Related Experiment Video
Updated: Jun 4, 2026

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
Published on: September 21, 2017
Redesign of a WW domain peptide for selective recognition of single-stranded DNA
Amanda L Stewart1, Jessica H Park, Marcey L Waters
1Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States.
Abstract:
A β-sheet miniprotein based on the FBP11 WW1 domain sequence has been redesigned for the molecular recognition of ssDNA. A previous report showed that a β-hairpin peptide dimer, (WKWK)(2), binds ssDNA with low micromolar affinity but with little selectivity over duplex DNA. This report extends those studies to a three-stranded β-sheet miniprotein designed to mimic the OB-fold. The new peptide binds ssDNA with low micromolar affinity and shows about 10-fold selectivity for ssDNA over duplex DNA. The redesigned peptide no longer binds its native ligand, the polyproline helix, confirming that the peptide has been redesigned for the function of binding ssDNA. Structural studies provide evidence that this peptide consists of a well-structured β-hairpin made of strands 2 and 3 with a less structured first strand that provides affinity for ssDNA but does not improve the stability of the full peptide. These studies provide insight into protein-DNA interactions as well as a novel example of protein redesign.
Related Concept Videos
Single-Strand DNA Binding Proteins
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Homologous Recombination
Restriction Enzymes
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

