Structure-guided design of a high affinity ligand for a riboswitch

Lin Huang, Jia Wang, Timothy Wilson, David Lilley (Lead / Corresponding author)

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Abstract

We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands have potential applications in chemical biology.
Original languageEnglish
JournalRNA: a Publication of the RNA Society
Early online date4 Jan 2019
DOIs
Publication statusE-pub ahead of print - 4 Jan 2019

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Riboswitch
Guanidine
Ligands
Binding Sites
X-Rays
RNA

Keywords

  • RNA ligand design
  • X-ray crystallography
  • molecular recognition
  • riboregulation

Cite this

@article{698767f181c94b81ba2e029ea06a271f,
title = "Structure-guided design of a high affinity ligand for a riboswitch",
abstract = "We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands have potential applications in chemical biology.",
keywords = "RNA ligand design, X-ray crystallography, molecular recognition, riboregulation",
author = "Lin Huang and Jia Wang and Timothy Wilson and David Lilley",
note = "Funding: Cancer Research UK (program grant A18604); Wellcome Trust (in-house diffractometer).",
year = "2019",
month = "1",
day = "4",
doi = "10.1261/rna.069567.118",
language = "English",
journal = "RNA: a Publication of the RNA Society",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",

}

TY - JOUR

T1 - Structure-guided design of a high affinity ligand for a riboswitch

AU - Huang, Lin

AU - Wang, Jia

AU - Wilson, Timothy

AU - Lilley, David

N1 - Funding: Cancer Research UK (program grant A18604); Wellcome Trust (in-house diffractometer).

PY - 2019/1/4

Y1 - 2019/1/4

N2 - We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands have potential applications in chemical biology.

AB - We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands have potential applications in chemical biology.

KW - RNA ligand design

KW - X-ray crystallography

KW - molecular recognition

KW - riboregulation

U2 - 10.1261/rna.069567.118

DO - 10.1261/rna.069567.118

M3 - Article

JO - RNA: a Publication of the RNA Society

JF - RNA: a Publication of the RNA Society

SN - 1355-8382

ER -