OligoR

OligoR processes hydrogen-deuterium exchange mass spectrometry (HDX/MS) data for oligonucleotides to analyze their conformational dynamics.

Key Features:

• Native HDX/MS data processing: Processes native HDX/MS experiments including multiple time points and mass-separated species for oligonucleotide analyses.
• Deconvolution of isotope distributions: Deconvolutes bimodal and highly overlapping isotope distributions by modeling physically possible isotope patterns.
• Chemical-formula-based isotope modeling: Generates isotope patterns derived from chemical formulae to constrain and interpret measured isotope envelopes.
• Cross-analyte applicability: The deconvolution and analysis methods can be applied to other analytes such as proteins, peptides, sugars, and small molecules.

Scientific Applications:

• Oligonucleotide conformational dynamics: Quantifies HDX-derived exchange behavior to study folding and structural dynamics of nucleic acids.
• Binding-induced structural characterization: Characterizes conformational changes of oligonucleotides upon binding with cations, small molecules, and proteins.

Methodology:

Deconvolution of complex (including bimodal) isotope distributions by modeling physically possible isotope patterns derived from chemical formulae, applied across multiple time points and mass-separated species.