Recognition of double-stranded RNA by proteins and small molecules

Coby B. Carlson, Olen M. Stephens, Peter A. Beal

Research output: Contribution to journalArticlepeer-review

54 Scopus citations


Molecular recognition of double-stranded RNA (dsRNA) is a key event for numerous biological pathways including the trafficking, editing, and maturation of cellular RNA, the interferon antiviral response, and RNA interference. Over the past several years, our laboratory has studied proteins and small molecules that bind dsRNA with the goal of understanding and controlling the binding selectivity. In this review, we discuss members of the dsRBM class of proteins that bind dsRNA. The dsRBM is a ∼70 amino acid sequence motif found in a variety of dsRNA-binding proteins. Recent results have led to a new appreciation of the ability of these proteins to bind selectivity to certain sites on dsRNA. This property is discussed in light of the RNA selectivity observed in the function of two proteins that contain dsRBMs, the RNA-dependent protein kinase (PKR) and an adenosine deaminase that acts on dsRNA (ADAR2). In addition, we introduce peptide-acridine conjugates (PACs), small molecules designed to control dsRBM-RNA interactions. These intercalating molecules bear variable peptide appendages at opposite edges of an acridine heterocycle. This design imparts the potential to exploit differences in groove characteristics and/or base-pair dynamics at binding sites to achieve selective binding.

Original languageEnglish (US)
Pages (from-to)86-102
Number of pages17
Issue number1
StatePublished - Sep 2003
Externally publishedYes


  • Adenosine deaminase
  • Double-stranded RNA
  • Double-stranded RNA binding motif
  • Molecular recognition
  • Peptide-acridine conjugates
  • Protein kinase

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics


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