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In silico molecular docking in DNA aptamer development.

Tholasi Nadhan Navien1, Ramesh Thevendran1, Hazrina Yusof Hamdani1

  • 1Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.

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|October 21, 2020
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Summary
This summary is machine-generated.

DNA aptamers, generated via SELEX, offer stability for diagnostics. This review details in silico molecular docking methods, software, and limitations for DNA aptamer development, complementing in vitro techniques.

Keywords:
DNA aptamerIn silicoIn silico maturationMolecular dockingStructural modeling

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Bioinformatics

Background:

  • Aptamers are single-stranded DNA or RNA oligonucleotides selected through SELEX, known for binding affinity and specificity.
  • DNA aptamers exhibit superior stability over RNA aptamers, making them ideal for diagnostic applications.
  • Traditional SELEX methods can be rigorous, prompting interest in computational approaches.

Purpose of the Study:

  • To provide an overview of in silico molecular docking approaches for DNA aptamer generation.
  • To detail the stepwise procedures and software utilized in computational DNA aptamer development.
  • To discuss in silico maturation strategies and the inherent limitations of these computational methods.

Main Methods:

  • Review of in silico molecular docking strategies for aptamer design.
  • Analysis of software tools employed in computational aptamer selection.
  • Exploration of integrated in silico and in vitro SELEX methodologies.

Main Results:

  • Detailed stepwise procedures for in silico DNA aptamer generation are presented.
  • Various software solutions for computational aptamer development are highlighted.
  • The review underscores the potential and limitations of in silico maturation strategies.

Conclusions:

  • In silico molecular docking offers a valuable adjunct to in vitro SELEX for DNA aptamer development.
  • Computational approaches can streamline the generation of stable and specific DNA aptamers for diagnostics.
  • Understanding the limitations of in silico methods is crucial for effective application in aptamer discovery.