Imaging Intracellular S-Adenosyl Methionine Dynamics in Live Mammalian Cells with a Genetically Encoded Red Fluorescent RNA-Based Sensor DOI
Xing Li, Liuting Mo, Jacob L. Litke

et al.

Journal of the American Chemical Society, Journal Year: 2020, Volume and Issue: 142(33), P. 14117 - 14124

Published: July 22, 2020

To understand the role of intracellular metabolites in cellular processes, it is important to measure dynamics and fluxes small molecules living cells. Although conventional metabolite sensors composed fluorescent proteins have been made detect some metabolites, an emerging approach use genetically encoded RNA. Because ability rapidly generate metabolite-binding RNA aptamers, RNA-based potential be designed more readily than protein-based sensors. Numerous strategies developed convert green-fluorescent Spinach or Broccoli fluorogenic aptamers into metabolite-regulated Nevertheless, red fluorescence particularly desirable because low level background However, variant aptamer, Red Broccoli, does not exhibit cells when imaged with its cognate fluorophore. It known why vitro but live mammalian Here, we develop a new fluorophore, OBI (3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime-1-benzoimidazole), which binds high affinity makes resistant thermal unfolding. We show that enables detected Furthermore, can fused S-adenosyl methionine (SAM)-binding aptamer sensor imaging SAM These results reveal functions

Language: Английский

Spectroscopy and dynamics of the hydrated electron at the water/air interface DOI Creative Commons
Caleb J. C. Jordan, Marc P. Coons, John M. Herbert

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 2, 2024

Abstract The hydrated electron, e – (aq) , has attracted much attention as a central species in radiation chemistry. However, less is known about at the water/air surface, despite its fundamental role electron transfer processes interfaces. Using time-resolved electronic sum-frequency generation spectroscopy, spectrum of interface and dynamics are measured here, following photo-oxidation phenoxide anion. spectral maximum agrees with that for bulk shows orbital density resides predominantly within aqueous phase, agreement supporting calculations. In contrast, chemistry interfacial differs from water, diffusing into leaving phenoxyl radical surface. Our work resolves long-standing questions highlights potential ubiquitous interface.

Language: Английский

Citations

21
Stimulated emission depletion microscopy DOI
Gražvydas Lukinavičius, Jonatan Alvelid, Rūta Gerasimaitė

et al.

Nature Reviews Methods Primers, Journal Year: 2024, Volume and Issue: 4(1)

Published: Aug. 8, 2024

Language: Английский

Citations

16
Analytical Derivative Coupling for Multistate CASPT2 Theory DOI
Jae Woo Park, Toru Shiozaki

Journal of Chemical Theory and Computation, Journal Year: 2017, Volume and Issue: 13(6), P. 2561 - 2570

Published: May 4, 2017

The probability of non-radiative transitions in photochemical dynamics is determined by the derivative couplings, couplings between different electronic states through nuclear degrees freedom. Efficient and accurate evaluation is, therefore, central importance to realize reliable computer simulations reactions. In this work, for multistate multireference second-order perturbation theory (MS-CASPT2) its 'extended' variant (XMS-CASPT2) are studied, which we present an algorithm their analytical evaluation. computational costs evaluating essentially same as those calculating energy gradients. geometries energies calculated with XMS-CASPT2 small molecules at minimum conical intersections (MECIs) good agreement computed configuration interaction. As numerical examples, MECIs optimized using stilbene a GFP model chromophore (the 4-para-hydroxybenzylidene-1,2-dimethyl-imidazolin-5-one anion).

Language: Английский

Citations

146
Fluorescent Probes for Nanoscopic Imaging of Mitochondria DOI Creative Commons
Soham Samanta, Ying He, Amit Sharma

et al.

Chem, Journal Year: 2019, Volume and Issue: 5(7), P. 1697 - 1726

Published: April 18, 2019

Language: Английский

Citations

129
Genetically encoded fluorescent tags DOI Creative Commons
Kurt S. Thorn

Molecular Biology of the Cell, Journal Year: 2017, Volume and Issue: 28(7), P. 848 - 857

Published: March 30, 2017

Genetically encoded fluorescent tags are protein sequences that can be fused to a of interest render it fluorescent. These have revolutionized cell biology by allowing nearly any imaged light microscopy at submicrometer spatial resolution and subsecond time in live or organism. They also used measure abundance thousands millions cells using flow cytometry. Here I provide an introduction the different genetic available, including both intrinsically proteins derive their fluorescence from binding either endogenous exogenous fluorophores. discuss optical biological properties guidelines for choosing appropriate experiment. Tools tagging nucleic acid reporter molecules detect presence biomolecules briefly discussed.

