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RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
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Direct selection of RNA beacon aptamers.

Daniel P Morse1

  • 1Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA. morse@usna.edu

Biochemical and Biophysical Research Communications
|May 30, 2007
PubMed
Summary

This study introduces a novel method to directly select RNA beacon aptamers for detecting specific molecules like the antibiotic tobramycin. The selected RNA molecules effectively signal tobramycin presence through fluorescence changes.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Nucleic Acid Aptamer Technology

Background:

  • Beacon aptamers are RNA molecules that signal ligand presence via fluorescence changes.
  • Existing methods for beacon aptamer selection are often indirect and complex.
  • Ligand binding typically induces conformational changes separating fluorophore/quencher pairs, altering fluorescence.

Purpose of the Study:

  • To develop a direct selection method for RNA beacon aptamers.
  • To select RNA molecules capable of detecting the aminoglycoside antibiotic tobramycin.
  • To ensure selected aptamers exhibit ligand-induced conformational changes for fluorescence signaling.

Main Methods:

  • A novel selection strategy was employed to simultaneously select for ligand binding and conformational change.

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  • RNA molecules were subjected to 14 rounds of selection against tobramycin.
  • Selected RNA sequences were converted into beacon aptamers for functional testing.

    • Main Results:

    • Two distinct RNA sequence families were identified after selection.
    • Beacon aptamers derived from these families specifically detected tobramycin.
    • A control RNA lacking selection pressure did not function as a tobramycin beacon aptamer.

    Conclusions:

    • The developed method efficiently selects functional RNA beacon aptamers.
    • This approach simplifies the generation of fluorescent biosensors for specific targets.
    • The selected aptamers demonstrate high specificity for tobramycin detection.