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

Piezoelectricity in a 2-D semiconductor: Berkeley Lab researchers discovery of piezoelectricty in molybdenum disulfide holds promise for future MEMS December 22nd, 2014

Quantum physics just got less complicated December 22nd, 2014

Enzyme Biosensor Used for Rapid Measurement of Drug December 22nd, 2014

Universality of charge order in cuprate superconductors: Charge order has been established in another class of cuprate superconductors, highlighting the importance of the phenomenon as a general property of these high-Tc materials December 22nd, 2014

Physics

Quantum physics just got less complicated December 22nd, 2014

Possible Futures

A novel method for identifying the body’s ‘noisiest’ networks November 19th, 2014

Researchers discern the shapes of high-order Brownian motions November 17th, 2014

VDMA Electronics Production Equipment: Growth track for 2014 and 2015 confirmed: Business climate survey shows robust industry sector November 14th, 2014

Open Materials Development Will Be Key for HP's Success in 3D Printing: HP can make a big splash in 3D printing, but it needs to shore up technology claims and avoid the temptation of the razor/razor blade business model in order to flourish November 11th, 2014

Academic/Education

SUNY Poly NanoCollege Faculty Member Selected as American Physical Society Fellow: SUNY Poly Associate Professor of Nanoscience Dr. Vincent LaBella Recognized for Significant Technological Innovations that Enable Interactive Learning December 17th, 2014

Nanomedicine expert joins Rice faculty: Gang Bao combines genetic, nano and imaging techniques to fight disease December 17th, 2014

FEI and Oregon Health & Science University Install a Complete Correlative Microscopy Workflow in Newly Built Collaborative Science Facility December 16th, 2014

Student Nanotechnology Laboratories Network Set Up in Iran December 15th, 2014

Nanomedicine

Enzyme Biosensor Used for Rapid Measurement of Drug December 22nd, 2014

Creation of 'Rocker' protein opens way for new smart molecules in medicine, other fields December 18th, 2014

Iranian Researchers Produce Electrical Pieces Usable in Human Body December 18th, 2014

Zenosense, Inc. - Hospital Collaboration - 400 Person Lung Cancer Detection Trial December 17th, 2014

Announcements

Piezoelectricity in a 2-D semiconductor: Berkeley Lab researchers discovery of piezoelectricty in molybdenum disulfide holds promise for future MEMS December 22nd, 2014

Quantum physics just got less complicated December 22nd, 2014

Enzyme Biosensor Used for Rapid Measurement of Drug December 22nd, 2014

Universality of charge order in cuprate superconductors: Charge order has been established in another class of cuprate superconductors, highlighting the importance of the phenomenon as a general property of these high-Tc materials December 22nd, 2014

Nanobiotechnology

Scientists trace nanoparticles from plants to caterpillars: Rice University study examines how nanoparticles behave in food chain December 16th, 2014

FEI and Oregon Health & Science University Install a Complete Correlative Microscopy Workflow in Newly Built Collaborative Science Facility December 16th, 2014

UCLA engineers first to detect and measure individual DNA molecules using smartphone microscope December 15th, 2014

Biomimetic dew harvesters: Understanding how a desert beetle harvests water from dew could improve drinking water collection in dew condensers December 8th, 2014

Quantum nanoscience

Quantum physics just got less complicated December 22nd, 2014

Universality of charge order in cuprate superconductors: Charge order has been established in another class of cuprate superconductors, highlighting the importance of the phenomenon as a general property of these high-Tc materials December 22nd, 2014

Fraud-proof credit card possible because of quantum physics December 16th, 2014

Nanoscale resistors for quantum devices: The electrical characteristics of new thin-film chromium oxide resistors that can be tuned by controlling the oxygen content detailed in the 'Journal of Applied Physics' December 9th, 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