The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application

Sabri, Mohamad Zulkeflee and Abdul Hamid, Azzmer Azzar and Sayed Hitam, Sharifah Mariam and Abdul Rahim, Mohd. Zulkhairi (2020) The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application. Biophysical Chemistry, 267. ISSN 03014622 E-ISSN 1873-4200

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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

Item Type:	Article (Journal)
Uncontrolled Keywords:	Aptamer, Non-SELEX, DNA hairpin, Computational chemistryThree-dimensional DNA designMolecular dynamics
Subjects:	Q Science > QD Chemistry
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Science > Department of Biotechnology
Depositing User:	Suhani Saarani
Date Deposited:	02 Feb 2021 09:18
Last Modified:	02 Feb 2021 09:18
URI:	http://irep.iium.edu.my/id/eprint/88194

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