g4dbr

g4dbr provides access to g4DB, a curated database of DNA G-quadruplex sequences validated under native electrospray mass spectrometry conditions to support structural characterization and MS-based screening of G-quadruplex–ligand interactions.

Key Features:

• Database Access: Access to g4DB containing detailed records of G-quadruplex sequences validated under native electrospray mass spectrometry (MS) conditions.
• Standardized Screening Assays: Supplies a short-list of G-quadruplex sequences that maintain consistent structures across NMR and MS environments to support interpretation of ligand binding stoichiometry and affinity.
• Data Processing and Reporting: Implemented in R and automates data processing, figure generation, and report production for G-quadruplex characterization.
• Integration of Multimodal Data: Integrates circular dichroism (CD) spectra, melting temperatures (Tm), NMR spectra, and electrospray mass spectra to analyze stability and conformational properties under varying ionic conditions including high K+ and low K+/high tetramethylammonium acetate (TMAA).
• Future Expansion: Supports incorporation of additional sequences into the database as new experimental data become available.

Scientific Applications:

• High-throughput characterization: Enables high-throughput characterization of G-quadruplex structures using integrated MS and spectroscopic data.
• Drug discovery and ligand studies: Facilitates interpretation of ligand binding stoichiometry and affinity for G-quadruplex–targeting compounds.
• Structural biology: Supports comparison of NMR- and MS-derived structural data to investigate DNA folding mechanisms and G-quadruplex conformational polymorphism.

Methodology:

Implemented in R to automate data processing and the generation of figures and reports.