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Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking.

Ricardo Oliveira1,2, Eva Pinho1,2, Ana Luísa Sousa1

  • 1INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, Vila do Conde, Portugal.

Plos One
|March 23, 2022
PubMed
Summary

This study introduces a computational workflow to predict aptamer structures and target binding. This method aids in designing novel nucleic acid mimic (NAM) aptamers with enhanced stability and specificity.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Molecular Biology

Background:

  • Aptamers are single-stranded oligonucleotides selected via SELEX for high-affinity target binding.
  • Their three-dimensional structure dictates binding specificity.
  • Nucleic acid mimic (NAM) aptamers incorporate unnatural nucleotides for improved stability and performance.

Purpose of the Study:

  • To present an accessible in silico workflow for predicting the tertiary structure of NAM, DNA, and RNA aptamers.
  • To predict the docking interactions between aptamers and their target molecules.
  • To validate the workflow using existing experimental data.

Main Methods:

  • Utilized free software and web servers for computational structure prediction.
  • Focused on predicting tertiary conformation and target docking.
  • Validated the workflow with 2'-O-methyl (2'OMe), LNA, DNA, and RNA aptamers from the Protein Data Bank.

Main Results:

  • Successfully predicted tertiary structures for all tested aptamers.
  • Achieved accurate docking models with good structural similarity to experimental data.
  • Demonstrated the workflow's efficacy for various aptamer types, including NAM aptamers.

Conclusions:

  • The developed in silico workflow accurately predicts aptamer tertiary structure and target docking.
  • This approach facilitates rational design and modification of aptamers, especially NAM aptamers.
  • It offers a valuable tool to avoid costly trial-and-error in aptamer development.