Biophysics
The basic question of how strands of nucleic acids (DNA and RNA) fold and hybridize has been studied thoroughly by biophysicists around the globe. In particular, there can be unexpected challenges in obtaining accurate kinetic data when studying the physics of how DNA and RNA fold and unfold at the single molecule level. One problem comes from temporal camera blur, as the cameras used to capture single聽photons emitted by these molecules do so in a finite time window that can blur the image and thereby skew the kinetics. In a paper published in the Journal of Physical Chemistry B, JILA Fellow David Nesbitt, and first author David Nicholson, propose an extremely simple yet broadly effective way to overcome this camera blur.
Most researchers would agree that it is much easier to write a paper聽about an observed effect than a paper proving the nonexistence of the effect when it is not observed. NIST JILA Fellow Ralph Jimenez found this to be the case聽in contributing to a recent paper published in Physical Review Applied. The authors of this paper were originally hoping to observe the increased efficiency in two-photon absorption, a special type of process used in microscopy of living tissue, that had been reported by other research labs. This increased efficiency would be determined by an additional absorption signal than the one being produced by classical light. This additional signal came from using entangled photons. Instead, Jimenez and his team of collaborators from NIST found no additional signal in their measurements, indicating a lack of absorption entirely from the entangled photons.
In a new paper, JILA physicist Thomas Perkins collaborated with CU Biochemistry Prof. Marcello Sousa to dissect the mechanisms of how certain bacteria become more virulent. The research brings together the Perkins lab expertise in single-molecule studies and the Sousa lab expertise in the type III secretion system, a key component of Salmonella bacteria.
A protein's function within a cell relies on how it folds, unfolds, and refolds. Using atomic force microscopy tools, the Perkins Group can precisely measure the free energy it takes to unfold and refold a few amino acids in the protein, which opens the door to making more precise measurements and alterations to a cell's membrane proteins.
Fluorescence and dyes are great tools to study cells, proteins, bacteria, or DNA. But scientists need to efficiently sort out the glowing material from the non-glowing stuff in their samples. The Jimenez Lab and the JILA Electronics Shop teamed up to create an improved flow cytometry system which can not only sort fluorescent material faster, it can sort by fluorescence lifetime and brightness faster than a commercially available system.
Researchers at JILA have developed a fast, simple method to prepare samples that enhances DNA imaging. The results are so clear that the double-helix shape of DNA can be seen clearly.
JILA researchers have demonstrated a much easier, faster and more precise way to understand the structure and function of the HIV RNA molecule, especially the HIV RNA hairpin. Furthermore, the techniques developed for this research promise to allow a wider range of users to study similar biological molecules, as they are built upon commercially available and user-friendly atomic force microscopes, or AFMs.
The actors are molecules. The plot, broken molecular bonds. JILA Fellow Ralph Jimenez and a team of detector experts at the National Institute of Standards and Technology (NIST) are working together to make X-ray movies of a molecular drama. The team at NIST built a microcalorimeter X-ray spectrometer capable of performing time-resolved spectroscopy; in other words: a camera to film molecules. They use this camera to learn how molecules break their bonds 鈥撀燿o the 颅electrons rearrange, do the other atoms quake?
JILA Fellows Dr. Tom Perkins and Dr. Konrad Lehnert both received medals from the Department of Commerce last night at the Ronald Reagan Amphitheater in Washington, D.C. Dr. Perkins received the Gold Medal, which is the highest honorary award given by the United States Department of Commerce, or DOC. Perkins was recognized for creating the world鈥檚 best atomic force microscope tailored to biological measurements. This device can 鈥済rab鈥 onto biological molecules, such as proteins, and measure the tiny forces involved in their folding and unfolding.
JILA Fellow and NIST Physicist Ralph Jimenez received the 2017 Arthur S. Flemming Award for outstanding public service as a Federal employee. Jimenez was one of 12 honorees across all parts of the Federal government to receive the Flemming Award this cycle. Jimenez was a winner in the Applied Science and Engineering category for his聽pioneering research聽on combining microfluidics, ultrafast lasers, biochemistry and molecular biology to dramatically accelerate the creation and characterization of specialized biomolecules to serve as sensors within living cells.