Designing Novel RNA Binders

Michael, Katja; Tor, Yitzhak

doi:10.1002/(sici)1521-3765(19981102)4:11<2091::aid-chem2091>3.0.co;2-3

Cited by 90 publications

(15 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…11À15 Much less is known, however, about the modulation of enzymatic activity by low molecular weight ligands. 16 The rapid generation of molecular diversity via combinatorial approaches provides new opportunities to further our understanding of RNA recognition. Large-scale investigations are hampered, however, by the inherent experimental difficulties associated with evaluating ribozyme function.…”

Section: Introductionmentioning

confidence: 99%

2-Aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammerhead ribozymes

Kirk

2001

Bioorganic &Amp; Medicinal Chemistry

View full text Add to dashboard Cite

Abstract-The design, synthesis and study of internally fluorescent hammerhead (HH) ribozymes, where changes in fluorescence parameters directly reflect the progress of the ribozyme's cleavage chemistry, are described. The approach relies on a HH substrate modified at position 1.1, proximal to the cleavage site, with 2-aminopurine (2AP), an intensely fluorescent adenosine isoster. The incorporation of 2AP, an unnatural nucleoside, does not interfere with the ribozyme folding and catalysis. Since 2AP is highly sensitive to environmental changes, its fluorescence is dramatically altered upon ribozyme-mediated cleavage of the substrate. This generates a measurable signal that directly reflects the progress of the ribozyme's reaction in real time. Identical pseudo first order rate constants are obtained for HH constructs using both continuous fluorescence monitoring and radioactive labeling. This rapid and real-time monitoring facilitates the study of ribozyme activity under different conditions (e.g., ionic strength, pH, etc.), and provides a useful assay to rapidly screen potential inhibitors. Three hitherto unknown HH inhibitors are presented and compared to neomycin B and chlortetracycline, two previously studied HH inhibitors. All three new small molecules, neo-acridine, guanidinoneomycin B, and [Á-(Eilatin)Ru(bpy) 2 ] 2+ , prove to be better inhibitors than neomycin B or chlortetracycline. Investigating HH inhibition under different ionic strengths reveals that the binding of neo-acridine, [Á-(Eilatin)Ru(bpy) 2 ] 2+ , and chlortetracycline to the HH involves hydrophobic interactions as their RNA affinities are largely unaffected by increasing salt concentrations. In contrast, neomycin B loses more than 50-fold of its inhibitory ability as the NaCl concentration is increased from 50 to 500 mM. #

show abstract

Section: Introductionmentioning

confidence: 99%

2-Aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammerhead ribozymes

Kirk

2001

Bioorganic &Amp; Medicinal Chemistry

View full text Add to dashboard Cite

show abstract

“…Their promiscuous binding to non-ribosomal RNAs and/or membrane components may be related to the multiple therapeutic side effects exhibited by these compounds [47][48][49]. Aminoglycosides bind to and inhibit the function of a wide range of unrelated RNAs with moderate activities (IC 50 ¼ 0.1-100 mM) [23,50]. Aminoglycosides do, however, show excellent specificity for RNA over DNA (Section 2.5.3).…”

Section: Ligand Specificitymentioning

confidence: 99%

“…In most cases, however, the binding stoichiometry of the inhibitor is not known, so its affinity to the RRE is evaluated by measuring the concentration of inhibitor needed to displace half of the Rev peptide from the RRE (defined as the ligand's IC 50 value). [34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50]. The peptide RevFl is used for fluorescence-based assays and is succinylated at its N-terminus, amidated at its C-terminus, and contains a four-alanine spacer to fluorescein.…”

Section: Fluorescence Anisotropymentioning

confidence: 99%

Targeting HIV RNA with Small Molecules

Luedtke¹,

Tor

2002

Small Molecule DNA and RNA Binders

Self Cite

View full text Add to dashboard Cite

“…3 Aminoglycosides, a clinically important class of antibiotics, act by binding to bacterial RNA. 4 High affinity binding of different aminoglycosides to specific sites in larger RNA molecules including ribosomal RNA, the hammerhead ribozyme 5 or smaller RNAs such as 16S rRNA and 23S rRNA has been extensively studied. 6,7 The interaction of aminoglycoside analogs with RNA has provided a detailed understanding of critical interactions responsible for selective aminoglycoside-RNA binding.…”

mentioning

confidence: 99%

“…6,7 The interaction of aminoglycoside analogs with RNA has provided a detailed understanding of critical interactions responsible for selective aminoglycoside-RNA binding. 4,8,9 Since electrostatic interactions play a key role in aminoglycoside-RNA recognition, the introduction of additional amine groups significantly improved binding while decreasing selectivity. Screening of a series of aminoglycoside analogs against the 16S rRNA, revealed a 1,3-hydroxyamine binding motif with micromolar affinity.…”

mentioning

confidence: 99%

Synthesis of Neomycin Analogs to Investigate Aminoglycoside-RNA Interactions

Seeberger¹,

Baumann²,

Zhang³

et al. 2003

Synlett

View full text Add to dashboard Cite

A series of novel aminoglycoside oligosaccharide analogs containing a 2,5-dideoxystreptamine core scaffold was prepared to study aminoglycoside binding to the small subunit of 16S rRNA. A set of monosaccharide building blocks carrying amino groups in different positions and conformations around the pyranose ring was utilized in the assembly of oligosaccharides. These aminoglycoside analogs were analyzed for their RNA-binding capacity using a high throughput mass spectroscopy assay.

show abstract

Designing Novel RNA Binders

Cited by 90 publications

References 27 publications

2-Aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammerhead ribozymes

2-Aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammerhead ribozymes

Targeting HIV RNA with Small Molecules

Synthesis of Neomycin Analogs to Investigate Aminoglycoside-RNA Interactions

Contact Info

Product

Resources

About