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Libraries for genomic SELEX

B S Singer1, T Shtatland, D Brown

  • 1Department of Molecular Biology, University of Colorado, Boulder 80309-0347, USA.

Nucleic Acids Research
|February 15, 1997
PubMed
Summary
This summary is machine-generated.

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Genomic SELEX identifies protein-nucleic acid interactions by analyzing genomic DNA. This method uses PCR libraries from E. coli, yeast, and human genomes for efficient network analysis.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Proteins regulating gene expression by binding nucleic acids in vivo are increasingly identified.
  • Understanding these protein-nucleic acid interactions is crucial for deciphering gene regulation networks.

Purpose of the Study:

  • To introduce and validate a method for constructing genomic DNA PCR libraries suitable for genomic SELEX.
  • To enable the rapid identification of protein-nucleic acid interaction networks within an organism's genome.

Main Methods:

  • Genomic SELEX, a method involving iterative binding, partitioning, and amplification of nucleic acids.
  • Construction of genomic DNA PCR libraries from Escherichia coli, Saccharomyces cerevisiae, and human genomes.
  • Transcription of DNA libraries using T7 RNA polymerase.

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Main Results:

  • Successfully constructed genomic DNA PCR libraries from three diverse organisms.
  • Libraries contain overlapping inserts originating from most genomic positions.
  • Demonstrated suitability of these libraries for genomic SELEX applications.

Conclusions:

  • The developed method provides a rapid and efficient way to generate genomic libraries for SELEX.
  • These libraries facilitate the large-scale identification of high-affinity protein-binding sites across genomes.
  • This approach is valuable for mapping protein-nucleic acid interactions in various organisms.