scholarly journals Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mateusz Mieczkowski ◽  
Christian Steinmetzger ◽  
Irene Bessi ◽  
Ann-Kathrin Lenz ◽  
Alexander Schmiedel ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Base Pair ◽  
Fluorescent Proteins ◽  
Stokes Shift ◽  
Fluorescence Emission ◽  
Rna Aptamers ◽  
Rna Aptamer ◽  
Time Resolved ◽  
Large Stokes Shift ◽  
Mechanistic Basis

AbstractFluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.

scholarly journals Structure–fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer

2019 ◽  
Author(s):  
Christian Steinmetzger ◽  
Irene Bessi ◽  
Ann-Kathrin Lenz ◽  
Claudia Höbartner
Keyword(s):  
Ligand Binding ◽  
Fluorescent Protein ◽  
Stokes Shift ◽  
Fluorescence Emission ◽  
Titration Calorimetry ◽  
Rna Aptamer ◽  
Large Stokes Shift ◽  
Molecular Features ◽  
G Quadruplex ◽  
Derivatives Of

Abstract The Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal key structure–fluorescence activation relationships (SFARs). The ligands under investigation form two categories with emission maxima of ∼540 or ∼590 nm, respectively, and bind with affinities in the nanomolar to low-micromolar range. Isothermal titration calorimetry was used to elucidate the enthalpic and entropic contributions to binding affinity for a cationic ligand that is unique to the Chili aptamer. In addition to fluorescence activation, ligand binding was also observed by NMR spectroscopy, revealing characteristic signals for the formation of a G-quadruplex only upon ligand binding. These data shed light on the molecular features required and responsible for the large Stokes shift and the strong fluorescence enhancement of red and green emitting RNA–chromophore complexes.

Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase

2021 ◽  
Vol 143 (37) ◽  
pp. 15091-15102
Author(s):  
Elizabeth M. Santos ◽  
Wei Sheng ◽  
Rahele Esmatpour Salmani ◽  
Setare Tahmasebi Nick ◽  
Alireza Ghanbarpour ◽  
...  
Keyword(s):  
Excited State ◽  
Proton Transfer ◽  
Fluorescent Proteins ◽  
Stokes Shift ◽  
Large Stokes Shift ◽  
Excited State Proton Transfer

Deciphering the grounds of the suitability of acylhydrazones as efficient photoswitches

2019 ◽  
Vol 21 (29) ◽  
pp. 16075-16082 ◽  
Author(s):  
Miquel Moreno ◽  
Ricard Gelabert ◽  
José M. Lluch
Keyword(s):  
Proton Transfer ◽  
Stokes Shift ◽  
Intramolecular Proton Transfer ◽  
Large Stokes Shift

Calculations on several acylhydrazones are carried out to explain their diverse photochemistry experimentally observed. Results disclose the role of the intramolecular proton transfer or the loss of the azidic proton in the large Stokes shift.

Mechanism Behind the Apparent Large Stokes Shift in LSSmOrange Investigated by Time-Resolved Spectroscopy

2015 ◽  
Vol 119 (47) ◽  
pp. 14880-14891 ◽  
Author(s):  
Eduard Fron ◽  
Herlinde De Keersmaecker ◽  
Susana Rocha ◽  
Yannick Baeten ◽  
Gang Lu ◽  
...  
Keyword(s):  
Stokes Shift ◽  
Time Resolved ◽  
Time Resolved Spectroscopy ◽  
Large Stokes Shift

scholarly journals Engineering ESPT Pathways Based on Structural Analysis of LSSmKate Red Fluorescent Proteins with Large Stokes Shift

2010 ◽  
Vol 132 (31) ◽  
pp. 10762-10770 ◽  
Author(s):  
Kiryl D. Piatkevich ◽  
Vladimir N. Malashkevich ◽  
Steven C. Almo ◽  
Vladislav V. Verkhusha
Keyword(s):  
Structural Analysis ◽  
Fluorescent Proteins ◽  
Stokes Shift ◽  
Large Stokes Shift ◽  
Red Fluorescent Proteins

scholarly journals Orange Fluorescent Proteins: Filling the Spectral Gap

2014 ◽  
Vol 70 (a1) ◽  
pp. C1670-C1670
Author(s):  
Sergei Pletnev ◽  
Daria Shcherbakova ◽  
Oksana Subach ◽  
Vladimir Malashkevich ◽  
Steven Almo ◽  
...  
Keyword(s):  
In Vivo Imaging ◽  
Spectral Properties ◽  
Molecular Mechanisms ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Stokes Shift ◽  
Emission Wavelength ◽  
Microscopy Imaging ◽  
Large Stokes Shift

