Synthesis and structure-activity relationship of Peptide Nucleic Acid Probes with improved Interstrand-Crosslinking abilities: Application to Biotin-mediated RNA-Pulldown

08 July 2022, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


The development of interstrand-crosslinking (ICL) probes for the covalent targeting of DNA and RNA sequences of interest has been extensively reported in the past decade. However, most of the reactions reported so far induce the formation of a stable adduct that cannot be reverted, thus ren-dering these chemistries less useful in applications where the reversibility of the reaction is need-ed for further downstream processing of the targeted and isolated sequences, such as enzymatic amplification steps. In this work, we report on the reversibility of the furan-mediated ICL reac-tion, conveniently triggered by either chemical (NBS) or luminous stimuli (light irradiation in presence of a photosensitizer), which can be conveniently achieved by heating the crosslinked sample at 95°C to induce the quantitative reversion of the reaction, while maintaining the struc-ture of the DNA/RNA targets intact. As a proof-of-concept and showing the benefits of the ICL reversibility, we apply furan-mediated ICL to the pulldown of a target RNA strand from cell ly-sate.


RNA pull-down
interstand crosslink
peptide nucleic acids
reversible crosslink

Supplementary materials

Supplementary information
Supplementary information available: Detailed synthesis of monomers, protocols for PNA synthesis, characterization of small molecules and PNA probes, complete list of the sequences used, ICL% of all experiments, HPLC-UV traces, PAGE and MALDI spectra of representative ICL experiments.


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