Nanotechnology Now

Our NanoNews Digest Sponsors





Heifer International

Wikipedia Affiliate Button


DHgate

Home > Press > Scientists Embed Computation in a DNA Crystal

Abstract:
California Institute of Technology computer scientists have succeeded in building a DNA crystal that computes as it grows.

Caltech computer scientists embed computation in a DNA crystal to create microscopic patterns

Pasadena, CA | December 06, 2004

In a demonstration that holds promise for future advances in nanotechnology, California Institute of Technology computer scientists have succeeded in building a DNA crystal that computes as it grows. As the computation proceeds, it creates a triangular fractal pattern in the DNA crystal.

This is the first time that a computation has been embedded in the growth of any crystal, and the first time that computation has been used to create a complex microscopic pattern. And, the researchers say, it is one step in the dream of nanoscientists to master construction techniques at the molecular level.

Reporting in the December issue of the journal Public Library of Science (PLoS) Biology, Caltech assistant professor Erik Winfree and his colleagues show that DNA "tiles" can be programmed to assemble themselves into a crystal bearing a pattern of progressively smaller "triangles within triangles," known as a Sierpinski triangle. This fractal pattern is more complex than patterns found in natural crystals because it never repeats. Natural crystals, by contrast, all bear repeating patterns like those commonly found in the tiling of a bathroom floor. And, because each DNA tile is a tiny knot of DNA with just 150 base pairs (an entire human genome has some 3 billion), the resulting Sierpinski triangles are microscopic. The Winfree team reports growing micron-size DNA crystals (about a hundredth the width of a human hair) that contain numerous Sierpinski triangles.

A key feature of the Caltech team's approach is that the DNA tiles assemble into a crystal spontaneously. Comprising a knot of four DNA strands, each DNA tile has four loose ends known as "sticky ends." These sticky ends are what binds one DNA tile to another. A sticky end with a particular DNA sequence can be thought of as a special type of glue, one that only binds to a sticky end with a complementary DNA sequence, a special "anti-glue''. For their experiments, the authors just mixed the DNA tiles into salt water and let the sticky ends do the work, self-assembling the tiles into a Sierpinski triangle. In nanotechnology this "hands off" approach to manufacturing is a desirable property, and a common theme.

The novel aspect of the research is the translation of an algorithm--the basic method underlying a computer program--into the process of crystal growth. A well-known algorithm for drawing a Sierpinski triangle starts with a sequence of 0s and 1s. It redraws the sequence over and over again, filling up successive rows on a piece of paper, each time performing binary addition on adjacent digits.

The result is a Sierpinski triangle built out of 0s and 1s. To embed this algorithm in crystal growth, the scientists represented written rows of binary "0s" and "1s" as rows of DNA tiles in the crystal--some tiles stood for 0, and others for 1. To emulate addition, the sticky ends were designed to ensure that whenever a free tile stuck to tiles already in the crystal, it represented the sum of the tiles it was sticking to.

The process was not without error, however. Sometimes DNA tiles stuck in the wrong place, computing the wrong sum, and destroying the pattern. The largest perfect Sierpinski triangle that grew contained only about 200 DNA tiles. But it is the first time any such thing has been done and the researchers believe they can reduce errors in the future.

In fact the work is the first experimental demonstration of a theoretical concept that Winfree has been developing since 1995--his proposal that any algorithm can be embedded in the growth of a crystal. This concept, according to Winfree's coauthor and Caltech research fellow Paul W. K. Rothemund, has inspired an entirely new research field, "algorithmic self-assembly," in which scientists study the implications of embedding computation into crystal growth.

"A growing group of researchers has proposed a series of ever more complicated computations and patterns for these crystals, but until now it was unclear that even the most basic of computations and patterns could be achieved experimentally," Rothemund says.

Whether larger, more complicated computations and patterns can be created depends on whether Winfree's team can reduce the errors. Whether the crystals will be useful in nanotechnology may depend on whether the patterns can be turned into electronic devices and circuits, a possibility being explored at other universities including Duke and Purdue.

Nanotechnology applications aside, the authors contend that the most important implication of their work may be a better understanding of how computation shapes the physical world around us. "If algorithmic concepts can be successfully adapted to the molecular context," the authors write, "the algorithm would join energy and entropy as essential concepts for understanding how physical processes create order."

Winfree is an assistant professor of computation and neural systems and computer science; Rothemund is a senior research fellow in computer science and computation and neural systems. The third author is Nick Papadakis, a former staff member in computer science.


Contact:
Robert Tindol (626) 395-3631 tindol@caltech.edu

Copyright California Institute of Technology

If you have a comment, please 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

Possible Futures

This could replace your silicon computer chips: A new semiconductor material made from black phosphorus may be a candidate to replace silicon in future tech July 30th, 2015

Smaller, faster, cheaper: A new type of modulator for the future of data transmission July 27th, 2015

Researchers predict material with record-setting melting point July 27th, 2015

Global Corrosion Resistant Nano Coatings Market To 2015: Acute Market Reports July 27th, 2015

Molecular Machines

Injectable electronics: New system holds promise for basic neuroscience, treatment of neuro-degenerative diseases June 8th, 2015

One step closer to a single-molecule device: Columbia Engineering researchers first to create a single-molecule diode -- the ultimate in miniaturization for electronic devices -- with potential for real-world applications May 25th, 2015

UCLA nanoscientists are first to model atomic structures of three bacterial nanomachines: Cryo electron microscope enables scientists to explore the frontiers of targeted antibiotics April 21st, 2015

Advances in molecular electronics: Lights on -- molecule on: Researchers from Dresden and Konstanz succeed in light-controlled molecule switching April 20th, 2015

Self Assembly

New computer model could explain how simple molecules took first step toward life: Two Brookhaven researchers developed theoretical model to explain the origins of self-replicating molecules July 28th, 2015

Spintronics: Molecules stabilizing magnetism: Organic molecules fixing the magnetic orientation of a cobalt surface/ building block for a compact and low-cost storage technology/ publication in Nature Materials July 25th, 2015

Imec introduces self-assembled monomolecular organic films to seal ultra-porous low- k materials: Method prevents leakage of barrier precursors during the interconnect metallization scheme July 15th, 2015

Clay sheets stack to form proton conductors: Model system demonstrates a new material property emerging from the assembly of nanoscale building blocks July 13th, 2015

Discoveries

Take a trip through the brain July 30th, 2015

This could replace your silicon computer chips: A new semiconductor material made from black phosphorus may be a candidate to replace silicon in future tech July 30th, 2015

Sol-gel capacitor dielectric offers record-high energy storage July 30th, 2015

Controlling Dynamic Behavior of Carbon Nanosheets in Structures Made Possible July 30th, 2015

Announcements

Take a trip through the brain July 30th, 2015

This could replace your silicon computer chips: A new semiconductor material made from black phosphorus may be a candidate to replace silicon in future tech July 30th, 2015

Sol-gel capacitor dielectric offers record-high energy storage July 30th, 2015

Controlling Dynamic Behavior of Carbon Nanosheets in Structures Made Possible July 30th, 2015

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