Affiliations 

  • 1 Bioengineering Section, Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET), Lot 1988, Bandar Vendor Taboh Naning, 78000 Alor Gajah, Melaka, Malaysia. Electronic address: [email protected]
  • 2 Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
  • 3 Bioengineering Section, Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET), Lot 1988, Bandar Vendor Taboh Naning, 78000 Alor Gajah, Melaka, Malaysia
  • 4 Technical Foundation Section, Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET), Lot 1988, Bandar Vendor Taboh Naning, 78000, Alor Gajah, Melaka, Malaysia
Biophys Chem, 2020 12;267:106492.
PMID: 33035750 DOI: 10.1016/j.bpc.2020.106492

Abstract

Aptamers are oligonucleotides and peptides around 15-100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validation tools, unlike protein structures. We suggest an approach to design the stem-loop/hairpin for the three dimensional structure of DNA aptamers through serial applications of computational prediction methods by comparing the simulated structures with the experimental data deposited in PDB Data bank, followed by MD simulations. The result shows minimal structural differences were observed between the designed and the original NMR aptamers, and the stem-loop conformational structures were also retained during the MD thus suggesting the proposed aptamers designing methods are able to synthesize a high quality molecular structure of hairpin aptamers, comparable to the NMR structures.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.