Computational Analysis of Sequence Editability in the Theophylline RNA Aptamer as a Functional RNA Module.

Aamir Aman, Leonhard Sidl, Nitchakan Darai, Peter Wolschann, Thanyada Rungrotmongkol, Michael T Wolfinger

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Article in International journal of molecular sciences, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

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6 authors.

Aamir AmanProgram in Bioinformatics and Computational Biology, College of Interdisciplinary and Integrative Studies, Chulalongkorn University, Bangkok 10330, Thailand.ORCID 0009-0002-0593-8180

Leonhard SidlDepartment of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.ORCID 0009-0006-6440-4807

Nitchakan DaraiFuturistic Science Research Center, School of Science, Walailak University, Nakhon Si Thammarat 80160, Thailand.ORCID 0009-0002-9802-3659

Peter WolschannDepartment of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.ORCID 0000-0001-6104-6596

Thanyada RungrotmongkolProgram in Bioinformatics and Computational Biology, College of Interdisciplinary and Integrative Studies, Chulalongkorn University, Bangkok 10330, Thailand.ORCID 0000-0002-7402-3235

Michael T WolfingerDepartment of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.ORCID 0000-0003-0925-5205

Funding

Chulalongkorn University GCUGR1125682071DFWF Austrian Science Fund 10.55776/I6440

6 · The paper itself

Abstract

RNA aptamers are often used as ligand-recognition modules in engineered RNA systems, but integration into larger RNA constructs can influence stability and ligand binding. As a result, aptamer sequences may need to be adapted to new environments while preserving essential properties. Here, we examine this sequence editability problem for the theophylline RNA aptamer. Starting from the experimentally determined structure, we introduced targeted mutations in peripheral structural elements while leaving the recognition site unchanged. The native aptamer, mutated variants, a Mg

Indexed as

Aptamers, NucleotideRNATheophyllineBinding SitesLigandsMolecular Dynamics SimulationMutationNucleic Acid ConformationThermodynamicsAptamers, NucleotideLigandsRNATheophyllinecaffeineMD simulationmodified RNA aptamerRNA aptamertheophyllinewaterswap

Identifiers

PMID42653233

DOI10.3390/ijms27167228

PMCPMC13513662

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.