Macrocyclic Helix‐Threading Peptides for Targeting RNA

Krishnamurthy, Malathy; Simon, Kristina; Orendt, Anita M.; Beal, Peter A.

doi:10.1002/anie.200702247

Cited by 67 publications

(44 citation statements)

References 30 publications

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“…Oligonucleotide-related molecules, such as PNAs (Avitabile et al 2012), and small molecules (Krishnamurthy et al 2007;Neubacher et al 2011;Bose et al 2012;Maiti et al 2012;Murata et al 2013) have been targeted to the Dicer cleavage sites in pre-miRNAs. However, less activity has been directed toward efforts to inhibit the cleavage by Drosha of specific pri-miRNAs.…”

Section: Introductionmentioning

confidence: 99%

Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha

Diaz

Chirayil

et al. 2014

RNA

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We have found a small molecule that specifically inhibits cleavage of a precursor to the oncogenic miRNA, miR-21, by the microprocessor complex of Drosha and DGCR8. We identified novel ligands for the apical loop of this precursor from a screen of 14,024 N-substituted oligoglycines (peptoids) in a microarray format. Eight distinct compounds with specific affinity were obtained, three having affinities for the targeted loop in the low micromolar range and greater than 15-fold discrimination against a closely related hairpin. One of these compounds completely inhibits microprocessor cleavage of a miR-21 primary transcript at concentrations at which cleavage of another miRNA primary transcript, pri-miR-16, is little affected. The apical loop of pri-miR-21, placed in the context of pri-miR-16, is sufficient for inhibition of microprocessor cleavage by the peptoid. This compound also inhibits cleavage of pri-miR-21 containing the pri-miR-16 apical loop, suggesting an additional site of association within pri-miR-21. The reported peptoid is the first example of a small molecule that inhibits microprocessor cleavage by binding to the apical loop of a pri-miRNA.

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Section: Introductionmentioning

confidence: 99%

Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha

Diaz

Chirayil

et al. 2014

RNA

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“…Often, however, on-bead screening techniques result in false-positive hits that can arise as a result of non-specific interactions of the RNA probe to the solid support or with the library members 17. To circumvent these potential problems, we have adapted a spectroscopic, solution phase nucleic acid binding assay to the screening of libraries of helix-threading peptides (HTPs) prepared in our laboratory 18–21. HTPs contain a heterocyclic chromophore embedded in a peptide backbone and can selectively bind stem-loop RNA structures that contain a 5’-PyPu-3’ intercalation site flanked by at least a single bulge on each strand, 3’ to this site 18, 20, 22.…”

Section: Introductionmentioning

confidence: 99%

“…HTPs contain a heterocyclic chromophore embedded in a peptide backbone and can selectively bind stem-loop RNA structures that contain a 5’-PyPu-3’ intercalation site flanked by at least a single bulge on each strand, 3’ to this site 18, 20, 22. We recently demonstrated that a macrocyclic variant binds a naturally occurring pre-miRNA containing such a binding site 21. In this paper, we describe the use of the fluorescent intercalator displacement assay to analyze the RNA binding properties of a small collection of HTPs 23, 24.…”

Section: Introductionmentioning

confidence: 99%

Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay

Krishnamurthy

Schirle

Beal

2008

Bioorganic & Medicinal Chemistry

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The fluorescent intercalator displacement assay using thiazole orange has been adapted to the study of RNA-binding helix-threading peptides (HTPs). This assay is highly sensitive with HTP-binding RNAs and provides binding affinity data in good agreement with quantitative ribonuclease footprinting without the need for radiolabeling or gel electrophoresis. The FID assay was used to define structure activity relationships for a small library of helix-threading peptides. Results of these studies indicate their RNA binding is dependent on peptide sequence, α-amino acid stereochemistry, and cyclization (versus linear peptides), but independent of macrocyclic ring size for the penta-, tetra- and tri peptides analyzed.

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“…Taken together our and Dervan's results emphasize that the distinct conformations of dsRNA and dsDNA make the molecular recognition of each of these biopolymers a unique task. Peptide based ligands have been previously used for molecular recognition of pri-miRNAs by helix-threading peptides 13, 14 and TAR RNA of HIV by Tat-derived 15 and, recently, de-novo designed branched peptides. 16 While good binding affinity and selectivity was observed, the structural details of peptide binding to dsRNA have not been elucidated.…”

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confidence: 99%

Sequence Selective Recognition of Double-Stranded RNA at Physiologically Relevant Conditions Using PNA-Peptide Conjugates

et al. 2013

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Conjugation of short peptide nucleic acids (PNA) with tetralysine peptides strongly enhanced triple helical binding to RNA at physiologically relevant conditions. The PNA hexamers and heptamers carrying cationic nucleobase and tetralysine modifications displayed high binding affinity for complementary double-stranded RNA without compromising sequence selectivity. The PNA-peptide conjugates had unique preference for binding double-stranded RNA, while having little, if any, affinity for double-stranded DNA. The cationic PNAs were efficiently taken up by HEK293 cells, while little uptake was observed for unmodified PNA.

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Macrocyclic Helix‐Threading Peptides for Targeting RNA

Cited by 67 publications

References 30 publications

Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha

Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha

Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay

Sequence Selective Recognition of Double-Stranded RNA at Physiologically Relevant Conditions Using PNA-Peptide Conjugates

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