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Computer-aided design of aptamers for cytochrome p450.

Dmitrii S Shcherbinin1, Oksana V Gnedenko1, Svetlana A Khmeleva1

  • 1Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.

Journal of Structural Biology
|July 14, 2015
PubMed
Summary

In silico selection of aptamers for proteins was developed. This method designed 15-mer DNA aptamers targeting cytochrome P450 51A1, showing high affinity in experimental validation.

Keywords:
AptamerBioinformaticsCytochrome P450 51A1Molecular dockingMolecular dynamicsRational designSELEX

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Area of Science:

  • Biotechnology
  • Computational Biology
  • Molecular Biology

Background:

  • Aptamers are DNA or RNA oligonucleotides selected via SELEX for high-affinity target binding.
  • In silico methods offer a potential alternative to experimental aptamer selection.
  • Cytochrome P450 51A1 is a key enzyme with implications in various biological processes.

Purpose of the Study:

  • To develop and validate an in silico approach for designing protein-specific aptamers.
  • To design novel aptamers targeting cytochrome P450 51A1 using computational methods.
  • To experimentally verify the binding affinity of the designed aptamers.

Main Methods:

  • In silico aptamer design involving identification of binding sites, recognition/structural element design, and affinity evaluation.
  • Docking and molecular dynamics simulations were employed for aptamer design.
  • Surface Plasmon Resonance (SPR) biosensor was used for experimental affinity assessment.

Main Results:

  • A set of 15-mer DNA aptamers targeting cytochrome P450 51A1 was successfully designed computationally.
  • Experimental validation confirmed the interaction of synthesized aptamers with cytochrome P450 51A1.
  • Dissociation constant (Kd) values in the range of 10(-6)-10(-7) M were determined for the aptamers.

Conclusions:

  • The described in silico approach is effective for designing functional aptamers against protein targets.
  • Computational methods can accelerate aptamer discovery and development.
  • The designed aptamers represent potential tools for studying cytochrome P450 51A1.