“The lock and key mechanism explains why this particular lead-specific DNAzyme makes such a sensitive and selective sensor,” said U. of I. chemistry professor Yi Lu, a corresponding author of a paper accepted for publication in Nature Chemical Biology, and posted on the journal’s Web site.
“Understanding the relationship between conformational change and reaction is important in obtaining deeper insight into how DNAzymes work and for designing more efficient sensors,” said Lu, who also is a researcher in the university’s department of biochemistry, the Beckman Institute, and the Center of Advanced Materials for the Purification of Water with Systems.
In the early 1980s, RNA molecules that can catalyze enzymatic reactions were discovered and named ribozymes. This discovery was followed by demonstrations in the 1990s that DNA also can act as enzymes, termed deoxyribozymes or DNAzymes.
With only four nucleotides as building blocks, versus 20 in proteins, nucleic acid enzymes may need to recruit cofactors (helper molecules) to perform some functions. Metal ions are a natural choice, and indeed most nucleic acid enzymes require metal ions for function under physiological conditions (and therefore are called metalloenzymes).
Metalloenzymes use various modes for functions for which metal-dependent conformational change (induced fit) is required in some cases but not in others (lock and key). In contrast, most ribozymes require conformation change that almost always precedes the enzyme reactions.
Using an extremely sensitive measurement technique called single-molecule fluorescence resonance energy transfer, Lu, physics professor Taekjip Ha and their research team studied the metal-dependent conformational change and cleavage activity of a particular lead-sensitive DNAzyme.
In single-molecule fluorescence resonance energy transfer, researchers add two dye molecules – one green and one red – to the molecule they want to study. Then they excite the green dye with a laser. Some of the energy moves from the green dye to the red dye, depending upon the distance between them.
“The changing ratio of the two intensities indicates the relative movement of the two dyes,” said Ha, who also is an affiliate of the university’s Institute for Genomic Biology and of the Howard Hughes Medical Institute. “By monitoring the brightness of the two dyes, we can measure conformational changes with nanometer precision.”
The researchers found that, in the presence of zinc or magnesium, a conformational change took place in the DNAzyme, followed by a cleavage reaction (behavior similar to many proteins and ribozymes). In the presence of lead, however, the cleavage reaction occurred without a preceding conformational change.
“This presents very strong evidence that the lead-specific enzyme uses the lock and key reaction mechanism,” Lu said. “This DNAzyme appears to be prearranged to accept lead for the activity.”
In previous work, Lu and his research group fashioned highly sensitive and selective fluorescent, colorimetric and magnetic resonance imaging sensors from the lead-specific DNAzyme used in this study. They have also constructed simple, disposable sensors using a different, uranium-specific DNAzyme.
“We think the answer to faster, more sensitive sensors lies with the lock and key mechanism,” Lu said. “Our next step is to look for other metals that use the lock and key mechanism with other specific DNAzymes. In addition, we want to investigate the structural details at the metal-binding sites and see how they change during catalysis.”
James E. Kloeppel | EurekAlert!
What happens in the cell nucleus after fertilization
06.12.2016 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt
Researchers uncover protein-based “cancer signature”
05.12.2016 | Universität Basel
Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...
A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.
Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...
In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.
“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...
The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.
The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...
Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water
In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...
16.11.2016 | Event News
01.11.2016 | Event News
14.10.2016 | Event News
06.12.2016 | Health and Medicine
06.12.2016 | Life Sciences
05.12.2016 | Power and Electrical Engineering