Universal DNA reader expedites code sequencing

February 16, 2010

ASU scientists have come up with a new twist in their efforts to develop a faster and cheaper way to read the DNA genetic code. They have developed the first, versatile DNA reader that can discriminate between DNA's four core chemical components – the key to unlocking the vital code behind human heredity and health.

Led by ASU Regents' Professor Stuart Lindsay, director of the Biodesign Institute's Center for Single Molecule Biophysics, the ASU team is one of a handful that has received stimulus funds for a National Human Genome Research Initiative, part of the National Institutes of Health, to make DNA genome sequencing as widespread as a routine medical checkup. Download Full Image

The broad goal of this "$1,000 genome" initiative is to develop a next-generation DNA sequencing technology to usher in the age of personalized medicine, where knowledge of an individual's complete, 3 billion-long code of DNA information, or genome, will allow for a more tailored approach to disease diagnosis and treatment. With current technologies taking almost a year to complete at a cost of several hundreds of thousands of dollars, less than 20 individuals on the planet have had their whole genomes sequenced to date.

To make their research dream a reality, Lindsay's team has envisioned building a tiny, nanoscale DNA reader that could work like a supermarket checkout scanner, distinguishing between the four chemical letters of the DNA genetic code, abbreviated by A, G, C and T, as they rapidly pass by the reader. To do so, they needed to develop the nanotechnology equivalent of threading the eye of a needle. In this case, the DNA would be the thread that could be recognized as it moved past the reader "eye."

During the past few years, Lindsay's team has made steady progress, and first demonstrated the ability to read individual DNA sequences in 2008 – but this approach was limited because they had to use four separate readers to recognize each of the DNA bases. More recently, they demonstrated the ability to thread DNA sequences through the narrow hole of a fundamental building block of nanotechnology, the carbon nanotube.

Lindsay's team relies on the eyes of nanotechnology, scanning tunneling- (STM) and atomic force- (ATM) microscopes, to make their measurements. The microscopes have a delicate electrode tip that is held very close to the DNA sample. In their latest innovation, Lindsay's team made two electrodes, one on the end of microscope probe, and another on the surface, that had their tiny ends chemically modified to attract and catch the DNA between a gap like a pair of chemical tweezers. The gap between these functionalized electrodes had to be adjusted to find the chemical bonding sweet spot, so that when a single chemical base of DNA passed through a tiny, 2.5 nanometer gap between two gold electrodes, it momentarily sticks to the electrodes and a small increase in the current is detected. Any smaller, and the molecules would be able to bind in many configurations, confusing the readout, any bigger and smaller bases would not be detected.

What we did was narrow the number of types of bound configurations to just one per DNA base," Lindsay said. "The beauty of the approach is that all the four bases just fit the 2.5 nanometer gap, so it is one size fits all, but only just so!"

At this scale, which is just a few atomic diameters wide, quantum phenomena are at play where the electrons can actually leak from one electrode to the other, tunneling through the DNA bases in the process. Each of the chemical bases of the DNA genetic code, abbreviated A, C, T or G, gives a unique electrical signature as they pass between the gap in the electrodes. By trial and error, and a bit of serendipity, they discovered that just a single chemical modification to both electrodes could distinguish between all 4 DNA bases.

"We've now made a generic DNA sequence reader and are the first group to report the detection of all 4 DNA bases in one tunnel gap," Lindsay said. "Also, the control experiments show that there is a certain (poor) level of discrimination with even bare electrodes (the control experiments) and this is in itself, a first too."

"We were quite surprised about binding to bare electrodes because, like many physicists, we had always assumed that the bases would just tumble through. But actually, any surface chemist will tell you that the bases have weak chemical interactions with metal surfaces."

Next, Lindsay's group is hard at work trying to adapt the reader to work in water-based solutions, a critically practical step for DNA sequencing applications. Also, the team would like to combine the reader capabilities with the carbon nanotube technology to work on reading short stretches of DNA.

If the process can be perfected, DNA sequencing could be performed much faster than current technology, and at a fraction of the cost. Only then will the promise of personalized medicine reach a mass audience.

The authors on the Nano Letters paper are: Shuai Chang, Shuo Huang, Jin He, Feng Liang, Peiming Zhang, Shengqing Li, Xiang Chen, Otto Sankey and Stuart Lindsay

The Nano Letters research article can be accessed online at URL: http://pubs.acs.org/doi/pdfplus/10.1021/nl1001185.">http://pubs.acs.org/doi/pdfplus/10.1021/nl1001185">http://pubs.acs.org/d...

Joe Caspermeyer

Manager (natural sciences), Media Relations & Strategic Communications


Study addresses living options for adults with autism, related disorders

February 16, 2010

Editor’s note: This press">http://www.autismcenter.org/news_details.aspx?id=41">press release first appeared on the Southwest Autism Research & Resource Center’s (SARRC) Web site and has been republished with permission.

