Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule

Lukas J. Aaldering, Vasanthanathan Poongavanam, Niels Langkjær, N. Arul Murugan, Per Trolle Jørgensen, Jesper Wengel, Rakesh N. Veedu*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3′-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.

Original languageEnglish
JournalChemBioChem
Volume18
Issue number8
Pages (from-to)755–763
ISSN1439-4227
DOIs
Publication statusPublished - 2017

Fingerprint

Carbon
Molecules
Thrombin
Nucleic Acids
Circular dichroism spectroscopy
Denaturation
Molecular modeling
thrombin aptamer
Structural dynamics
Chemical modification
Circular Dichroism
Anticoagulants
Experiments

Keywords

  • Aptamers
  • G-quadruplex
  • Modified DNA
  • Thrombin
  • Unlocked nucleic acid

Cite this

@article{c71bdd24943e436dbb8d43476bee16f5,
title = "Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule",
abstract = "The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3′-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.",
keywords = "Aptamers, G-quadruplex, Modified DNA, Thrombin, Unlocked nucleic acid",
author = "Aaldering, {Lukas J.} and Vasanthanathan Poongavanam and Niels Langkj{\ae}r and Murugan, {N. Arul} and J{\o}rgensen, {Per Trolle} and Jesper Wengel and Veedu, {Rakesh N.}",
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doi = "10.1002/cbic.201600654",
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Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule. / Aaldering, Lukas J.; Poongavanam, Vasanthanathan; Langkjær, Niels; Murugan, N. Arul; Jørgensen, Per Trolle; Wengel, Jesper; Veedu, Rakesh N.

In: ChemBioChem, Vol. 18, No. 8, 2017, p. 755–763.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule

AU - Aaldering, Lukas J.

AU - Poongavanam, Vasanthanathan

AU - Langkjær, Niels

AU - Murugan, N. Arul

AU - Jørgensen, Per Trolle

AU - Wengel, Jesper

AU - Veedu, Rakesh N.

PY - 2017

Y1 - 2017

N2 - The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3′-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.

AB - The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3′-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.

KW - Aptamers

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KW - Modified DNA

KW - Thrombin

KW - Unlocked nucleic acid

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