Open AccessStructure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide
Author(s) -
Raphael I. Benhamou,
Alicia J. Angelbello,
Ryan J. Andrews,
Eric T. Wang,
Walter N. Moss,
Matthew D. Disney
Publication year - 2020
Publication title -
acs chemical biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.899
H-Index - 111
eISSN - 1554-8937
pISSN - 1554-8929
DOI - 10.1021/acschembio.9b00958
Subject(s) - rna , oligonucleotide , rna splicing , biology , rna binding protein , nucleic acid , cleavage (geology) , dna , microbiology and biotechnology , biochemistry , gene , paleontology , fracture (geology)
Myotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy that is caused by an expanded repeat of r(CCUG) [r(CCUG) exp ] in intron 1 of a CHC-type zinc finger nucleic acid binding protein ( CNBP ) pre-mRNA. Various mechanisms contribute to DM2 pathology including pre-mRNA splicing defects caused by sequestration of the RNA splicing regulator muscleblind-like-1 (MBNL1) by r(CCUG) exp . Herein, we study the biological impacts of the molecular recognition of r(CCUG) exp 's structure by a designer dimeric small molecule that directly cleaves the RNA in patient-derived cells. The compound is comprised of two RNA-binding modules conjugated to a derivative of the natural product bleomycin. Careful design of the chimera affords RNA-specific cleavage, as attachment of the bleomycin cleaving module was done in a manner that disables DNA cleavage. The chimeric cleaver is more potent than the parent binding compound for alleviating DM2-associated defects. Importantly, oligonucleotides targeting the r(CCUG) exp sequence for cleavage exacerbate DM2 defects due to recognition of a short r(CCUG) sequence that is embedded in CNBP , argonaute-1 ( AGO1 ), and MBNL1 , reducing their levels. The latter event causes a greater depletion of functional MBNL1 than the amount already sequestered by r(CCUG) exp . Thus, compounds targeting RNA structures can have functional advantages over oligonucleotides that target the sequence in some disease settings, particularly in DM2.