Non-enzymatic conversion of RNA sequence information into DNA by squaramide ligation for accurate RNA quantification
Non-enzymatic conversion of RNA sequence information into DNA by squaramide ligation for accurate RNA quantification
RNA is an important biomarker for research and diagnostics. However, its transient nature and fragility require its conversion to DNA prior to detection. To this end, enzymatic approaches have been used but are limited by biological constraints, while chemical methods hold much promise but have not been competitive alternatives. Here, we demonstrate that chemical ligation of DNA oligonucleotides hybridised to a complementary RNA template to form an artificial squaramide backbone can be used to quantify sub-attomoles of RNA. This reaction requires mildly buffered, monovalent salt solutions with no extra chemical reagents, and can be performed at a range of temperatures within minutes. We describe the careful design of a three-component ligation system that minimises false-positives and demonstrate its use in qPCR to detect long RNAs in complex systems. Detection limits of 0.3 attomoles are achieved making it one of the most sensitive and specific chemical ligation systems to the best of our knowledge.
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Taemaitree, Lapatrada
c069b3ef-6d34-4a85-a351-2576fb01af64
Burba, Friedrich
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Harvey, Nina
161bd516-2289-42fe-9a58-da4aa806d79f
Shivalingam, Arun
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Brown, Tom
890edb72-2009-44e2-8e8b-30be41e60c7e
El-Sagheer, Afaf H.
05b8295a-64ad-4fdf-ad57-c34934a46c04
Taemaitree, Lapatrada, Burba, Friedrich, Harvey, Nina, Shivalingam, Arun, Brown, Tom and El-Sagheer, Afaf H.
(2026)
Non-enzymatic conversion of RNA sequence information into DNA by squaramide ligation for accurate RNA quantification.
Nature Communications, 9 (1), [272].
(doi:10.1038/s42004-026-02069-5).
Abstract
RNA is an important biomarker for research and diagnostics. However, its transient nature and fragility require its conversion to DNA prior to detection. To this end, enzymatic approaches have been used but are limited by biological constraints, while chemical methods hold much promise but have not been competitive alternatives. Here, we demonstrate that chemical ligation of DNA oligonucleotides hybridised to a complementary RNA template to form an artificial squaramide backbone can be used to quantify sub-attomoles of RNA. This reaction requires mildly buffered, monovalent salt solutions with no extra chemical reagents, and can be performed at a range of temperatures within minutes. We describe the careful design of a three-component ligation system that minimises false-positives and demonstrate its use in qPCR to detect long RNAs in complex systems. Detection limits of 0.3 attomoles are achieved making it one of the most sensitive and specific chemical ligation systems to the best of our knowledge.
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s42004-026-02069-5_reference
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Accepted/In Press date: 5 May 2026
e-pub ahead of print date: 19 May 2026
Published date: 19 May 2026
Identifiers
Local EPrints ID: 513160
URI: https://eprints.soton.ac.uk/id/eprint/513160
ISSN: 2041-1723
PURE UUID: bcb2fed5-2871-4cc0-b550-fd4ca6fb71a6
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Date deposited: 05 Aug 2026 16:32
Last modified: 13 Sep 2026 15:50
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Contributors
Author:
Lapatrada Taemaitree
Author:
Friedrich Burba
Author:
Nina Harvey
Author:
Arun Shivalingam
Author:
Tom Brown
Author:
Afaf H. El-Sagheer
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