Within the next 15 years, more than 500,000 children with autism spectrum disorders (ASDs) will enter adulthood. Today, many adults with autism are being cared for by aging parents who in most cases will not outlive their children, leaving them limited options for lifelong support. This growing new subset of the developmentally disabled population―too old for continued support through the special education services of a public school system and too fragile to live without support in the larger world―and their families face a complicated system of vocational rehabilitation services, Medicaid, disconnected government agencies and a lack of appropriate residential care options beyond the obvious ones of keeping them at home or within institutional settings. Download Full Image

Opening">http://www.autismcenter.org/openingdoors.aspx">Opening Doors: A Discussion of Residential Options for Adults Living with Autism and Related Disorders, is a newly released collaborative study by the Urban Land Institute (ULI) Arizona, Southwest Autism Research and Resource Center (SARRC), the Arizona State University (ASU) Stardust Center for Affordable Homes and the Family and the ASU Herberger Institute School of Architecture and Landscape Architecture. The study focuses on the residential concerns of adults with autism and related disorders and is designed to advance the development of replicable residential models that offer quality, affordable housing options within the fabric of their communities. It also addresses current and projected demand for life-long living options that support the segment of individuals with autism spectrum and related disorders unable to live on their own. Further, the study explores the financial catalysts needed to spur new investment by the private and public sectors to meet projected demand and advocates for the creation of public-private-nonprofit collaborations to address long-term living, residential concerns.

The companion study for Opening Doors is Advancing">http://stardust.asu.edu/research_resources/detail.php?id=60">Advancing Full Spectrum Housing: Designing for Adults with Autism Spectrum Disorders, was produced by the Arizona State University Stardust Center for Affordable Homes and the Family, and ASU Herberger Institute School of Architecture and Landscape Architecture.   

These studies were funded through grants by Urban Land Foundation, Pivotal Foundation and SARRC.

“Our goal is to respond to the pressing question that’s looming today for millions of parents of children with autism and related disorders: Who will care for my child when I’m no longer able to do so? The dramatic increase in the population of affected individuals gives rise to serious concern among families, service providers, government and the community at-large that residential services for post-school-age adults with autism and developmental disorders must be created as an integral part of a healthy community’s housing plan and opportunities,” said Denise D. Resnik, SARRC Co-founder, Editor of Opening Doors and mother of an 18-year-old son with autism.

“We must restructure the way existing government funding is allocated to housing resources for the developmentally disabled in order to grow a sustainable real estate supply over time,” said George Bosworth, Urban Land Institute Arizona Executive Director.

The studies are intended to highlight existing residential options and support services, and guide the development of new options so they may serve as organic living and learning laboratories for scholars, social workers and families. Opening Doors proposes actionable steps that address the increasing demand for supportive housing and communities, which maximize independent living.

“Although there are a variety of sources for capital funding, organizations most often use two to three sources to cobble together a workable financial model for the projects,” said Joe Blackbourn, SARRC Board Member, Everest Holdings President and CEO, and former ULI Arizona Chairman.

Based on the synthesis of existing research and field research of several case studies, an inventory profile was developed of more than 100 "best practice" residential developments for adults with ASDs or other special needs conditions.

Advancing Full Spectrum Housing, introduces housing providers, architects, developers, planners, public officials and others involved in the residential development industry to conditions and aspirations of adults with autism that demand a new approach to the design and development of homes,” said Sherry Ahrentzen, Associate Director of Research for the ASU Stardust Center for Affordable Homes and the Family, a research entity in the ASU Herberger Institute School of Architecture and Landscape Architecture.

“Directed by 10 resident-based design goals, the design guidelines – ranging from neighborhood amenities to technological assistive devices in the home – provide a robust platform that architects, housing providers, families and residents can use to identify and select design features that best respond to specific needs and aspirations of residents,” said Kim Steele, Associate Professor of Landscape Architecture in the ASU Herberger Institute School of Architecture and Landscape Architecture.

Urban Land Institute is the preeminent, multidisciplinary real estate forum, facilitating the open exchange of ideas, information and experience among local, national and international industry leaders and policy makers dedicated to creating better places. The mission of the ULI is to provide responsible leadership in the use of land to enhance the total environment. For more information, visit www.uli.org.


The Southwest Autism Research & Resource Center, founded in 1997, is a nonprofit, community-based organization in Phoenix, Arizona, dedicated to autism research, education and outreach to individuals with autism and their families. SARRC undertakes self-directed and collaborative research, serves as a satellite site for national and international projects, and provides up-to-date information, training and assistance to families and professionals about autism spectrum disorders (ASDs). For more information, visit www.autismcenter.org.

The">http://www.autismcenter.org">www.autismcenter.org.... School of Architecture and Landscape Architecture in the Herberger Institute for Design and the Arts at Arizona State University offers a holistic approach to environmental design, lending teaching and research in a forward-thinking environment. Our more than 900 students are challenged to think creatively about architecture, landscape architecture, energy innovation and urban design. Phoenix and the Southwestern desert’s extreme environmental conditions provide an innovative laboratory for teaching and applied research. To learn more, visit: http://design.asu.edu/sala/.

The">http://design.asu.edu/sala/">http://design.asu.edu/sala/. ASU Stardust Center for Affordable Homes and the Family, a research entity in the ASU Herberger Institute School of Architecture and Landscape Architecture, supports organizations, neighborhoods and professionals in their efforts to improve the growth of quality affordable homes and sustainable communities through research, educational outreach, advocacy and design innovation. The center opened its doors in January 2005 with initial funding from a gift from Jerry Bisgrove and the Stardust Foundation. For more information, visit http://stardust.asu.edu/.

Denise">http://stardust.asu.edu/">http://stardust.asu.edu/. D. Resnik, denise">mailto:denise@resnikpr.com">denise@resnikpr.com
(602) 956-8834
Denise Resnik and Associates 

Wendy Craft

Marketing and communications manager, Business and Finance Communications Group