Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button

Home > Press > Caltech Scientists Control Complex Nucleation Processes using DNA Origami Seeds

Ribbon-like DNA tile crystals grown from DNA origami seeds. Credit: Caltech/Winfree, Rothemund, Barish, Schulman
Ribbon-like DNA tile crystals grown from DNA origami seeds. Credit: Caltech/Winfree, Rothemund, Barish, Schulman

Abstract:
The construction of complex man-made objects--a car, for example, or even a pizza--almost invariably entails what are known as "top-down" processes, in which the structure and order of the thing being built is imposed from the outside (say, by an automobile assembly line, or the hands of the pizza maker).

Caltech Scientists Control Complex Nucleation Processes using DNA Origami Seeds

Pasadena, CA | Posted on April 10th, 2009

"Top-down approaches have been extremely successful," says Erik Winfree of the California Institute of Technology (Caltech). "But as the object being manufactured requires higher and higher precision--such as silicon chips with smaller and smaller transistors--they require enormously expensive factories to be built."

The alternative to top-down manufacturing is a "bottom-up" approach, in which the order is imposed from within the object being made, so that it "grows" according to some built-in design.

"Flowers, dogs, and just about all biological objects are created from the bottom up," says Winfree, an associate professor of computer science, computation and neural systems, and bioengineering at Caltech. Along with his coworkers, Winfree is seeking to integrate bottom-up construction approaches with molecular fabrication processes to construct objects from parts that are just a few billionths of a meter in size that essentially assemble themselves.

In a recent paper in the Proceedings of the National Academy of Sciences (PNAS), Winfree and his colleagues describe the development of an information-containing DNA "seed" that can direct the self-assembled bottom-up growth of tiles of DNA in a precisely controlled fashion. In some ways, the process is similar to how the fertilized seeds of plants or animals contain information that directs the growth and development of those organisms.

"The big potential advantage of bottom-up construction is that it can be cheap"--just as the mold that grows in your kitchen does so for free--"and can be massively parallel, because the objects construct themselves," says Winfree.

But, he adds, while bottom-up approaches have been extremely useful in biology, they haven't played as significant a role in technology, "because we don't have a great grasp on how to design systems that build themselves. Most examples of bottom-up technologies are specific chemical processes that work great for a particular task, but don't easily generalize for constructing more complex structures."

To understand how complexity can be programmed into bottom-up molecular fabrication processes, Winfree and his colleagues study and understand the processes--or algorithms--that generate organization not just in computers but also in the natural world.

"Tasks can be solved by carrying out well-defined rules, and these rules can be carried out by a mindless mechanism such as a computer," he says. "The same set of rules can perform different tasks when given different inputs, and there exist 'universal programs' that can perform any task required of it, as specified in its input. Your laptop is such a universal computer; it can run any software that you download, and in principle, any feasible task could be programmed."

These principles also have been exploited by natural evolution, Winfree says: "Every cell, it appears, is a kind of universal computer that can be instructed in seemingly limitless ways by a DNA genome that specifies what chemical processes to execute, thus building an active organism. The aim of my lab has been to understand algorithms and information within molecular systems."

Winfree's investigations into algorithmic self-assembly earned him a MacArthur "genius" prize in 2000; his collaborator, Paul W. K. Rothemund, a senior research associate at Caltech and a coauthor of the PNAS paper, was awarded the same no-strings-attached grant in 2007 for his work designing scaffolded "DNA origami" structures that self-assemble into nearly arbitrary shapes (such as a smiley face and a map of the Western Hemisphere).

The structures designed by Rothemund, which could eventually be used in smaller, faster computers, were used as the seeds for the programmed self-assembly of DNA tiles described in the current paper.

In the work, the researchers designed several different versions of a DNA origami rectangle, 95 by 75 nanometers, which served as the seeds for the growth of different types of ribbon-like crystals of DNA. The seeds were combined in a test tube with other bits of DNA, called "tiles," heated, and then cooled slowly.

"As it cools, the first origami seed and the individual tiles form, as their component DNA molecules begin sticking to each other and folding into shape--but the tiles and origami don't stick to each other yet," Winfree explains.

