Featured Research

from universities, journals, and other organizations

Scientists use blur to sharpen DNA mapping

October 9, 2013
Rice University
Researchers have found a simple way to pinpoint the location of specific sequences along single strands of DNA, a technique that could someday help diagnose genetic diseases.

Bright spots captured by a camera in a new technique called mbPAINT, developed at Rice University, helped researchers pinpoint the specific location of a short, known DNA sequence along a single strand of DNA. The technique may someday help find mutations suspected in genetic diseases.
Credit: Landes Lab/Rice University

With high-tech optical tools and sophisticated mathematics, Rice University researchers have found a way to pinpoint the location of specific sequences along single strands of DNA, a technique that could someday help diagnose genetic diseases.

Proof-of-concept experiments in the Rice lab of chemist Christy Landes identified DNA sequences as short as 50 nucleotides at room temperature, a feat she said is impossible with standard microscopes that cannot see targets that small, or electron microscopes that require targets to be in a vacuum or cryogenically frozen.

The technique called "super-localization microscopy" has been known for a while, Landes said, but its application in biosensing is just beginning. Scientists have seen individual double-stranded DNA molecules under optical microscopes for years, but the ability to see single-stranded DNA is a new achievement, and breaking the diffraction limit of light adds value, she said.

The work by Landes, Rice postdoctoral associate Jixin Chen and undergraduate student Alberto Bremauntz is detailed in the American Chemical Society journal Applied Materials and Interfaces.

The Rice researchers call their super-resolution technique "motion blur point accumulation for imaging in nanoscale topography" (mbPAINT). With it, they resolved structures as small as 30 nanometers (billionths of a meter) by making, essentially, a movie of fluorescent DNA probes flowing over a known target sequence along an immobilized single strand of DNA.

The probes are labeled with a fluorescent dye that lights up only when attached to the target DNA. In the experimental setup, most would flow by unseen, but some would bind to the target for a few milliseconds, just long enough to be captured by the camera before the moving liquid pulled them away. Processing images of these brief events amidst the background blur allows the researchers to image objects smaller than the natural diffraction limits of light-based imaging, which do not allow for the resolution of targets smaller than the wavelength of light used to illuminate them.

Even the Landes lab's system is subject to these physical limitations. Individual images of fluorescing probes on targets are just a pixelated blur. But it's a blur with a bright spot, and careful analysis of multiple images allows the researchers to pinpoint that spot along the strand.

"The probes are moving so fast that in real time, all we would see with the camera is a line," Chen said. But when the camera firing at 30-millisecond intervals happened to catch a bound probe, it clearly stood out. The probes sometime picked out two sequences along a strand that would have been seen as a single blur via regular fluorescent microscopy.

Landes said one goal for mbPAINT is to map ever-smaller fragments of DNA. "Eventually, we'd like to get down to a couple of nucleotides," she said. "Some diseases are characterized by one amino acid mutation, which is three nucleotides, and there are many diseases associated with very small genetic mutations that we'd like to be able to identify.

"We're thinking this method will be ideally suited for diseases associated with small, localized mutations that are not possible to detect in any other inexpensive way," she said.

Landes sees mpPAINT as not only more cost-effective but also able to capture information electron microscopes cannot.

"One of the reasons people invented electron microscopy is to image objects smaller than light's diffraction limit, because biomolecules such as proteins and DNAs are smaller than that," she said. "But electron microscopy requires cryogenic temperatures or a vacuum. You can't easily watch things react in solution.

"The advent of this technology allows us to see the biological processes of nano-sized objects as they happen in water, with buffers and salts, at room temperature, at body temperature or even in a cell. It's very exciting," Landes said.

Story Source:

The above story is based on materials provided by Rice University. Note: Materials may be edited for content and length.

Journal Reference:

  1. Jixin Chen, Alberto Bremauntz, Lydia Kisley, Bo Shuang, Christy F. Landes. Super-Resolution mbPAINT for Optical Localization of Single-Stranded DNA. ACS Applied Materials & Interfaces, 2013; 5 (19): 9338 DOI: 10.1021/am403984k

Cite This Page:

Rice University. "Scientists use blur to sharpen DNA mapping." ScienceDaily. ScienceDaily, 9 October 2013. <www.sciencedaily.com/releases/2013/10/131009111151.htm>.
Rice University. (2013, October 9). Scientists use blur to sharpen DNA mapping. ScienceDaily. Retrieved August 1, 2014 from www.sciencedaily.com/releases/2013/10/131009111151.htm
Rice University. "Scientists use blur to sharpen DNA mapping." ScienceDaily. www.sciencedaily.com/releases/2013/10/131009111151.htm (accessed August 1, 2014).

Share This

More Health & Medicine News

Friday, August 1, 2014

Featured Research

from universities, journals, and other organizations

Featured Videos

from AP, Reuters, AFP, and other news services

House Republicans Vote to Sue Obama Over Healthcare Law

House Republicans Vote to Sue Obama Over Healthcare Law

Reuters - US Online Video (July 31, 2014) The Republican-led House of Representatives votes to sue President Obama, accusing him of overstepping his executive authority in making changes to the Affordable Care Act. Mana Rabiee reports. Video provided by Reuters
Powered by NewsLook.com
Despite Health Questions, E-Cigs Are Beneficial: Study

Despite Health Questions, E-Cigs Are Beneficial: Study

Newsy (July 31, 2014) Citing 81 previous studies, new research out of London suggests the benefits of smoking e-cigarettes instead of regular ones outweighs the risks. Video provided by Newsy
Powered by NewsLook.com
Dangerous Bacteria Kills One in Florida

Dangerous Bacteria Kills One in Florida

AP (July 31, 2014) Sarasota County, Florida health officials have issued a warning against eating raw oysters and exposing open wounds to coastal and inland waters after a dangerous bacteria killed one person and made another sick. (July 31) Video provided by AP
Powered by NewsLook.com
Health Insurers' Profits Slide

Health Insurers' Profits Slide

Reuters - Business Video Online (July 30, 2014) Obamacare-related costs were said to be behind the profit plunge at Wellpoint and Humana, but Wellpoint sees the new exchanges boosting its earnings for the full year. Fred Katayama reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.


Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News


Free Subscriptions

Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile

Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?

Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins