Duplex RNA‐Binding Enzymes: Headliners from Neurobiology, Virology, and Development

Beal, Peter A.

doi:10.1002/cbic.200400303

Cited by 4 publications

(2 citation statements)

References 120 publications

(143 reference statements)

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“…The dsRBM is an evolutionarily conserved motif expressed in many proteins both on and off the RNAi pathway. The motif consists of ∼70 amino acids and binds to duplex RNA in a largely sequence-independent fashion − . One dsRBM protein in particular, PKR, is well-known for its role in siRNA-dependent immunostimulation and off-target effects , .…”

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confidence: 99%

Minor-Groove-Modulating Adenosine Replacements Control Protein Binding and RNAi Activity in siRNAs

2010

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Short-interfering RNAs (siRNAs) are common tools in molecular biology, however the development of RNAi-based therapeutics is limited by immunostimulatory and non-specific effects mediated by off-target RNA-binding proteins. PKR and ADAR1 are two proteins implicated in RNAi off-target effects, and share a common means of interaction with siRNAs through double-stranded RNA binding motifs (dsRBMs). Here we report the site-specific introduction of N2- propargyl 2-aminopurine into siRNAs and subsequent conversion to two bulky products via copper-catalyzed azide alkyne cycloaddition (CuAAC) with either Nazidoacetyl-mannosamine azide or N-ethylpiperidine azide. We observed position-specific effects on RNAi activity for modifications made to both the passenger and guide strands. These findings are rationalized in light of recent structural studies of components of the RNA-induced silencing complex (RISC) and RISC-loading complex (RLC). The most active siRNAs were assayed for binding affinity to the RNA-dependent protein kinase (PKR) and adenosine deaminase that acts on RNA 1 (ADAR1). PKR binding was significantly reduced by multiple modifications, regardless of size, and ADAR1 binding was reduced in a position and size-sensitive manner. Our findings present a strategy for designing siRNAs that reduce off-target dsRBM-protein binding while retaining native RNAi activity.

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Minor-Groove-Modulating Adenosine Replacements Control Protein Binding and RNAi Activity in siRNAs

2010

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“…1,2 Various enzymes recognize dsRNA and function at specific positions. For example, adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that recognize dsRNA substrates and convert adenosine (A) to inosine (I) at specific locations in the duplex.…”

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confidence: 99%

Synthesis of native-like crosslinked duplex RNA and study of its properties

Onizuka

Hazemi

Thomas

et al. 2017

Bioorganic & Medicinal Chemistry

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A variety of enzymes have been found to interact with double-stranded RNA (dsRNA) in order to carry out its functions. We have endeavored to prepare the covalently crosslinked native-like duplex RNA, which could be useful for biochemical studies and RNA nanotechnology. In this study, the interstrand covalently linked duplex RNA was formed by a crosslinking reaction between vinylpurine (VP) and the target cytosine or uracil in RNA. We measured melting temperatures and CD spectra to identify the properties of the VP crosslinked duplex RNA. The crosslinking formation increased the thermodynamic stability without disturbing the natural conformation of dsRNA. In addition, a competitive binding experiment with the duplex RNA binding enzyme, ADAR2, showed the crosslinked dsRNA bound the protein with nearly the same binding affinity as the natural dsRNA, confirming that it has finely preserved the natural traits of duplex RNA.

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Protein Interactions with Double-Stranded RNA in Eukaryotic Cells

Hammann

2006

Small RNAs

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Duplex RNA‐Binding Enzymes: Headliners from Neurobiology, Virology, and Development

Cited by 4 publications

References 120 publications

Minor-Groove-Modulating Adenosine Replacements Control Protein Binding and RNAi Activity in siRNAs

Minor-Groove-Modulating Adenosine Replacements Control Protein Binding and RNAi Activity in siRNAs

Synthesis of native-like crosslinked duplex RNA and study of its properties

Protein Interactions with Double-Stranded RNA in Eukaryotic Cells

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