Nanotechnology Now

Our NanoNews Digest Sponsors





Heifer International

Wikipedia Affiliate Button


android tablet pc

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

Materials for the next generation of electronics and photovoltaics: MacArthur Fellow develops new uses for carbon nanotubes October 21st, 2014

Special UO microscope captures defects in nanotubes: University of Oregon chemists provide a detailed view of traps that disrupt energy flow, possibly pointing toward improved charge-carrying devices October 21st, 2014

Super stable garnet ceramics may be ideal for high-energy lithium batteries October 21st, 2014

Could I squeeze by you? Ames Laboratory scientists model molecular movement within narrow channels of mesoporous nanoparticles October 21st, 2014

Physics

Solid nanoparticles can deform like a liquid: Unexpected finding shows tiny particles keep their internal crystal structure while flexing like droplets October 12th, 2014

Unconventional photoconduction in an atomically thin semiconductor: New mechanism of photoconduction could lead to next-generation excitonic devices October 9th, 2014

Nanoparticles Break the Symmetry of Light October 6th, 2014

Quantum environmentalism: Putting a qubit's surroundings to good use October 2nd, 2014

Possible Futures

Imaging electric charge propagating along microbial nanowires October 20th, 2014

Superconducting circuits, simplified: New circuit design could unlock the power of experimental superconducting computer chips October 18th, 2014

Nanocoatings Market By Product Is Expected To Reach USD 8.17 Billion By 2020: Grand View Research, Inc. October 15th, 2014

Perpetuus Carbon Group Receives Independent Verification of its Production Capacity for Graphenes at 140 Tonnes per Annum: Perpetuus Becomes the First Manufacturer in the Sector to Allow Third Party Audit October 7th, 2014

Academic/Education

First Canada Excellence Research Chair gets $10 million from the federal government for oilsands research at the University of Calgary: Federal government announces prestigious research chair to study improving oil production efficiency October 19th, 2014

Raytheon, UMass Lowell open on-campus research institute: Industry leader’s researchers to collaborate with faculty, students to move key technologies forward through first-of-its-kind partnership October 11th, 2014

SUNY Colleges of Nanoscale Science and Engineering and National Institute for Occupational Safety and Health Announce Expanded Partnership October 2nd, 2014

Yale University and Leica Microsystems Partner to Establish Microscopy Center of Excellence: Yale Welcomes Scientists to Participate in Core Facility Opening and Super- Resolution Workshops October 20 Through 31, 2014 September 30th, 2014

Nanomedicine

Detecting Cancer Earlier is Goal of Rutgers-Developed Medical Imaging Technology: Rare earth nanocrystals and infrared light can reveal small cancerous tumors and cardiovascular lesions October 21st, 2014

Design of micro and nanoparticles to improve treatments for Alzheimers and Parkinsons: At the Faculty of Pharmacy of the UPV/EHU-University of the Basque Country encapsulation techniques are being developed to deliver correctly and effectively certain drugs October 20th, 2014

Non-Toxic Nanocatalysts Open New Window for Significant Decrease in Reaction Process October 19th, 2014

European Commission opens the gate towards the implementation of Nanomedicine Translation Hub October 16th, 2014

Announcements

Special UO microscope captures defects in nanotubes: University of Oregon chemists provide a detailed view of traps that disrupt energy flow, possibly pointing toward improved charge-carrying devices October 21st, 2014

Super stable garnet ceramics may be ideal for high-energy lithium batteries October 21st, 2014

Could I squeeze by you? Ames Laboratory scientists model molecular movement within narrow channels of mesoporous nanoparticles October 21st, 2014

Detecting Cancer Earlier is Goal of Rutgers-Developed Medical Imaging Technology: Rare earth nanocrystals and infrared light can reveal small cancerous tumors and cardiovascular lesions October 21st, 2014

Nanobiotechnology

Crystallizing the DNA nanotechnology dream: Scientists have designed the first large DNA crystals with precisely prescribed depths and complex 3D features, which could create revolutionary nanodevices October 20th, 2014

Scientists Map Key Moment in Assembly of DNA-Splitting Molecular Machine: Crucial steps and surprising structures revealed in the genesis of the enzyme that divides the DNA double helix during cell replication October 15th, 2014

DNA nano-foundries cast custom-shaped metal nanoparticles: DNA's programmable assembly is leveraged to form precise 3D nanomaterials for disease detection, environmental testing, electronics and beyond October 10th, 2014

Charged graphene gives DNA a stage to perform molecular gymnastics October 9th, 2014

Quantum nanoscience

NIST quantum probe enhances electric field measurements October 8th, 2014

Quantum environmentalism: Putting a qubit's surroundings to good use October 2nd, 2014

Rice launches Center for Quantum Materials: RCQM will immerse global visitors in cross-disciplinary research September 30th, 2014

Big Results Require Big Ambitions: Three young UCSB faculty receive CAREER awards from the National Science Foundation September 18th, 2014

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







© Copyright 1999-2014 7th Wave, Inc. All Rights Reserved PRIVACY POLICY :: CONTACT US :: STATS :: SITE MAP :: ADVERTISE