Radical-Induced Dissociation for Oligonucleotide Sequencing by TiO2/ZnAl-Layered Double Oxide-Assisted Laser Desorption/Ionization Mass Spectrometry

De novo sequencing of oligonucleotides remains challenging, especially for oligonucleotides with post-transcriptional or synthetic modifications. Mass spectrometry (MS) sequencing can reliably detect and locate all of the modification sites in oligonucleotides via m/z variance. However, current MS-b...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2023-11, Vol.95 (45), p.16505-16513
Main Authors: Zhou, Shiwen, Qi, Menghui, Luo, Yuanqing, Li, Wangyu, Liu, Yaqin, Guo, Cheng, Wei, Wei, Chen, Guanru, Tu, Peijun, Feng, Hongru, Pan, Yuanjiang
Format: Article
Language:English
Subjects:
Density functional theory
Desorption
Energy of dissociation
Fragments
Instrumentation
Ionization
Mass spectrometry
Mass spectroscopy
Nucleotide sequence
Oligonucleotides
Post-transcription
Scientific imaging
siRNA
Spectra
Titanium dioxide
Ultraviolet radiation
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Summary:De novo sequencing of oligonucleotides remains challenging, especially for oligonucleotides with post-transcriptional or synthetic modifications. Mass spectrometry (MS) sequencing can reliably detect and locate all of the modification sites in oligonucleotides via m/z variance. However, current MS-based sequencing methods exhibit complex spectra and low ion abundance and usually require coupled instrumentation. Herein, we demonstrate a method of oligonucleotide sequencing using TiO2/ZnAl-layered double oxide (LDO)-assisted laser desorption/ionization (LDI)-MS based on radical-induced dissociation (RID). ·CH2OH radicals can be produced on the surface of a TiO2/ZnAl-LDO matrix via ultraviolet light, inducing an attack on the active site of the oligonucleotide phosphate skeleton to create typical “a-, a-B-, c·-, d-, w-, and y”-type fragments. Compared with the spectra obtained via collision-based methods, such as collision-induced dissociation and higher-energy collisional dissociation, the LDI-MS spectra based on RID exhibit single-charged signals, fewer types of fragments, and a lower proportion of unknown noise peaks. We demonstrate full sequence coverage for a 6-mer 2′-O-methyl-modified oligonucleotide and a 21-mer small interfering RNA and show that RID can sequence oligonucleotides with modifications. Importantly, the mechanism responsible for the RID of the oligonucleotide phosphate skeleton was investigated through offline experiments, demonstrating consistent results with density functional theory calculations.
ISSN:0003-2700
1520-6882
DOI:10.1021/acs.analchem.3c02166