Deoxynucleotide substitution: a new technique for sequence analysis of RNA
Related Experiment Video
Updated: Oct 16, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
Published on: July 10, 2020
Abstract:
It is possible to replace in a normal transcription reaction catalyzed by E.coli RNA polymerase one of the four precursors by the corresponding deoxynucleoside triphosphate. These deoxynucleotide-substituted RNA's offer interesting prospects for nucleotide sequence analysis. Indeed by the use of U(2)-RNase with dG-RNA, or pancreatic RNase with dC-RNA or dU-RNA, base specific cleavage can be obtained at any of the four residues. In this way overlap of at least six residues in length can be obtained for any site in the RNA. The technique offers also great benefit for solving the sequence of the more difficult T(1)-oligonucleotides. Some examples in the sequence analysis of SV40 DNA-Hind fragments are reported.
Related Concept Videos
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
RNA Editing
Sanger Sequencing
Nonsense-mediated mRNA Decay
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Complementary DNA

