In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain

Progesterone receptor plays an important role in the progression of breast cancer. Currently, antibody-based Immunohistochemistry is used in pathological assessment of PR levels for the detection of breast cancer. The shortcomings associated with antibodies pave the path to use aptamers as the al...

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Main Author:	Nadhan, Navien Tholasi
Format:	Thesis
Language:	English
Published:	2022
Subjects:	R5-130.5 General works
Online Access:	http://eprints.usm.my/59309/1/NAVIEN%20AL%20THOLASI%20NADHAN%20-%20TESIS%20cut.pdf
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spelling	my-usm-ep.593092023-09-01T02:29:33Z In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain 2022-08 Nadhan, Navien Tholasi R5-130.5 General works Progesterone receptor plays an important role in the progression of breast cancer. Currently, antibody-based Immunohistochemistry is used in pathological assessment of PR levels for the detection of breast cancer. The shortcomings associated with antibodies pave the path to use aptamers as the alternatives. Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that are capable of binding to their cognate target molecules with high affinity and specificity based on their unique structural folding capacity. The tediousness and rigor associated with certain steps of the conventional SELEX intensify the efforts to select DNA aptamers using in silico-docking approach. That said, we report an in silico selection and validation of DNA aptamer to the progesterone receptor DNA binding domain (PR DBD) using ssDNA sequences derived from human progesterone response elements (PREs). Firstly, a library of sixty-four different nearnative ssDNA analogs of the corresponding PRE sequences was designed and subjected to secondary and tertiary structural determination. After that, docking between the ssDNA tertiary structures with the PR DBD was carried out using PatchDock. The sequence with the highest docking score was chosen as the aptamer candidate and further validated by in vitro direct ELASA. Among the candidates, we selected the ssDNA sequence (PRDBDapt17; 5′- AGAACAGCGTGTTCT -3′), which showed the highest docking scores of 11334 as a promising PR DBD binding aptamer. In addition, the PRDBDapt17 detected recombinant PR DBD in direct ELASA with a limit of detection of 3.91 nM. 2022-08 Thesis http://eprints.usm.my/59309/ http://eprints.usm.my/59309/1/NAVIEN%20AL%20THOLASI%20NADHAN%20-%20TESIS%20cut.pdf application/pdf en public masters Universiti Sains Malaysia Institut Perubatan & Pergigian Termaju
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	R5-130.5 General works
spellingShingle	R5-130.5 General works Nadhan, Navien Tholasi In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain
description	Progesterone receptor plays an important role in the progression of breast cancer. Currently, antibody-based Immunohistochemistry is used in pathological assessment of PR levels for the detection of breast cancer. The shortcomings associated with antibodies pave the path to use aptamers as the alternatives. Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that are capable of binding to their cognate target molecules with high affinity and specificity based on their unique structural folding capacity. The tediousness and rigor associated with certain steps of the conventional SELEX intensify the efforts to select DNA aptamers using in silico-docking approach. That said, we report an in silico selection and validation of DNA aptamer to the progesterone receptor DNA binding domain (PR DBD) using ssDNA sequences derived from human progesterone response elements (PREs). Firstly, a library of sixty-four different nearnative ssDNA analogs of the corresponding PRE sequences was designed and subjected to secondary and tertiary structural determination. After that, docking between the ssDNA tertiary structures with the PR DBD was carried out using PatchDock. The sequence with the highest docking score was chosen as the aptamer candidate and further validated by in vitro direct ELASA. Among the candidates, we selected the ssDNA sequence (PRDBDapt17; 5′- AGAACAGCGTGTTCT -3′), which showed the highest docking scores of 11334 as a promising PR DBD binding aptamer. In addition, the PRDBDapt17 detected recombinant PR DBD in direct ELASA with a limit of detection of 3.91 nM.
format	Thesis
qualification_level	Master's degree
author	Nadhan, Navien Tholasi
author_facet	Nadhan, Navien Tholasi
author_sort	Nadhan, Navien Tholasi
title	In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain
title_short	In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain
title_full	In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain
title_fullStr	In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain
title_full_unstemmed	In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain
title_sort	in silico selection and validation of dna aptamer against progesterone receptor dna binding domain
granting_institution	Universiti Sains Malaysia
granting_department	Institut Perubatan & Pergigian Termaju
publishDate	2022
url	http://eprints.usm.my/59309/1/NAVIEN%20AL%20THOLASI%20NADHAN%20-%20TESIS%20cut.pdf
_version_	1776101284954243072

In Silico Selection And Validation Of Dna Aptamer Against Progesterone Receptor Dna Binding Domain

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