"Then, at a lower temperature, the tiles start to stick to each other and to the origami. The critical concept here is that the DNA tiles will only form crystals if the process gets started by a seed, upon which they can grow," he says.

In this way, the DNA ribbons self-assemble themselves, but only into forms such as ribbons with particular widths and ribbons with stripe patterns prescribed by the original seed.

The work, Winfree says, "exhibits a degree of control over information-directed molecular self-assembly that is unprecedented in accuracy and complexity, which makes me feel that we are finally beginning to understand how to program information into molecules and have that information direct algorithmic processes."

The paper, "An information-bearing seed for nucleating algorithmic self-assembly," was published in the March 24 issue of the Proceedings of the National Academy of Sciences.

The other authors of the paper are undergraduate Robert D. Barish and visiting scholar Rebecca Schulman. The work was supported by grants from the National Aeronautics and Space Administration's astrobiology program, the National Science Foundation, and the Focus Center Research Program, and a gift from Microsoft Research.

####

About Caltech
The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.

For more information, please click here

Contacts:
Kathy Svitil
(626) 395-8022

Copyright © Caltech

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related News Press

News and information

Keeping electric car design on the right road: A closer look at the life-cycle impacts of lithium-ion batteries and proton exchange membrane fuel cells December 9th, 2016

Further improvement of qubit lifetime for quantum computers: New technique removes quasiparticles from superconducting quantum circuits December 9th, 2016

Chemical trickery corrals 'hyperactive' metal-oxide cluster December 8th, 2016

Scientists track chemical and structural evolution of catalytic nanoparticles in 3-D: Up-close, real-time, chemical-sensitive 3-D imaging offers clues for reducing cost/improving performance of catalysts for fuel-cell-powered vehicles and other applications December 8th, 2016

Possible Futures

Keeping electric car design on the right road: A closer look at the life-cycle impacts of lithium-ion batteries and proton exchange membrane fuel cells December 9th, 2016

Further improvement of qubit lifetime for quantum computers: New technique removes quasiparticles from superconducting quantum circuits December 9th, 2016

Researchers peer into atom-sized tunnels in hunt for better battery: May improve lithium ion for larger devices, like cars December 8th, 2016

Scientists track chemical and structural evolution of catalytic nanoparticles in 3-D: Up-close, real-time, chemical-sensitive 3-D imaging offers clues for reducing cost/improving performance of catalysts for fuel-cell-powered vehicles and other applications December 8th, 2016

Molecular Machines

Micro-bubbles make big impact: Research team develops new ultrasound-powered actuator to develop micro robot November 25th, 2016

Scientists come up with light-driven motors to power nanorobots of the future: Researchers from Russia and Ukraine propose a nanosized motor controlled by a laser with potential applications across the natural sciences and medicine November 11th, 2016

HKU chemists develop world's first light-seeking synthetic Nanorobot November 9th, 2016

Light drives single-molecule nanoroadsters: Rice University scientists part of international team demonstrating untethered 3-wheelers November 4th, 2016

Molecular Nanotechnology

Tip-assisted chemistry enables chemical reactions at femtoliter scale November 16th, 2016

Scientists come up with light-driven motors to power nanorobots of the future: Researchers from Russia and Ukraine propose a nanosized motor controlled by a laser with potential applications across the natural sciences and medicine November 11th, 2016

New Book by Nobel Laureate Tells Story of Chemistry’s New Field: Fraser Stoddart explains the mechanical bond and where it is taking scientists November 11th, 2016

HKU chemists develop world's first light-seeking synthetic Nanorobot November 9th, 2016

Self Assembly

Computers made of genetic material? HZDR researchers conduct electricity using DNA-based nanowires November 9th, 2016

First multicellular organism inspires the design of better cancer drugs September 15th, 2016

A versatile method to pattern functionalized nanowires: A team of researchers from Hokkaido University has developed a versatile method to pattern the structure of 'nanowires,' providing a new tool for the development of novel nanodevices September 9th, 2016

Location matters in the self-assembly of nanoclusters: Iowa State University scientists have developed a new formulation to explain an aspect of the self-assembly of nanoclusters on surfaces that has broad applications for nanotechnology September 8th, 2016

NanoNews-Digest
The latest news from around the world, FREE




  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoTech-Transfer
University Technology Transfer & Patents
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project