Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination

Abstract

Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilized T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discovered alternative transcription termination in the origin of replication sequence. Next, we employed circular DNA without transcription terminators to perform rolling circle transcription. This allowed us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.

Nanopore translocation reveals electrophoretic force on non-canonical RNA:DNA double helix

“…Further studies involving different forms of nucleic acids such as RR duplexes, C-DNA, and Z-DNA in ionic liquids would contribute to a better understanding of molecular transport of nucleic acids (60). The higher velocity of RD duplexes has implications for the density of labels in RNA identifiers used for nanopore RNA analysis (29, 61), which is important for their design and detection. This poses a challenge when applying nanopores for the analysis of shorter RNA molecules (<2 kbp), and additional strategies for slowing down RNA identifiers may be necessary.…”