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 C n linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a 10-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 has potential applications in chemical biology.

Original languageEnglish
Pages (from-to)423-430
Number of pages8
JournalRNA: a Publication of the RNA Society
Volume25
Issue number4
Early online date4 Jan 2019
DOIs
Publication statusPublished - Apr 2019

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Riboswitch
Guanidine
Ligands
Binding Sites
X-Rays
RNA

Keywords

  • Molecular recognition
  • RNA ligand design
  • Riboregulation
  • X-ray crystallography

Cite this

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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 C n linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a 10-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 has potential applications in chemical biology.",
keywords = "Molecular recognition, RNA ligand design, Riboregulation, X-ray crystallography",
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",
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doi = "10.1261/rna.069567.118",
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journal = "RNA: a Publication of the RNA Society",
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publisher = "Cold Spring Harbor Laboratory Press",
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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 - 2019/4

Y1 - 2019/4

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 C n linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a 10-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 has 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 C n linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a 10-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 has potential applications in chemical biology.

KW - Molecular recognition

KW - RNA ligand design

KW - Riboregulation

KW - X-ray crystallography

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DO - 10.1261/rna.069567.118

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