Search research articles

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Dibenzoacridinium derivatives: a new class of G-quadruplex ligands with anti-HIV-1 properties.

RSC medicinal chemistry·2026

Same author

Helical aromatic oligoamide foldamers as selective G-quadruplex ligands.

Nucleic acids research·2025

Same author

Eps2Fold: a rapid method to characterize G-quadruplex DNA structures using single absorbance spectra.

Nucleic acids research·2025

Same author

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.

Proteins·2025

Same author

Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.

bioRxiv : the preprint server for biology·2025

Same author

New 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinazoline and 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinoline Derivatives: Synthesis and Biological Evaluation as Novel Anticancer Agents by Targeting G-Quadruplex.

Pharmaceuticals (Basel, Switzerland)·2024

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Jul 26, 2025

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides.

Eric Largy¹, Matthieu Ranz¹

¹CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, Univ. Bordeaux, F-33600 Pessac, France.

Analytical Chemistry

|June 13, 2023

Summary

This study introduces OligoR, a web application for analyzing DNA hydrogen-deuterium exchange mass spectrometry (HDX/MS) data. OligoR simplifies processing and visualizes complex oligonucleotide dynamics and binding interactions.

More Related Videos

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Published on: May 17, 2016

Related Experiment Videos

Last Updated: Jul 26, 2025

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Published on: May 17, 2016

Area of Science:

Biochemistry and Biophysics
Analytical Chemistry
Computational Biology

Background:

Hydrogen-deuterium exchange mass spectrometry (HDX/MS) is a powerful technique for studying molecular dynamics.
Native MS coupled with HDX/MS enables characterization of oligonucleotides, including their interactions with various ligands.
Existing software solutions often lack specialized features for oligonucleotide HDX/MS data analysis.

Purpose of the Study:

To develop a dedicated software solution for processing and visualizing native HDX/MS data of oligonucleotides.
To enable robust deconvolution of complex isotope distributions for accurate analysis of folding dynamics.
To provide an accessible platform for researchers studying DNA structural dynamics.

Main Methods:

Development of OligoR, a web-browser-based application for native HDX/MS data analysis.
Implementation of a novel approach for deconvoluting bimodal isotope distributions based on chemical formulae.
Processing of raw data from open formats to interactive visualizations and exportable results.

Main Results:

OligoR efficiently processes HDX/MS experiments for oligonucleotides, handling multiple time points and mass-separated species within minutes.
The developed deconvolution method accurately resolves overlapping isotope distributions, revealing valuable folding dynamics.
The application generates interactive data tables and customizable, publication-quality figures.

Conclusions:

OligoR provides a comprehensive and user-friendly solution for native HDX/MS analysis of oligonucleotides.
The deconvolution approach is robust and applicable to a wide range of analytes beyond oligonucleotides.
This tool facilitates deeper understanding of oligonucleotide structural dynamics and interactions.