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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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A computational study of alternate SELEX.

Yeon-Jung Seo1, Marit Nilsen-Hamilton, Howard A Levine

  • 1Department of Statistics, Iowa State University, Ames, IA, 50011, USA, syeonj@iastate.edu.

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|June 1, 2014
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Summary

This study introduces an improved Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. By alternating positive and negative selection rounds, this alternate SELEX enhances nucleic acid (NA) specificity for desired targets.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Biology

Background:

  • Systematic Evolution of Ligands by Exponential Enrichment (SELEX) identifies nucleic acid (NA) molecules with specific target affinities.
  • Existing SELEX protocols can lead to enrichment of nonspecifically binding NAs, especially with multiple targets.

Purpose of the Study:

  • To develop and analyze an alternate SELEX protocol incorporating negative selection into positive SELEX.
  • To enhance the selectivity and specificity of NA pools for desired targets in multi-target scenarios.

Main Methods:

  • Iterative alternating rounds of positive and negative selection.
  • Polymerase Chain Reaction (PCR) amplification of selected NA pools.
  • Mathematical modeling of the alternate SELEX process as a discrete-time dynamical system using chemical potential.

Main Results:

  • The alternate SELEX process refines NA populations for high selectivity and specificity.
  • Mathematical formulations for negative and alternate selection efficiencies were defined.
  • Asymptotic behavior and global asymptotic stability conditions for the alternate SELEX system were analyzed.

Conclusions:

  • Alternating positive and negative selection rounds effectively minimizes nonspecific NA binding.
  • The alternate SELEX method yields NA pools with improved binding specificity.
  • Conditions for the global asymptotic stability of the alternate SELEX process were established.