Nanotechnology Now

Our NanoNews Digest Sponsors





Heifer International

Wikipedia Affiliate Button


DHgate

Home > Press > A new read on DNA sequencing

Stuart Lindsay is a biohysicist at the Biodesign Institute at Arizona State University. Credit: The Biodesign Institute at Arizona State University
Stuart Lindsay is a biohysicist at the Biodesign Institute at Arizona State University. Credit: The Biodesign Institute at Arizona State University

Abstract:
Stuart Lindsay, of the Biodesign Institute at Arizona State University, has demonstrated a technique that may lead to rapid, low cost reading of whole genomes

A new read on DNA sequencing

Phoenix, AZ | Posted on November 15th, 2010

The twisting, ladder-like form of the DNA molecule—the architectural floor plan of life—contains a universe of information critical to human health. Enormous effort has been invested in deciphering the genetic code, including, most famously, the Human Genome Project. Nevertheless, the process of reading some three-billion nucleotide "letters" to reveal an individual's full genome remains a costly and complex undertaking.

Now biophysicist Stuart Lindsay, of the Biodesign Institute at Arizona State University, has demonstrated a technique that may lead to rapid, low cost reading of whole genomes, through recognition of the basic chemical units—the nucleotide bases that make up the DNA double helix. An affordable technique for DNA sequencing would be a tremendous advance for medicine, allowing routine clinical genomic screening for diagnostic purposes; the design of a new generation of custom-fit pharmaceuticals; and even genomic tinkering to enhance cellular resistance to viral or bacterial infection.

Lindsay is an ASU Regents' Professor and Carson Presidential Chair of Physics and Chemistry as well as director of the Biodesign Institute's Center for Single Molecule Biophysics. His group's research appears in the current issue of the journal Nature Nanotechnology.

Lindsay's technique for reading the DNA code relies on a fundamental property of matter known as quantum tunneling, which operates at the subatomic scale. According to quantum theory, elementary particles like electrons can do some very strange and counter-intuitive things, in defiance of classical laws of physics. Such sub-atomic, quantum entities possess both a particle and a wave-like nature. Part of the consequence of this is that an electron has some probability of moving from one side of a barrier to the other, regardless of the height or width of such a barrier.

Remarkably, an electron can accomplish this feat, even when the potential energy of the barrier exceeds the kinetic energy of the particle. Such behavior is known as quantum tunneling, and the flow of electrons is a tunneling current. Tunneling is confined to small distances—so small that a tunnel junction should be able to read one DNA base (there are four of them in the gentic code, A,T,C and G) at a time without interference from flanking bases. But the same sensitivity to distance means that vibrations of the DNA, or intervening water molecules, ruin the tunneling signal. So the Lindsay group has developed "recognition molecules" that "grab hold" of each base in turn, clutching the base against the electrodes that read out the signal. They call this new method "recognition tunneling."

The current paper in Nature Nanotechnology shows that single bases inside a DNA chain can indeed be read with tunneling, without interference from neighboring bases. Each base generates a distinct electronic signal, current spikes of a particular size and frequency that serve to identify each base. Surprisingly, the technique even recognizes a small chemical change that nature sometimes uses to fine-tune the expression of genes, the so called "epigenetic" code. While an individual's genetic code is the same in every cell, the epigenetic code is tissue and cell specific and unlike the genome itself, the epigenome can respond to environmental changes during an individual's life.

To read longer lengths of DNA, Lindsay's group is working to couple the tunneling readout to a nanopore—a tiny hole through which DNA is dragged, one base at a time, by an electric field. The paper in Nature Nanotechnology has something to say about this problem too. "It has always been believed that the problem with passing DNA through a nanopore is that it flies through so quickly that there is no time to read the sequence" Lindsay says. Surprisingly, the tunneling signals reported in the Nanture Nanotechnology paper last for a long time—nearly a second per base read.

To test this result, Lindsay teamed with a colleague, Robert Ros, to measure how hard one has to pull to break the complex of a DNA base plus the recognition molecules. They did this with an atomic force microscope. "These measurements confirmed the long lifetime of the complex, and also showed that the reading time could be speeded up at will by the application of a small additional pulling force" says Ros. "Thus the stage is set for combining tunneling reads with a device that passes DNA through a nanopore" says Lindsay.

