Self-Replication Process Holds Promise for Production of New Materials

NYU scientists have developed artificial structures that can self-replicate, a process that has the potential to yield new types of materials. These structures consist of triple helix molecules containing three DNA double helices. (Credit: Image courtesy of Nature.)

Science Daily  — New York University scientists have developed artificial structures that can self-replicate, a process that has the potential to yield new types of materials. In the natural world, self-replication is ubiquitous in all living entities, but artificial self-replication has been elusive. The new discovery is the first steps toward a general process for self-replication of a wide variety of arbitrarily designed seeds. The seeds are made from DNA tile motifs that serve as letters arranged to spell out a particular word. The replication process preserves the letter sequence and the shape of the seed and hence the information required to produce further generations.

This process holds much promise for the creation of new materials. DNA is a robust functional entity that can organize itself and other molecules into complex structures. More recently DNA has been used to organize inorganic matter, such as metallic particles, as well. The re-creation by the NYU scientists of this type of assembly in a laboratory raises the prospect for the eventual development of self-replicating materials that possess a wide range of patterns and that can perform a variety of functions. The breakthrough the NYU researchers have achieved is the replication of a system that contains complex information. Thus, the replication of this material, like that of DNA in the cell, is not limited to repeating patterns.

The work, conducted by researchers in NYU's Departments of Chemistry and Physics and its Center for Soft Matter Research, appears in the latest issue of the journal Nature.

To demonstrate this self-replication process, the NYU scientists created artificial DNA tile motifs -- short, nanometer-scale arrangements of DNA. Each tile serves as a letter -- A or B -- that recognizes and binds to complementary letters A' or B'. In the natural world, the DNA replication process involves complementary matches between bases -- adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C) -- to form its familiar double helix. By contrast, the NYU researchers developed an artificial tile or motif, called BTX (bent triple helix molecules containing three DNA double helices), with each BTX molecule composed of 10 DNA strands. Unlike DNA, the BTX code is not limited to four letters -- in principle, it can contain quadrillions of different letters and tiles that pair using the complementarity of four DNA single strands, or "sticky ends," on each tile, to form a six-helix bundle.

In order to achieve self-replication of the BTX tile arrays, a seed word is needed to catalyze multiple generations of identical arrays. BTX's seed consists of a sequence of seven tiles -- a seven-letter word. To bring about the self-replication process, the seed is placed in a chemical solution, where it assembles complementary tiles to form a "daughter BTX array" -- a complementary word. The daughter array is then separated from the seed by heating the solution to ~ 40 oC. The process is then repeated. The daughter array binds with its complementary tiles to form a "granddaughter array," thus achieving self-replication of the material and of the information in the seed -- and hence reproducing the sequence within the original seed word. Significantly, this process is distinct from the replication processes that occur within the cell, because no biological components, particularly enzymes, are used in its execution -- even the DNA is synthetic.

"This is the first step in the process of creating artificial self-replicating materials of an arbitrary composition," said Paul Chaikin, a professor in NYU's Department of Physics and one of the study's co-authors. "The next challenge is to create a process in which self-replication occurs not only for a few generations, but long enough to show exponential growth."

"While our replication method requires multiple chemical and thermal processing cycles, we have demonstrated that it is possible to replicate not just molecules like cellular DNA or RNA, but discrete structures that could in principle assume many different shapes, have many different functional features, and be associated with many different types of chemical species," added Nadrian Seeman, a professor in NYU's Department of Chemistry and a co-author of the study.

The research was supported by grants from the W.M. Keck Foundation, the MRSEC Program of the National Science Foundation, the National Institute of General Medical Sciences, the Army Research Office, NASA, and the Office of Naval Research.

Brilliant 10: The Robot Trainer

Crowdsourcing will help robots learn complex tasks the same way children do

By Gregory Mone

Chad Jenkins Courtesy Chad Jenkins/Brown University

As an Atari-addicted kid, all Chad Jenkins wanted was to someday become a videogame designer. But once he got to grad school, he switched his obsession to robots.

Jenkins, now at Brown University, aims to program robots so that they learn the way children do: through mimicry andrepetition. To teach his first virtual humanoid robot how to do the Cabbage Patch, he programmed it to study his moves and replicate them. Now he’s turned his attention to more-complex tasks, such as setting a table or preparing a meal. The key is repetition. The more a robot observes, and the greater the variety of approaches to a given task that it observes, the better it will be able to understand the underlying essence of the act itself.

Such teaching takes a lot of repetition. rather than do all the dancing or table-setting himself, though, Jenkins has figured out a way to crowdsource the work. Prescreened users will log on to his Brown lab’s website and, through simple keystrokes, guide a robot—such as the PR2, a humanoid robot made by the Silicon Valley company Willow Garage—through a job. Instead of observing the person, the robot will learn by observing itself, recording its every movement and action, and using learning algorithms to find the most efficient way to complete a task. eventually, after someone demonstrates to the PR2 how to successfully pick up and set down a wineglass, the robot should be able to master it.

Jenkins’s training lab will also be testing new applications and tasks for the robots. Most robots run on specialized code, but Jenkins made his robots run on a common Web language so that more developers would be able to program them. “He’s democratizing access to robots,” says Willow Garage roboticist Brian Gerkey. Although Jenkins isn’t sure what applications the geek masses will devise, the father of three does have a task in mind for his own house: “I’d love for a robot to sort the toys and put them away."

Brilliant 10: Neuron Observer

Staring into the brains of fruit flies could clarify the connection between genes and behaviors

By Mara Grunbaum

Gaby Maimon Courtesy Gaby Maimon

Gaby Maimon, of Rockefeller University, can read fruit flies’ minds. As their wings buzz under his microscope, he watches the neurons fire in their poppy-seed-size brains. By doing so, he is able to discern how the firing of certain neurons corresponds to certain behaviors. His goal is to untangle precisely how genes and neuron activation trigger behavioral disorders like autism and ADHD.

To achieve such insights, Maimon needed to be able to to study fly neurons while the insects were awake and behaving as they normally would while flapping their wings. He built a plastic platform that immobilizes the flies’ heads in a saline bath—where he can surgically insert electrodes into their brains—but allows their wings to stay dry and flap freely as they “fly” through a simulated environment. His recordings of neuron activity, the first recordings of active, awake insects rather than sedated ones, lets him see which cells are working as the insects make simple decisions, such as whether to turn left or right during flight.

Maimon, who was raised in Israel, has always been curious about complex behavior. In grad school he worked with monkeys, but he grew frustrated with the pace of the work, so after finishing his doctorate, he switched to insects. He knew that fruit flies, with their 100,000 neurons and easily manipulated genetics, could help him correlate gene activation with neural function and complex behaviors.

For his next project, Maimon will record the activity of the same neurons in different flies to see if cellular variations make them behave differently. After that, he’ll search their genomes for the code that builds those cells. The research could reveal how they—and we—make choices. It will take a lot of steady hands and fly-scale brain surgeries, but he has the surgical procedure down now. The trick? “You don’t drink coffee that morning.”