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A small molecule microarray platform to select RNA internal loop-ligand interactions

Academic Article
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Overview

authors

  • Childs-Disney, J. L.
  • Wu, M. L.
  • Pushechnikov, A.
  • Aminova, O.
  • Disney, Matthew

publication date

  • November 2007

journal

  • ACS Chemical Biology  Journal

abstract

  • Herein, we report the development of a microarray platform to select RNA motif-ligand interactions that allows simultaneous screening of both RNA and chemical space. We used this platform to identify the RNA internal loops that bind 6'- N-5-hexynoate kanamycin A ( 1). Selected internal loops that bind 1 were studied in detail and commonly display an adenine across from a cytosine independent of the size of the loop. Additional preferences are also observed. For 3 x 3 nucleotide loops, there is a preference for purines, and for 2 x 2 nucleotide loops there is a preference for pyrimidines neighbored by an adenine across from a cytosine. This technique has several advantageous features for selecting RNA motif-ligand interactions: (1) higher affinity RNA motif-ligand interactions are identified by harvesting bound RNAs from lower ligand loadings; (2) bound RNAs are harvested from the array via gel extraction, mitigating kinetic biases in selections; and (3) multiple selections are completed on a single array surface. To further demonstrate that multiple selections can be completed in parallel on the same array surface, we selected the RNA internal loops from a 4096-member RNA internal loop library that bound a four-member aminoglycoside library. These experiments probed 16,384 (4 aminoglycoside x 4096-member RNA library) interactions in a single experiment. These studies allow for parallel screening of both chemical and RNA space to improve our understanding of RNA-ligand interactions. This information may facilitate the rational and modular design of small molecules targeting RNA.

subject areas

  • Base Sequence
  • Kanamycin
  • Ligands
  • Oligonucleotide Array Sequence Analysis
  • RNA
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Identity

International Standard Serial Number (ISSN)

  • 1554-8929

Digital Object Identifier (DOI)

  • 10.1021/6700174r

PubMed ID

  • 17975888
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Additional Document Info

start page

  • 745

end page

  • 754

volume

  • 2

issue

  • 11

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