Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting

2008 ◽  
Vol 3 (2) ◽  
pp. 288-302 ◽  
Author(s):  
Inna Shcherbakova ◽  
Michael Brenowitz
Keyword(s):  
Nucleic Acids ◽  
Hydroxyl Radical ◽  
Time Resolution ◽  
Structural Changes ◽  
Hydroxyl Radical Footprinting

Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting

The Analyst ◽  
2018 ◽  
Vol 143 (4) ◽  
pp. 798-807 ◽  
Author(s):  
Emily E. Chea ◽  
Lisa M. Jones
Keyword(s):  
Nucleic Acids ◽  
Hydroxyl Radical ◽  
Live Cells ◽  
Cellular Environment ◽  
Hydroxyl Radical Footprinting

Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins in live cells.

scholarly journals Mapping Functionally Important Motifs SPF and GGQ of the Decoding Release Factor RF2 to theEscherichia coliRibosome by Hydroxyl Radical Footprinting

2002 ◽  
Vol 278 (17) ◽  
pp. 15095-15104 ◽  
Author(s):  
Debbie-Jane G. Scarlett ◽  
Kim K. McCaughan ◽  
Daniel N. Wilson ◽  
Warren P. Tate
Keyword(s):  
Hydroxyl Radical ◽  
Release Factor ◽  
Hydroxyl Radical Footprinting

scholarly journals Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

2018 ◽  
Vol 13 (11) ◽  
pp. 2535-2556 ◽  
Author(s):  
Alexey K. Shaytan ◽  
Hua Xiao ◽  
Grigoriy A. Armeev ◽  
Daria A. Gaykalova ◽  
Galina A. Komarova ◽  
...  
Keyword(s):  
High Resolution ◽  
Hydroxyl Radical ◽  
Structural Interpretation ◽  
Hydroxyl Radical Footprinting

scholarly journals First steps towards time-resolved 'in-house' X-ray diffraction experiments

2014 ◽  
Vol 70 (a1) ◽  
pp. C775-C775 ◽  
Author(s):  
Radoslaw Kaminski ◽  
Jason Benedict ◽  
Elzbieta Trzop ◽  
Katarzyna Jarzembska ◽  
Bertrand Fournier ◽  
...  
Keyword(s):  
Excited State ◽  
Time Resolution ◽  
Structural Changes ◽  
Laser Pulses ◽  
High Repetition Rate ◽  
X Ray Diffraction ◽  
Laboratory Equipment ◽  
Time Resolved ◽  
X Ray ◽  
Ligand Charge Transfer

High-intensity X-ray sources, such as synchrotrons or X-ray free electron lasers, providing up to 100 ps time-resolution allow for studying very short-lived excited electronic states in molecular crystals. Some recent examples constitute investigations of Rh...Rh bond shortening,[1] or metal-to-ligand charge transfer processes in CuI complexes.[2] Nevertheless, in cases in which the lifetime of excited state species exceeds 10 μs it is now possible, due to the dramatic increase in the brightness of X-ray sources and the sensitivity of detectors, to use laboratory equipment to explore structural changes upon excitation. Consequently, in this contribution we present detailed technical description of the 'in-house' X-ray diffraction setup allowing for the laser-pump X-ray-probe experiments within the time-resolution at the order of 10 μs or larger. The experimental setup consists of a modified Bruker Mo-rotating-anode diffractometer, coupled with the high-frequency Nd:YAG laser (λ = 355 nm). The required synchronization of the laser pulses and the X-ray beam is realized via the optical chopper mounted across the beam-path. Chopper and laser capabilities enable high-repetition-rate experiments reaching up to 100 kHz. In addition, the laser shutter is being directly controlled though the original diffractometer software, allowing for collection of the data in a similar manner as done at the synchrotron (alternating light-ON & light-OFF frames). The laser beam itself is split into two allowing for improved uniform light delivery onto the crystal specimen. The designed setup was tested on the chosen set of crystals exhibiting rather long-lived excited state, such as, the Cu2Br2L2 (L = C5H4N-NMe2) complex, for which the determined lifetime is about 100 μs at 90 K. The results shall be presented. Research is funded by the National Science Foundation (CHE1213223). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.

scholarly journals Quick-EXAFS setup at the SuperXAS beamline forin situX-ray absorption spectroscopy with 10 ms time resolution

2016 ◽  
Vol 23 (1) ◽  
pp. 260-266 ◽  
Author(s):  
Oliver Müller ◽  
Maarten Nachtegaal ◽  
Justus Just ◽  
Dirk Lützenkirchen-Hecht ◽  
Ronald Frahm
Keyword(s):  
Absorption Spectra ◽  
Absorption Spectroscopy ◽  
Time Resolution ◽  
Structural Changes ◽  
Oscillation Period ◽  
Low Noise ◽  
Bragg Angle ◽  
Absorption Data ◽  
Quick Exafs ◽  
Paul Scherrer

The quick-EXAFS (QEXAFS) method adds time resolution to X-ray absorption spectroscopy (XAS) and allows dynamic structural changes to be followed. A completely new QEXAFS setup consisting of monochromator, detectors and data acquisition system is presented, as installed at the SuperXAS bending-magnet beamline at the Swiss Light Source (Paul Scherrer Institute, Switzerland). The monochromator uses Si(111) and Si(311) channel-cut crystals mounted on one crystal stage, and remote exchange allows an energy range from 4.0 keV to 32 keV to be covered. The spectral scan range can be electronically adjusted up to several keV to cover multiple absorption edges in one scan. The determination of the Bragg angle close to the position of the crystals allows high-accuracy measurements. Absorption spectra can be acquired with fast gridded ionization chambers at oscillation frequencies of up to 50 Hz resulting in a time resolution of 10 ms, using both scan directions of each oscillation period. The carefully developed low-noise detector system yields high-quality absorption data. The unique setup allows both state-of-the-art QEXAFS and stable step-scan operation without the need to exchange whole monochromators. The long-term stability of the Bragg angle was investigated and absorption spectra of reference materials as well as of a fast chemical reaction demonstrate the overall capabilities of the new setup.

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