Related Experiment Video
Updated: May 5, 2026

Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight MALDI-TOF Mass Spectrometry
Published on: June 10, 2018
Structural Characterization of Normal and Modified Oligonucleotides by Matrix-assisted Laser Desorption Fourier
1Analytical Chemistry Division, Oak Ridge National Laboratory, 37831-6120, Tennessee, Oak Ridge, USA.
Abstract:
Matrix-assisted UV laser desorption Fourier transform mass spectrometry (266 nm, nicotinic acid matrix) can be used for the detailed structural characterization of normal and modified oligonucleotides. The negative ion spectra for these compounds revealed abundant (M - H) (-) ions as well as fragment ions that provided the information necessary to determine oligomer sequence and to differentiate isomers. The nicotinic acid matrix was required for the production of (M - H) (-) ions for the oligonucleotide dimers, trimers, tetramers, and hexamers examined in this study. Elimination of the nicotinic acid matrix resulted in complete loss of the (M -H) (-) ions as well as most of the larger fragment ions for the oligomers. The primary fragmentation pathway was observed to be phosphate ester bond cleavage with the resulting charge retained on the 3' end of the oligomer and enabled isomeric differentiation of compounds such as d(S'-CGCG-3') and d(S'-CCGG-3'). Collisioninduced dissociation experiments of the (M - H) (-) ions for these compounds confirmed the preferential loss of nucleotides from the 5' end of the oligomers. The presence and location of modifications such as methyl and ethyl alkyl groups to the oligonucleotides could also be identified.
More Related Videos
11:37Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism
Published on: July 28, 2017
09:38Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
Published on: November 26, 2013
Related Concept Videos
Matrix-Assisted Laser Desorption Ionization (MALDI)
MALDI-TOF Mass Spectrometry
Mass Spectrometry: Complex Analysis
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
Mass Spectrum: Interpretation
Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Mass Spectrometry: Overview