Combined molecular study techniques reveal more about DNA proteins

March 2, 2011

Illinois researchers have combined two molecular imaging technologies to create an instrument with incredible sensitivity that provides new, detailed insight into dynamic molecular processes.

Physics professors Taekjip Ha and Yann Chemla and combined their expertise in single-molecule biophysics – fluorescence microscopy and optical traps, respectively – to study binding and unbinding of individual DNA segments to a larger strand. They and their joint postdoctoral researcher Matthew Comstock detail their technique in a paper published in the Feb. 20 online edition of Nature Methods.

Both professors have particularly studied proteins and enzymes that regulate DNA, such as the enzyme helicase that unwinds DNA for duplication or transcription to RNA. Fluorescent microscopy techniques allow researchers to observe proteins as they conform and move, but often lack the spatial range to track the protein's motion over distance.

Optical traps, meanwhile, enable researchers to study a protein's translocation, but not its conformation. Chemla compares traditional optical traps to fishing. A single molecule of DNA is tethered between two attachment points, and the activity of a bound to it is only inferred from how it tugs on the tether, much like a fish at the end of a line. This can reveal a lot about a protein's activity and motion, but the technique has glaring limitations as well. For example, it is difficult to know how many proteins or the types of proteins that are involved.

"Also, these proteins may do all sorts of things beyond tugging on our line that we may not be sensitive to," Chemla said. "Fluorescence allows you to have an additional readout to actually see these things, and the key is that we can now measure them simultaneously. This work was a real synthesis of the expertise of two groups at the Center for the Physics of Living Cells at the U. of I."

The combination allows Chemla, Ha and their group to measure both a protein's motion – sensitive to translocation as small as one base pair, a distance of only a few angstroms – and also conformational changes as it acts. This can reveal details about its mechanism that would not have been accessible before.

"It was a major technical challenge, but the final product is a one-of-a-kind instrument with unique capabilities," Chemla said. "It's like taking a rudimentary, real-time 'movie' of what individual molecules are doing."

Explore further: Molecule by molecule, new assay shows real-time gene activity

More information: "Ultrahigh-Resolution Optical Trap With Single-Fluorophore Sensitivity," www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1574.html

Related Stories

Molecule by molecule, new assay shows real-time gene activity

March 15, 2006

Chemists at Harvard University have developed the first technique providing a real-time, molecule-by-molecule "movie" of protein production in live cells. Their direct observation of fluorescently tagged molecules in single ...

FSU researchers make observing cell functions easier

May 8, 2008

Now that the genome (DNA) of humans and many other organisms have been sequenced, biologists are turning their attention to discovering how the many thousands of structural and control genes -- the “worker bees” of living ...

Using a light touch to measure protein bonds

June 30, 2008

MIT researchers have developed a novel technique to measure the strength of the bonds between two protein molecules important in cell machinery: Gently tugging them apart with light beams.

Team finds a better way to watch bacteria swim

October 4, 2009

Researchers have developed a new method for studying bacterial swimming, one that allows them to trap Escherichia coli bacteria and modify the microbes' environment without hindering the way they move.

Recommended for you

Genomes uncover life's early history

August 24, 2015

A University of Manchester scientist is part of a team which has carried out one of the biggest ever analyses of genomes on life of all forms.

Rare nautilus sighted for the first time in three decades

August 25, 2015

In early August, biologist Peter Ward returned from the South Pacific with news that he encountered an old friend, one he hadn't seen in over three decades. The University of Washington professor had seen what he considers ...

Why a mutant rice called Big Grain1 yields such big grains

August 24, 2015

(Phys.org)—Rice is one of the most important staple crops grown by humans—very possibly the most important in history. With 4.3 billion inhabitants, Asia is home to 60 percent of the world's population, so it's unsurprising ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.