Language: Английский

Citations

118
Electrostatic control of photoisomerization pathways in proteins DOI Open Access
Matthew G. Romei, Chi‐Yun Lin, Irimpan I. Mathews

et al.

Science, Journal Year: 2020, Volume and Issue: 367(6473), P. 76 - 79

Published: Jan. 3, 2020

Electrostatics guide chromophore twist Photoisomerization—the twisting of bonds in a molecule response to absorption light—is exploited biology sense light and can influence the photophysical properties fluorescent proteins used imaging applications. Romei et al. studied this behavior by introducing unnatural amino acids into photoswitchable green protein Dronpa2, thus systematically altering electronic (see Perspective Hu ). Crystal structures spectroscopic analyses series these variants support model which electrostatic interactions between its environment barrier heights for around different during photoisomerization. These insights may future design with desired properties. Science , issue p. 76 ; see also 26

Language: Английский

Citations

105
Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science DOI Open Access
Anna I. Krylov, Theresa L. Windus, Taylor Barnes

et al.

The Journal of Chemical Physics, Journal Year: 2018, Volume and Issue: 149(18)

Published: Nov. 8, 2018

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding phenomena that underlie and control chemical processes, which is manifested in a large number community software projects codes. CMS now poised take next transformative steps better training modern design engineering methods tools, increasing interoperability through more systematic adoption agreed upon standards accepted best-practices, overcoming unnecessary redundancy effort along with greater reproducibility, deployment new onto hardware platforms from in-house clusters mid-range computing systems supercomputers. This turn will have future impact on be created address grand challenge science we illustrate here: formulation diverse catalysts, descriptions long-range charge excitation transfer, development structural ensembles for intrinsically disordered proteins.

Language: Английский

Citations

96
Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy DOI
Fadi M. Jradi, Luke D. Lavis

ACS Chemical Biology, Journal Year: 2019, Volume and Issue: 14(6), P. 1077 - 1090

Published: April 17, 2019

Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing “super-resolution” fluorescence below the diffraction limit light. The past decade seen an explosion not only optical hardware for SMLM but also development or repurposing fluorescent proteins and small-molecule probes this technique. In review, written by chemists chemists, we detail history collate collection with demonstrated utility SMLM. We hope it will serve as primer probe choice well inspiration new fluorophores that enable imaging samples exquisite detail.

Language: Английский

Citations

95
A critical comparison of lanthanide based upconversion nanoparticles to fluorescent proteins, semiconductor quantum dots, and carbon dots for use in optical sensing and imaging DOI
Sandy F. Himmelstoß, Thomas Hirsch

Methods and Applications in Fluorescence, Journal Year: 2019, Volume and Issue: 7(2), P. 022002 - 022002

Published: March 1, 2019

The right choice of a fluorescent probe is essential for successful luminescence imaging and sensing especially concerning in vivo vitro applications, the development new classes have gained more attention last years. One most promising class are upconversion nanoparticles (UCNPs)—inorganic nanocrystals capable to convert near-infrared light high energy radiation. In this review we will compare UCNPs with other probes terms (a) optical properties probes, such as their brightness, photostability excitation wavelength; (b) chemical dispersibility, stability under experimental or physiological conditions, availability modification strategies labelling; (c) potential toxicity biocompatibility probe. Thereby want provide better understanding advantages drawbacks address future challenges design nanocrystals.

Language: Английский

Citations

78
Artificial-Intelligence-Enhanced On-the-Fly Simulation of Nonlinear Time-Resolved Spectra DOI
Sebastian V. Pios, Maxim F. Gelin, Arif Ullah

et al.

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(9), P. 2325 - 2331

Published: Feb. 22, 2024

Time-resolved spectroscopy is an important tool for unraveling the minute details of structural changes in molecules biological and technological significance. The nonlinear femtosecond signals detected such systems must be interpreted, but it a challenging task which theoretical simulations are often indispensable. Accurate transient absorption or two-dimensional electronic spectra are, however, computationally very expensive, prohibiting wider adoption existing first-principles methods. Here, we report artificial-intelligence-enhanced protocol to drastically reduce computational cost simulating time-resolved spectra, makes affordable polyatomic increasing size. based on doorway–window approach on-the-fly surface-hopping simulations. We show its applicability prototypical molecule pyrazine produces with high precision respect ab initio reference while cutting by at least 95% compared pure

Language: Английский

Citations

14