A tunable assay for modulators of genome-destabilizing DNA structures

Imee M.A. Del Mundo, Eun Jeong Cho, Kevin N. Dalby, Karen M. Vasquez

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Regions of genomic instability are not random and often co-localize with DNA sequences that can adopt alternative DNA structures (i.e. non-B DNA, such as H-DNA). Non-B DNA-forming sequences are highly enriched at translocation breakpoints in human cancer genomes, representing an endogenous source of genetic instability. However, a further understanding of the mechanisms involved in non-B DNA-induced genetic instability is needed. Small molecules that can modulate the formation/stability of non-B DNA structures, and therefore the subsequent mutagenic outcome, represent valuable tools to study DNA structure-induced genetic instability. To this end, we have developed a tunable Förster resonance energy transfer (FRET)-based assay to detect triplex/H-DNA-destabilizing and -stabilizing ligands. The assay was designed by incorporating a fluorophore-quencher pair in a naturally-occurring H-DNA-forming sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. By tuning triplex stability via buffer composition, the assay functions as a dual-reporter that can identify stabilizers and destabilizers, simultaneously. The assay principle was demonstrated using known triplex stabilizers, BePI and coralyne, and a complementary oligonucleotide to mimic a destabilizer, MCRa2. The potential of the assay was validated in a 384-well plate with 320 custom-assembled compounds. The discovery of novel triplex stabilizers/destabilizers may allow the regulation of genetic instability in human genomes.

Original languageEnglish (US)
Pages (from-to)e73
JournalNucleic acids research
Volume47
Issue number13
DOIs
StatePublished - Jul 26 2019

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Genome
DNA
coralyne
Human Genome
Genetic Structures
Genomic Instability
Energy Transfer
Oncogenes
Oligonucleotides
Buffers
Ligands
triplex DNA
Neoplasms

ASJC Scopus subject areas

  • Genetics

Cite this

A tunable assay for modulators of genome-destabilizing DNA structures. / Del Mundo, Imee M.A.; Cho, Eun Jeong; Dalby, Kevin N.; Vasquez, Karen M.

In: Nucleic acids research, Vol. 47, No. 13, 26.07.2019, p. e73.

Research output: Contribution to journalArticle

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