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

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 predi...

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Main Authors: Sabri, Mohamad Zulkeflee, Abdul Hamid, Azzmer Azzar, Sayed Hitam, Sharifah Mariam, Abdul Rahim, Mohd. Zulkhairi
Format: Article
Language:English
English
English
Published: Elsevier B.V. 2020
Subjects:
QD Chemistry
Online Access:http://irep.iium.edu.my/88194/1/88194_The%20assessment%20of%20three%20dimensional%20modelling.pdf
http://irep.iium.edu.my/88194/2/88194_The%20assessment%20of%20three%20dimensional%20modelling_SCOPUS.pdf
http://irep.iium.edu.my/88194/3/88194_The%20assessment%20of%20three%20dimensional%20modelling_WoS.pdf
http://irep.iium.edu.my/88194/
https://www.sciencedirect.com/science/article/abs/pii/S0301462220302003
https://doi.org/10.1016/j.bpc.2020.106492
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spelling my.iium.irep.881942021-02-02T01:18:29Z http://irep.iium.edu.my/88194/ The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application Sabri, Mohamad Zulkeflee Abdul Hamid, Azzmer Azzar Sayed Hitam, Sharifah Mariam Abdul Rahim, Mohd. Zulkhairi QD Chemistry 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 Elsevier B.V. 2020-12 Article PeerReviewed application/pdf en http://irep.iium.edu.my/88194/1/88194_The%20assessment%20of%20three%20dimensional%20modelling.pdf application/pdf en http://irep.iium.edu.my/88194/2/88194_The%20assessment%20of%20three%20dimensional%20modelling_SCOPUS.pdf application/pdf en http://irep.iium.edu.my/88194/3/88194_The%20assessment%20of%20three%20dimensional%20modelling_WoS.pdf 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 https://www.sciencedirect.com/science/article/abs/pii/S0301462220302003 https://doi.org/10.1016/j.bpc.2020.106492
institution Universiti Islam Antarabangsa Malaysia
building IIUM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider International Islamic University Malaysia
content_source IIUM Repository (IREP)
url_provider http://irep.iium.edu.my/
language English
English
English
topic QD Chemistry
spellingShingle QD Chemistry
Sabri, Mohamad Zulkeflee
Abdul Hamid, Azzmer Azzar
Sayed Hitam, Sharifah Mariam
Abdul Rahim, Mohd. Zulkhairi
The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
description 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
format Article
author Sabri, Mohamad Zulkeflee
Abdul Hamid, Azzmer Azzar
Sayed Hitam, Sharifah Mariam
Abdul Rahim, Mohd. Zulkhairi
author_facet Sabri, Mohamad Zulkeflee
Abdul Hamid, Azzmer Azzar
Sayed Hitam, Sharifah Mariam
Abdul Rahim, Mohd. Zulkhairi
author_sort Sabri, Mohamad Zulkeflee
title The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
title_short The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
title_full The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
title_fullStr The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
title_full_unstemmed The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
title_sort assessment of three dimensional modelling design for single strand dna aptamers for computational chemistry application
publisher Elsevier B.V.
publishDate 2020
url http://irep.iium.edu.my/88194/1/88194_The%20assessment%20of%20three%20dimensional%20modelling.pdf
http://irep.iium.edu.my/88194/2/88194_The%20assessment%20of%20three%20dimensional%20modelling_SCOPUS.pdf
http://irep.iium.edu.my/88194/3/88194_The%20assessment%20of%20three%20dimensional%20modelling_WoS.pdf
http://irep.iium.edu.my/88194/
https://www.sciencedirect.com/science/article/abs/pii/S0301462220302003
https://doi.org/10.1016/j.bpc.2020.106492
_version_ 1691732925798678528
score 13.211869

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