. In this manner, we intend to expand upon our design rules from thermodynamic minima and to develop design rules for systematically programmed kinetically trapped states.