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
How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH
A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)
An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.
Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...
Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.
Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...
Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.
As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...
Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.
With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...
Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine
Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...
19.06.2017 | Event News
13.06.2017 | Event News
13.06.2017 | Event News
23.06.2017 | Physics and Astronomy
23.06.2017 | Physics and Astronomy
23.06.2017 | Information Technology