Anyone who has ever battled a stuck zipper knows it's a good idea to see what's stuck, where and how badly -- and then to pull hard.
A Cornell research team's experiments involve the "unzipping" of single DNA molecules. By mapping the hiccups, stoppages and forces along the way, they have gained new insight into how genes are packed and expressed within cells.
The research, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” published online Jan. 11, 2009, in Nature Structural and Molecular Biology, was led by Michelle Wang, associate professor of physics and Howard Hughes Medical Institute Investigator. Collaborators on the project included physics graduate student Michael Hall and John Lis, the Barbara McClintock Professor of Molecular Biology and Genetics.
DNA – the molecules that contain genetic information – are nucleic acids often illustrated as long, thin strands of double helices. DNA fits inside cell nuclei by being wound like thread around proteins called histones, forming tightly packed bundles called nucleosomes. But that same DNA must often be uncoiled and accessed by such enzymes as RNA polymerase, which the researchers liken to a motor because it moves along the DNA in the process of gene transcription.
"There is this paradox," Lis explained. "On one hand you need compaction and the packing away of DNA. On the other hand, you need accessibility, so the cellular machines can read the information contained in the DNA."
Trying to understand what happens during that unwrapping process is at the heart of this research team's efforts. By unzipping each DNA double helix through a nucleosome using an optical trap -- a technique developed in Wang's lab -- they unwrapped strands of DNA from their histone cores, observing, with near-base pair accuracy, the interactions that took place along the way.
"Our hope is that if we can establish and understand the interactions within the nucleosome, we can begin to understand how the motor proteins can invade the nucleosome," Wang said.
Optical trapping involves a focused beam of light that can "trap" small objects. A refractive sphere is chemically attached to the DNA strand, and the optical trap moves the sphere, allowing the researchers to unzip the DNA strands apart by pulling, Hall explained. By doing so, the researchers re-created what happens in the cell when DNA uncoils from the histone core, and they measured the blips along the way -- for example, when the DNA strand had to be pulled apart from a protein molecule -- and how much force was needed to keep going.
"It's really like a zipper," Hall said. "And when there is a protein in there, it's kind of like you have a piece of cloth stuck. You know you can get it out, but you just have to pull harder, and then it pops out. That's basically the same way we can detect where the interactions are with the proteins."
The researchers have performed the first direct, precise measurements of histone-DNA interactions. Their findings could help uncover how changes to the histones or DNA sequences affect how motor proteins access genetic information in cells.
"If we have that knowledge, we can extrapolate that information to apply to different scenarios and different motor motions," Wang said.
Blaine Friedlander | Newswise Science News
Further reports about: > Cells > DNA > DNA molecules > DNA sequence > High-resolution dynamic mapping > Interaction between water and forest > Molecular > Molecular Biology > Molecules > RNA polymerase > double helices > gene transcription > genetic information > hiccups > histone-DNA interactions > nucleic acids > synthetic biology > unzipping
A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau
On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...
16.08.2017 | Event News
04.08.2017 | Event News
26.07.2017 | Event News
18.08.2017 | Life Sciences
18.08.2017 | Physics and Astronomy
18.08.2017 | Materials Sciences