scholarly journals Probing ligand and cation binding sites in G-quadruplex nucleic acids by mass spectrometry and electron photodetachment dissociation sequencing

The Analyst ◽  
2019 ◽  
Vol 144 (11) ◽  
pp. 3518-3524 ◽  
Author(s):  
Dababrata Paul ◽  
Adrien Marchand ◽  
Daniela Verga ◽  
Marie-Paule Teulade-Fichou ◽  
Sophie Bombard ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Ligand Binding ◽  
Binding Sites ◽  
Cation Binding ◽  
Tandem Mass ◽  
Top Down ◽  
G Quadruplex ◽  
Ligand Binding Sites ◽  
Electron Photodetachment

Tandem mass spectrometry: native top-down sequencing by electron photodetachment dissociation (EPD) reveals ligand binding sites on DNA G-quadruplexes.

scholarly journals Probing Ligand and Cation Binding Sites in G-Quadruplex Nucleic Acids by Mass Spectrometry and Electron Photodetachment Dissociation Sequencing

2019 ◽  
Author(s):  
Dababrata Paul ◽  
Adrien Marchand ◽  
Daniela Verga ◽  
Marie-Paule Teulade-Fichou ◽  
Sophie Bombard ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ligand Binding ◽  
Binding Sites ◽  
Binding Mode ◽  
Cation Binding ◽  
Potassium Cation ◽  
Telomeric Sequences ◽  
G Quadruplex ◽  
Electron Photodetachment ◽  
Noncovalent Bonds

ABSTRACTMass spectrometry provides exquisite detail on ligand and cation binding stoichiometries with a DNA target. The next important step is to develop reliable methods to determine the cation and ligand binding sites in each complex separated by the mass spectrometer. To circumvent the caveat of ligand derivatization for cross-linking, which may alter the ligand binding mode, we explored a tandem mass spectrometry (MS/MS) method that does not require ligand derivatization, and is therefore also applicable to localize metal cations. By obtaining more negative charge states for the complexes using supercharging agents, and by creating radical ions by electron photodetachment, oligonucleotide bonds become weaker than the DNA-cation or DNA-ligand noncovalent bonds upon collision-induced dissociation of the radicals. This electron photodetachment (EPD) method allows to locate the binding regions of cations and ligands by top-down sequencing of the oligonucleotide target. The very potent G-quadruplex ligands 360A and PhenDC3 were found to replace a potassium cation and bind close to the central loop of 4-repeat human telomeric sequences.

Top-Down ESI-ECD-FT-ICR Mass Spectrometry Localizes Noncovalent Protein-Ligand Binding Sites

2006 ◽  
Vol 128 (45) ◽  
pp. 14432-14433 ◽  
Author(s):  
Yongming Xie ◽  
Jennifer Zhang ◽  
Sheng Yin ◽  
Joseph A. Loo
Keyword(s):  
Mass Spectrometry ◽  
Ligand Binding ◽  
Binding Sites ◽  
Top Down ◽  
Ligand Binding Sites ◽  
Noncovalent Protein ◽  
Ft Icr

scholarly journals Nano-LC FTICR Tandem Mass Spectrometry for Top-Down Proteomics: Routine Baseline Unit Mass Resolution of Whole Cell Lysate Proteins up to 72 kDa

2012 ◽  
Vol 84 (5) ◽  
pp. 2111-2117 ◽  
Author(s):  
Jeremiah D. Tipton ◽  
John C. Tran ◽  
Adam D. Catherman ◽  
Dorothy R. Ahlf ◽  
Kenneth R. Durbin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Mass Resolution ◽  
Unit Mass ◽  
Tandem Mass ◽  
Top Down ◽  
Whole Cell ◽  
Whole Cell Lysate ◽  
Cell Lysate ◽  
Unit Mass Resolution

scholarly journals A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome

2009 ◽  
Vol 20 (12) ◽  
pp. 2183-2191 ◽  
Author(s):  
Ji Eun Lee ◽  
John F. Kellie ◽  
John C. Tran ◽  
Jeremiah D. Tipton ◽  
Adam D. Catherman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Two Dimensional ◽  
Top Down ◽  
Low Mass

scholarly journals Top-Down Proteomic Identification of Shiga Toxin 1 and 2 from Pathogenic Escherichia coli Using MALDI-TOF-TOF Tandem Mass Spectrometry

2019 ◽  
Vol 7 (11) ◽  
pp. 488 ◽  
Author(s):  
Clifton K. Fagerquist ◽  
William J. Zaragoza ◽  
Michelle Q. Carter
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Tandem Mass Spectrometry ◽  
Disulfide Bond ◽  
Shiga Toxin ◽  
Tandem Mass ◽  
Top Down ◽  
E Coli ◽  
B Subunit ◽  
Proteomic Identification

Shiga-toxin-producing Escherichia coli (STEC) are a burden on agriculture and a threat to public health. Rapid methods are needed to identify STEC strains and characterize the Shiga toxin (Stx) they produce. We analyzed three STEC strains for Stx expression, using antibiotic induction, matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) mass spectrometry, and top-down proteomic analysis. E. coli O157:H- strain 493/89 is a clinical isolate linked to an outbreak of hemolytic uremic syndrome (HUS) in Germany in the late 1980s. E. coli O145:H28 strains RM12367-C1 and RM14496-C1 were isolated from an agricultural region in California. The stx operon of the two environmental strains were determined by whole genome sequencing (WGS). STEC strain 493/89 expressed Shiga toxin 2a (Stx2a) as identified by tandem mass spectrometry (MS/MS) of its B-subunit that allowed identification of the type and subtype of the toxin. RM12367-C1 also expressed Stx2a as identified by its B-subunit. RM14496-C1 expressed Shiga toxin 1a (Stx1a) as identified from its B-subunit. The B-subunits of Stx1 and Stx2 both have an intramolecular disulfide bond. MS/MS was obtained on both the disulfide-bond-intact and disulfide-bond-reduced B-subunit, with the latter being used for top-down proteomic identification. Top-down proteomic analysis was consistent with WGS.

scholarly journals Automated Capillary Isoelectric Focusing-Tandem Mass Spectrometry for Qualitative and Quantitative Top-Down Proteomics

2020 ◽  
Vol 92 (24) ◽  
pp. 15890-15898
Author(s):  
Tian Xu ◽  
Xiaojing Shen ◽  
Zhichang Yang ◽  
Daoyang Chen ◽  
Rachele A. Lubeckyj ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Isoelectric Focusing ◽  
Tandem Mass ◽  
Capillary Isoelectric Focusing ◽  
Top Down ◽  
Qualitative And Quantitative
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