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Related Concept Videos

RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Related Experiment Video

Updated: Jun 23, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Aptamers targeting RNA molecules.

Marguerite Watrin1, Eric Dausse, Isabelle Lebars

  • 1Institut Européen de Chimie et Biologie, Pessac, France, Université Victor Segalen, Bordeaux, France.

Methods in Molecular Biology (Clifton, N.J.)
|April 21, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces genomic SELEX and 2D-SELEX methods for aptamer discovery, focusing on RNA structures like stem-loops. These techniques enable selection of modified aptamers for studying viral RNA, such as HIV-1 trans-activating responsive element.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Oligonucleotides often struggle to bind folded RNA targets effectively.
  • In vitro selection (SELEX) can yield aptamers that exploit non-double-stranded RNA features, offering insights into RNA tertiary structures and ligand interactions.

Purpose of the Study:

  • To describe a genomic SELEX approach for recognizing RNA stem-loop structures involved in kissing complexes.
  • To detail a 2D-SELEX procedure combining in vitro selection with dynamic combinatorial chemistry for modified aptamer discovery.
  • To present optimized in vitro transcription conditions for producing RNA suitable for NMR studies.

Main Methods:

  • Genomic SELEX for aptamer selection against specific RNA structures.
  • 2D-SELEX incorporating dynamic combinatorial chemistry to generate aptamer derivatives with modified nucleotides.
  • Optimization of in vitro transcription for large-scale RNA production for structural analysis.

Main Results:

  • Demonstration of genomic SELEX for identifying aptamers targeting stem-loop structures prone to kissing complex formation.
  • Successful application of 2D-SELEX to select aptamer variants with non-natural nucleotides.
  • Establishment of conditions for high-yield RNA transcription suitable for NMR.

Conclusions:

  • The described SELEX technologies are effective for aptamer discovery against complex RNA targets.
  • These methods were successfully applied to the human immunodeficiency virus type 1 trans-activating responsive element, crucial for viral transcription.