Analysis of double-stranded RNA using an innovative nanopore sequencing method with an integrated biosensor (Sens-Nanopore)

Programme

GFF/ FTI-Strategy Lower Austria 2021-2027

Project coordination

Danube Private University, Prof. Dr. Mandana Amiri

Project partner

• CNRS Délégation Alsace 

Researchers involved at DPU

• Hon.-Prof. Prof. Dr. Wolfgang Knoll
• Univ.-Prof. DI Dr. Christoph Kleber

Abstract

Double-stranded RNA (dsRNA) is associated with viral infections. In RNA viruses, dsRNA constitutes the viral genome, whereas in DNA viruses it is generated during viral replication within host cells. Nearly all organisms possess the ability to detect dsRNA, primarily as a mechanism to mitigate potential infections. Therefore, the presence of long viral dsRNA can be regarded as a universal biomarker for viral infections. The development of reliable and rapid quantitative and qualitative dsRNA analysis methods could, in the future, contribute significantly to effective epidemic control.

The novel nanopore technology concept enables simple and successful sequencing of viral variants; however, it currently still requires labor-intensive sample preparation steps. Rapid and direct fingerprinting of viral dsRNA for clinical bedside diagnostics using nanopore technology therefore remains an unresolved challenge. The aim of the Sens-Nanopore project is to bridge this gap by combining nanopore-based dsRNA sequencing with biosensor technology and efficient, specific bioreceptor–analyte surface interactions.

Sens-Nanopore proposes the integration of viral dsRNA-binding proteins onto carbon-based sensors, particularly laser-induced graphene (LIG)-based field-effect transistors (FETs), which are fabricated through laser processing of polyimide thin films for the quantitative detection of viral dsRNA. Subsequent dsRNA fingerprinting will then be performed. The key functional characteristics of this novel dsRNA sensor system will be evaluated in this project using model systems.

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