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Benchmarking the Base Randomization Algorithm as a Possible Tool for the Initial Step of Generating a Virtual RNA

Kabelo P Mokgopa1, Shina D Oloniiju2, Kevin A Lobb1,3

  • 1Department of Chemistry, Rhodes University, Makhanda 6140, South Africa.

Biotech (Basel (Switzerland))
|September 22, 2025
PubMed
Summary

A new Base Randomization Algorithm (BRA) addresses the scarcity of aptamer databases. This method statistically generates valid aptamer sequences, advancing aptamer research and applications.

Keywords:
AlgorithmsAptamersBRAMFERNARandomizationvirtual library

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Computational Biology

Background:

  • Aptamer databases are scarce, hindering research and applications in healthcare, environmental monitoring, and biotechnology.
  • Existing databases lack comprehensive resources for aptamer discovery and utilization.
  • Aptamer databases are crucial for advancing molecular modeling and machine learning in the field.

Purpose of the Study:

  • To introduce and benchmark the Base Randomization Algorithm (BRA) as a solution for aptamer database scarcity.
  • To statistically analyze sequence properties generated by the BRA, including MFE, base composition, and arrangement.
  • To investigate the impact of sequence length on aptamer folding at secondary and tertiary levels.

Main Methods:

  • Development and benchmarking of the Base Randomization Algorithm (BRA).
  • Statistical analysis of generated aptamer sequences, focusing on MFE, base composition, and distribution.
  • Mathematical examination of base selection principles for sequence validity and statistical optimization.
  • Exploration of sequence length effects on aptamer structure folding.

Main Results:

  • The BRA generates aptamer sequences that follow a Gaussian distribution pattern.
  • Statistical analysis confirmed the validity and optimization of sequences generated by the BRA.
  • The study provides a mathematical approximation for the base mean in generated aptamer datasets.
  • Sequence length significantly influences aptamer secondary and tertiary structure folding.

Conclusions:

  • The Base Randomization Algorithm (BRA) offers a viable method for generating statistically sound aptamer sequences.
  • BRA can contribute to the development of much-needed aptamer databases.
  • This work facilitates further advancements in aptamer research, design, and application through improved sequence generation and analysis.