Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution

Coby B. Carlson, Momchilo Vuyisich, Barry D. Gooch, Peter A. Beal

Research output: Contribution to journalArticlepeer-review

38 Scopus citations


In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5′-CpG-3′ sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (KD = 20 nM) contains a base-paired 5′-CpG-3′ step flanked on the 5′ side by a 4 nt internal loop and the 3′ side by a bulged U. Several viral 5′- and 3′-UTR RNA sequences that likely form binding sites for this PAC are identified.

Original languageEnglish (US)
Pages (from-to)663-672
Number of pages10
JournalChemistry and Biology
Issue number7
StatePublished - Jul 1 2003
Externally publishedYes

ASJC Scopus subject areas

  • Organic Chemistry


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