Working Night and Day

Day-night changes in light and temperature power a low-cost material assembly that mimics biological self-copying.

Image courtesy of Paul Chaikin, New York University

For materials, a new process achieves self-replication and selective control of evolving properties. Seven million copies were made in just 24 cycles that mimicked the light and temperature pattern of Earth’s days and nights. On the left are schematics with corresponding atomic force microscopy images below. A seed of two rafts labeled “T” has protruding sticky ends (red vertical rods). At “night” during low temperatures, the sticky ends on “A” rafts reversibly assemble on the complementary ends of the “T” seed. At “sunrise,” the ultraviolet light causes the two “A” rafts to bind together. As the temperature rises during the “day,” the bound “A” offspring are released from the parent “T”. On the right, the offspring after several cycles are shown (scale bar is 100 nanometer).

The Science

Self-replication makes identical copies of an initial seed. A new, autonomous method allows for selective and fast copying of materials—producing more than 7 million copies in only 24 cycles. The structures grow from seeds based on synthetic DNA. The seeds are referred to as DNA origami rafts. Daily changes in light and temperature power the low-cost growth. This new self-copying process can be designed to make and control multi-component materials with evolving functionality.

The Impact

In nature, self-replication and selective control of evolving properties are vital. In producing new materials, this technique could be used to make ideal materials in various environments. This study realized autonomous assembly of materials with specific properties. Pressure from the environment selectively guided the growth rates. This technique could transform how we construct materials.

Summary

Self-replication is a dynamic process that results in the assembly of identical copies of an initial seed structure. Self-replication along with evolution to favor specific traits are critical capabilities in nature for adapting to changing needs and circumstances. Few synthetic methods for fabricating materials approach the exquisite ability of biological systems to use these processes for growth and adaptation. Some approaches mimic a few of the attributes of these biological processes, but not the most desired capabilities of extremely rapid (exponential) self-directed replication in response to particular environmental signals.

Scientists at New York University have designed a system of DNA building blocks that exponentially replicates a seed pattern. The number of copies doubles in each cycle of temperature and ultraviolet illumination that mimics the Earth’s day-night pattern. The system produced more than 7 million copies in 24 cycles. The information encoded by the specific ordering of the nucleotide bases within the original seeds is transmitted from the parental pattern to the offspring and ensuing generations. The encoded information can be used with DNA assemblies of different shapes. This process exploits the selective pairing of nucleotide bases within DNA strands that commonly occurs in biology and DNA nanotechnology assembly processes. The parent is a seed consisting of two ordered DNA rafts. First, DNA strands on the parent rafts assemble daughter rafts from the surrounding liquid by reversibly binding at low temperature to their complementary, but distinct, DNA strands. The binding is temperature-sensitive base-pairing that occurs during a temperature swing that mimics the “day” to “night” transition. Next, the daughter rafts are covalently bound to each other using ultraviolet-photocrosslinking. This artificial “sunlight at dawn” illumination provides the light that permanently fixes the monomers. The increasing heat of the day is used to release the new daughter assemblies from the parents. Both parent and daughter motifs guide the continuing formation of new descendants upon the addition of new monomers, doubling the population each generation.

This simple process uses the temperature-reversible association of nucleotide monomers to a parent, followed by their irreversible coupling to form offspring. This process allows self-replication of predetermined structures. The material with the desired properties is selectively produced from a range of possible structures. The growth of its unique seed instead of others within the same pool is biased by favoring its ability to replicate. As an example, replication is sensitive to bath acidity. Some types of base-pairing favor replication under acidic conditions, while others favor growth under basic conditions (higher pH). Remarkably, this sensitivity could be leveraged to favor replication of one population of seeds over other chemically distinct ones. This is achieved by incorporating pH-sensitive binding in each population. When both types of seeds are present in an acidic environment, the acid-preferring seeds replicated much faster and produced many more copies of the original seed than the population that prefers higher pH. Switching from acidic to basic conditions allows the originally slower-replicating population to speed up the replication process, catching up to the previously fast-growing population.

Contact

Paul Chaikin
New York University
[email protected]

Funding

This work was supported primarily by the Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (initiation, design, analysis, and imaging). This work was partially supported by the Gordon and Betty Moore Foundation, National Institutes of Health, National Science Foundation, Army Research Office, and Office of Naval Research for DNA sequencing, origami preparation, and infrastructure. This research was also supported by the Hong Kong Government and Project 985 in China.

Publications

X. He, R. Sha, R. Zhuo, Y. Mi, P.M. Chaikin and N.C. Seeman, “Exponential growth and selection in self-replicating materials from DNA origami rafts.” Nature Materials 16, 993 (2017). [DOI:  10.1038/NMAT4986]

Highlight Categories

Program: BES , MSE

Performer: University

Additional: Collaborations , Non-DOE Interagency Collaboration , International Collaboration