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In this chapter, we present the possibility of using ultraviolet (UV) and circular dichroism (CD) spectroscopies to analyze RNA–RNA interactions as an alternative or complementary technique to the classical RNA gel mobility shift assay. We present relevant, detailed protocols and the results obtained for a specific biological model to investigate all three methods. In this model, we studied the binding of small noncoding sRNA molecules of bacteriophage origin to fragments of bacterial mRNAs that were selected based on in silico analysis. We conclude that spectroscopic methods can be especially useful in analyzing the interactions of small RNAs with target transcripts and in the experimental validation of their target sites of action.

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Application of Ultraviolet (UV) and Circular Dichroism (CD) Spectroscopies to Study RNA-RNA Interactions of Regulatory RNAs of Bacteriophage Origin

  • 实验方案

  • 发表日期：

    2026年

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  • Natalia Lewandowska,
  • Sylwia Bloch,
  • Agnieszka Chylewska,
  • Aleksandra M. Dąbrowska,
  • Monika Mazur,
  • Joanna Zwolenkiewicz,
  • Wojciech Wesołowski,
  • Aleksandra Łukasiak,
  • Emilia Węglińska,
  • Mikołaj Olejniczak,
  • Grzegorz Węgrzyn,
  • Bożena Nejman-Faleńczyk

摘要

In this chapter, we present the possibility of using ultraviolet (UV) and circular dichroism (CD) spectroscopies to analyze RNA–RNA interactions as an alternative or complementary technique to the classical RNA gel mobility shift assay. We present relevant, detailed protocols and the results obtained for a specific biological model to investigate all three methods. In this model, we studied the binding of small noncoding sRNA molecules of bacteriophage origin to fragments of bacterial mRNAs that were selected based on in silico analysis. We conclude that spectroscopic methods can be especially useful in analyzing the interactions of small RNAs with target transcripts and in the experimental validation of their target sites of action.