DNA makes nano barcode
Technology Research News
To keep Moore's Law going -- the tenet
that computer speed will roughly double every 18 months -- manufacturers
must make faster circuits, and that usually means making them smaller.
If an electronic signal has less distance to travel, it will make the
trip more quickly.
But as the components that make up electronic devices grow smaller
it is becoming increasingly difficult for manufacturers to assemble them
using traditional lithography methods, which employ light and chemicals
to etch materials into shape. The transistors that form the bulk of the
Pentium 4 computer chip, for instance, are already about 130 nanometers
across, which is one-tenth the girth of an E. coli bacterium, or about
the size of a row of 1,300 hydrogen atoms.
Lithography is ultimately limited in scale to the wavelength of
light, said John Reif, a professor of computer science at Duke University.
"Within one or two decades, the ultimate limitations of these top-down
patterning methods will be reached," he said.
Another tack is assembling materials from the bottom up -- molecule-by-molecule.
Reif and several colleagues at Duke University have moved the
bottom-up method a step forward by programming strands of synthetic DNA
to self-assemble into a structure that makes the pattern encoded in a
DNA strand readable by microscope.
Key to the method is coaxing columns of looped and non-looped
strands of DNA stack into a barcode-like lattice.
DNA is made up of sequences of four bases - adenine, cytosine,
guanine and thymine -- attached to a sugar-phosphate backbone. Complementary
bases combine -- thiamine with adenine, and cytosine with guanine -- to
form the familiar double-stranded helix of biological DNA.
The researchers used a single DNA "scaffolding" strand that contained
sections of base sequences that were complementary to portions of DNA
barcoding strands. They used two types of DNA barcoding strands -- strands
that contained hairpin loops, and strands that did not. The barcoding
strands also contained sections of base sequences that caused barcoding
strands to combine with like barcoding strands.
The researchers mixed the scaffolding strand with barcoding strands
to form a two-dimensional lattice, with an initial row of barcoding strands
ordered by the scaffolding strand and additional barcoding strands stacked
up on the originals, forming columns with loops and columns without loops.
The columns were large enough that they could be sensed with an atomic
force microscope and read like a barcode. "The barcode patterns... are
determined by a scaffold strand of synthetic DNA. The other strands of
DNA assemble around the scaffold strand to form the 2D barcode patterned
lattice," said Reif.
The researchers programmed the process to produce two different
barcodes -- 01101 and 10010. The prototype DNA barcodes stored the five
bits of information in a 75-nanometer long lattice of DNA.
The method is "a nice advance in assembling nano-objects," said
David Harlan Wood, a professor of computer science at the University of
Delaware. The ability to directly observe the assembly by looking through
a microscope at the loops makes nano construction more practical, he said.
"Readout techniques are sorely needed for DNA computing," he added.
This type of readout, however, is limited by the number of distinct
objects. "When many multiple molecules are important, other methods, such
as biochips, may be more appropriate," said Wood.
The method could eventually be used to make templates that will
enable molecule-by-molecule construction of electronic circuits, said
Reif. The process should yield more complicated patterns than columns
if the scaffolding strand is wound back and forth, according to Reif.
"Using these patterned DNA lattices as scaffolds, we intend... to self-assemble
molecular electronic circuit components... with the goal of forming molecular-scale
electronic circuitry," said Reif.
Molecular electronics and robotics components can be precisely
positioned at specific locations on such a scaffolding, according to Reif.
There have been notable successes in constructing individual molecular
components like carbon nanotubes, said Reif. The DNA scaffolding is one
way to hold, shape and assemble these molecular components into complex
machines and systems, he said.
The method could be ready for practical use in five to eight years,
according to Reif
Reif's research colleagues were Hao Yan, Thomas H. LaBean and
Liping Feng. The work appeared in the June 23, 2003 Proceedings of
the National Academy of Sciences. The research was funded by the Defense
Advanced Research Projects Agency (DARPA), the Air Force Office of Scientific
Research (AFOSR), and the National Science Foundation (NSF).
Timeline: 5-8 years
TRN Categories: Biological, Chemical, DNA and Molecular
Story Type: News
Related Elements: Technical paper, "Directed Nucleation
Assembly of DNA Tile Complexes for Barcode-Patterned Lattices," Proceedings
of the National Academy Of Sciences, June 23, 2003.
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