Sequencing through recognition tunneling, if proven successful for whole genome reading, could represent a substantial savings in cost and hopefully, in time as well. Existing methods of DNA sequencing typically rely on cutting the full molecule into thousands of component bits, snipping apart the ladder of complementary bases and reading these fragments. Later, the pieces must be meticulously re-assembled, with the aid of massive computing power. "Direct readout of the epigenetic code holds the key to understanding why cells in different tissues are different, despite having the same genome" Lindsay adds, a reference to the new ability to read epigenetic modifications with tunneling.

Lindsay stresses much work remains to be done before the application of sequencing by recognition can become a clinical reality. "Right now, we can only read two or three bases as the tunneling probe drifts over them, and some bases are more accurately identified than others," he says. However, the group expects this to improve as future generations of recognition molecules are synthesized.

"The basic physics is now demonstrated" Lindsay says, adding "perhaps it will soon be possible to incorporate these principles into mass produced computer chips." The day of the "genome on a lap-top" might be coming sooner than previously thought possible.

####

For more information, please click here

Contacts:
Joseph Caspermeyer

480-727-0369

Copyright © Arizona State University

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

Controlling phase changes in solids: Controlling phase changes in solids July 29th, 2015

Liquipel Debuts Eyesight-Saving ION-Glass Blue Light Protection for iPhones and Androids at RadioShack Stores Nationwide: Liquipel's Unique Protective Screen, Available at RadioShack, Cuts Harmful Blue Light Implicated in Macular Degeneration by 10x July 28th, 2015

Nanophase to present paper on slurry pH impact at Optics + Photonics conference July 28th, 2015

Laboratorial Performance of Nanocomposite Membrane Improved in Water Purification July 28th, 2015

Physics

Make mine a decaf: Breakthrough in knowledge of how nanoparticles grow: University of Leicester and CNRS researchers observe how nanoparticles grow when exposed to helium July 23rd, 2015

Drawing a line between quantum and classical world: Bell's Inequality fails as a test of the boundary July 21st, 2015

Spintronics just got faster July 20th, 2015

Density-near-zero acoustical metamaterial made in China: Researchers create a tunable membrane 'metamaterial' with near-zero density, effectively recreating the quantum tunneling effect for sound waves July 14th, 2015

Possible Futures

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

Global Zinc oxide nanopowders Industry 2015: Acute Market Reports July 25th, 2015

Academic/Education

Deben reports on the use of their CT500 in the X-ray microtomography laboratory at La Trobe University, Melbourne, Australia July 22nd, 2015

JPK reports on the use of SPM in the Messersmith Group at UC Berkeley looking at biologically inspired polymer adhesives. July 21st, 2015

Renishaw adds Raman analysis to Scanning Electron Microscopy at the University of Sydney, Australia July 9th, 2015

Oxford Instruments’ TritonXL Cryofree dilution refrigerator selected for the Oxford NQIT Quantum Technology Hub project June 30th, 2015

Nanomedicine

Stretching the limits on conducting wires July 25th, 2015

UT Dallas nanotechnology research leads to super-elastic conducting fibers July 24th, 2015

Nanopaper as an optical sensing platform July 23rd, 2015

Albany College of Pharmacy and Health Sciences to Host One Week Symposium on Nanomedicine July 23rd, 2015

Announcements

Controlling phase changes in solids: Controlling phase changes in solids July 29th, 2015

Perfect Optical Properties in Production of Aluminum Oxide Colloid Nanoparticles July 28th, 2015

Short wavelength plasmons observed in nanotubes: Berkeley Lab researchers create Ludinger liquid plasmons in metallic SWNTs July 28th, 2015

'Seeing' molecular interactions could give boost to organic electronics July 28th, 2015

Nanobiotechnology

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

Programming adult stem cells to treat muscular dystrophy and more by mimicking nature July 22nd, 2015

Biophotonics - Global Strategic Business Report 2015 July 21st, 2015

Quantum nanoscience

Drawing a line between quantum and classical world: Bell's Inequality fails as a test of the boundary July 21st, 2015

World first: Significant development in the understanding of macroscopic quantum behavior: Researchers from Polytechnique Montréal and Imperial College London demonstrate the wavelike quantum behavior of a polariton condensate on a macroscopic scale and at room temperature July 14th, 2015

The quantum physics of artificial light harvesting: How molecular vibrations make photosynthesis efficient July 13th, 2015

A 'movie' of ultrafast rotating molecules at a hundred billion per second: A quantum wave-like nature was successfully observed in rotating nitrogen molecules July 4th, 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