Ligand specificity and affinity in the sulforhodamine B binding RNA aptamer

Kyle A Piccolo; Brooke McNeil; Jeff Crouse; Su Ji Lim; Sarah C Bickers; W Scott Hopkins; Thorsten Dieckmann

doi:10.1016/j.bbrc.2020.06.056

Ligand specificity and affinity in the sulforhodamine B binding RNA aptamer

Biochem Biophys Res Commun. 2020 Aug 27;529(3):666-671. doi: 10.1016/j.bbrc.2020.06.056. Epub 2020 Jul 18.

Authors

Kyle A Piccolo¹, Brooke McNeil¹, Jeff Crouse², Su Ji Lim², Sarah C Bickers¹, W Scott Hopkins², Thorsten Dieckmann³

Affiliations

¹ Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
² Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
³ Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada. Electronic address: thorsten.dieckmann@uwaterloo.ca.

PMID: 32736690
DOI: 10.1016/j.bbrc.2020.06.056

Abstract

Binding affinity and selectivity are critical properties of aptamers that must be optimized for any application. The sulforhodamine B binding RNA aptamer (SRB-2) is a somewhat promiscuous aptamer that can bind ligands that vary markedly in shape, size and charge. Here we categorize potential ligands based on their binding mode and structural characteristics required for high affinity and selectivity. Several known and potential ligands of SRB-2 were screened for binding affinity using LSPR, ITC and NMR spectroscopy. The study shows that rhodamine B has the ideal structural and electrostatic properties for selective and high-affinity binding of the SRB-2 aptamer.

Keywords: Aptamer; Binding affinity; Ligand; SRB-2; Selectivity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alkylation
Aptamers, Nucleotide / chemistry
Aptamers, Nucleotide / metabolism*
Base Sequence
Binding Sites
Coloring Agents / chemistry
Coloring Agents / metabolism*
Ligands
Nucleic Acid Conformation
Rhodamines / chemistry
Rhodamines / metabolism*
Static Electricity

Substances

Aptamers, Nucleotide
Coloring Agents
Ligands
Rhodamines
lissamine rhodamine B