Fluorescent proteins (FPs) have become valuable tools for molecular biology, biochemistry, medicine, and cancer research. Starting from parent green fluorescent protein (GFP), most challenging task of the FPs studies was the development of FPs with longer excitation/emission wavelength. This pursuit was motivated by advantages of so-called red-shifted FPs, namely, lower background of cellular autofluorescence in microscopy, lower light scattering and reduced tissue absorbance of longer wavelengths for in vivo imaging. In addition to FPs with regular spectral properties, there are proteins of other types available, including FPs with a large Stokes shift and photoconvertible FPs. These special kinds of FPs have become useful in super-resolution microscopy, imaging of enzyme activities, protein-protein interactions, photolabeling, and in vivo imaging. According to their emission wavelength, red-shifted FPs could be divided in the following groups: 520-540 nm yellow FPs (YFPs), 540-570 nm orange FPs (OFPs), 570-620 nm red FPs (RFPs), and > 620 nm far-RFPs. Red shift of the excitation/emission bands of these FPs is predominantly achieved by extension of the conjugated system of the chromophore and its protonation/deprotonation. The variety of spectral properties of FPs (excitation and emission wavelength, quantum yield, brightness, photo- and pH- stability, photoconversion, large Stokes shift, etc) results from the different chromophore structures and its interactions with surrounding amino acid residues. In this work we focus on structural studies and molecular mechanisms of FPs with orange emission.

scholarly journals A Multicolor Large Stokes Shift Fluorogen‐Activating RNA Aptamer with Cationic Chromophores

2019 ◽  
Vol 25 (8) ◽  
pp. 1931-1935 ◽  
Author(s):  
Christian Steinmetzger ◽  
Navaneethan Palanisamy ◽  
Kiran R. Gore ◽  
Claudia Höbartner
Keyword(s):  
Stokes Shift ◽  
Rna Aptamer ◽  
Large Stokes Shift

scholarly journals An NIR-emitting lysosome-targeting probe with large Stokes shift via coupling cyanine and excited-state intramolecular proton transfer

2017 ◽  
Vol 53 (26) ◽  
pp. 3697-3700 ◽  
Author(s):  
Dipendra Dahal ◽  
Lucas McDonald ◽  
Xiaoman Bi ◽  
Chathura Abeywickrama ◽  
Farai Gombedza ◽  
...  
Keyword(s):  
Excited State ◽  
Proton Transfer ◽  
Stokes Shift ◽  
Intramolecular Proton Transfer ◽  
Large Stokes Shift

A NIR-emitting probe with a large Stokes shift (Δλ ≈ 234 nm) can selectively show lysosome organelles without exhibiting “an alkalinizing effect”.

A novel 2-(2′-aminophenyl)benzothiazole derivative displays ESIPT and permits selective detection of Zn2+ ions: experimental and theoretical studies

RSC Advances ◽  
2016 ◽  
Vol 6 (75) ◽  
pp. 71496-71500 ◽  
Author(s):  
Subramaniyan Janakipriya ◽  
Selvaraj Tamilmani ◽  
Sathiah Thennarasu
Keyword(s):  
Excited State ◽  
Proton Transfer ◽  
Stokes Shift ◽  
Intramolecular Proton Transfer ◽  
Theoretical Studies ◽  
Selective Detection ◽  
Large Stokes Shift ◽  
Benzothiazole Derivative ◽  
Experimental And Theoretical Studies

Synthesis of a novel 2-(2′-aminophenyl)benzothiazole based probe (1) and demonstration of excited state intramolecular proton transfer (ESIPT) with a large Stokes shift (∼246 nm) are presented.

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