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Nucleic Acids Res. 2019 Jun 20;47(11):5502-5510. doi: 10.1093/nar/gkz215.

Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol.

Author information

1
Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France.
2
Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, Canada.

Abstract

Guanine-rich DNA and RNA sequences can fold into higher-order structures known as G-quadruplexes (or G4-DNA and G4-RNA, respectively). The prevalence of the G4 landscapes in the human genome, transcriptome and ncRNAome (non-coding RNA), collectively known as G4ome, is strongly suggestive of biological relevance at multiple levels (gene expression, replication). Small-molecules can be used to track G4s in living cells for the functional characterization of G4s in both normal and disease-associated changes in cell biology. Here, we describe biotinylated biomimetic ligands referred to as BioTASQ and their use as molecular tools that allow for isolating G4s through affinity pull-down protocols. We demonstrate the general applicability of the method by purifying biologically relevant G4s from nucleic acid mixtures in vitro and from human cells through the G4RP-RT-qPCR protocol. Overall, the results presented here represent a step towards the optimization of G4-RNAs identification, a key step in studying G4s in cell biology and human diseases.

PMID:
30949698
PMCID:
PMC6582334
DOI:
10.1093/nar/gkz215
[Indexed for MEDLINE]
Free PMC Article

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