ArticleNucleic acids research2021
DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 42 citations in OpenAlex.
- Helical aromatic oligoamide foldamers as selective G-quadruplex ligands.Nucleic acids research · 2025Article
- Stability of G/C DNA Tetraplexes at Physiological pH Formed at the Promoter-UTR Intersection of theACS omega · 2025Article
- A Flexible Quadruple-Stranded Helicate Demonstrates a Strong Binding Preference for DNA Three-Way Junctions by Induced Fit.Journal of the American Chemical Society · 2025Article
- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- Eps2Fold: a rapid method to characterize G-quadruplex DNA structures using single absorbance spectra.Nucleic acids research · 2025Article
- Molecular recognition and effects of a benzothiazole derivative targeting the MYC G-quadruplex.Nucleic acids research · 2025Article
- Comprehensive datasets for RNA design, machine learning, and beyond.Scientific reports · 2025Article
- Unraveling Ribonucleic Acid Unfolding: A Quantitative Comparison of Solution and Gas-Phase Unfolding.Analytical chemistry · 2025Article
- Ion Mobility-Mass Spectrometry Captures the Structural Consequences of Lipid Nanoparticle Encapsulation on Ribonucleic Acid Cargo.Journal of the American Chemical Society · 2024Article
- Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry.International journal of mass spectrometry · 2024Article
- Collision-Induced Unfolding Reveals Disease-Associated Stability Shifts in Mitochondrial Transfer Ribonucleic Acids.Journal of the American Chemical Society · 2024Article
- A High-Throughput Workflow for Mass Spectrometry Analysis of Nucleic Acids by Nanoflow Desalting.Analytical chemistry · 2024Article
- EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database.Nucleic acids research · 2024Article
- G4Bank: A database of experimentally identified DNA G-quadruplex sequences.Interdisciplinary sciences, computational life sciences · 2023Article
- Spacer Fidelity Assessments of Guide RNA by Top-Down Mass Spectrometry.ACS central science · 2023Article
- OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides.Analytical chemistry · 2023Article
- Optimization of G-Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones).Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- GAIA: G-quadruplexes in alive creature database.Nucleic acids research · 2023Article
- Design, Synthesis, and Antiprotozoal Evaluation of New Promising 2,9-Pathogens (Basel, Switzerland) · 2022Article
- Phen-DCAngewandte Chemie (International ed. in English) · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.