“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!
Cells communicate in a dynamic code
19.02.2018 | California Institute of Technology
Studying mitosis' structure to understand the inside of cancer cells
19.02.2018 | Biophysical Society
For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.
In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...
Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale
Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...
For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.
But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...
Scientists from the University of Zurich have succeeded for the first time in tracking individual stem cells and their neuronal progeny over months within the intact adult brain. This study sheds light on how new neurons are produced throughout life.
The generation of new nerve cells was once thought to taper off at the end of embryonic development. However, recent research has shown that the adult brain...
Theoretical physicists propose to use negative interference to control heat flow in quantum devices. Study published in Physical Review Letters
Quantum computer parts are sensitive and need to be cooled to very low temperatures. Their tiny size makes them particularly susceptible to a temperature...
15.02.2018 | Event News
13.02.2018 | Event News
12.02.2018 | Event News
19.02.2018 | Materials Sciences
19.02.2018 | Materials Sciences
19.02.2018 | Life Sciences