Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles
The E6 region has higher protuberant probability annealing than consensus probe focusing on another region in the human papillomavirus (HPV) genome in terms of detection and screening method. Here, we designed the first multiple virus single-stranded deoxyribonucleic acid (ssDNA) for multiple detect...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Published: |
Wiley
2021
|
| _version_ | 1796983269838815232 |
|---|---|
| author | Jaapar, F. Nadhirah Parmin, Nor Azizah A. Halim, N. Hamidah Hashim, Uda Gopinath, Subash Chandra Bose Halim, F. Syakirah A. Rahim, Ruslinda Voon, C. H. M. N., Afnan Uda Sharifah Nadzirah Rejali, Zulida Mohd Jamil, Amilia Afzan Zakaria, Iffah Izzati |
| author_facet | Jaapar, F. Nadhirah Parmin, Nor Azizah A. Halim, N. Hamidah Hashim, Uda Gopinath, Subash Chandra Bose Halim, F. Syakirah A. Rahim, Ruslinda Voon, C. H. M. N., Afnan Uda Sharifah Nadzirah Rejali, Zulida Mohd Jamil, Amilia Afzan Zakaria, Iffah Izzati |
| author_sort | Jaapar, F. Nadhirah |
| collection | UPM |
| description | The E6 region has higher protuberant probability annealing than consensus probe focusing on another region in the human papillomavirus (HPV) genome in terms of detection and screening method. Here, we designed the first multiple virus single-stranded deoxyribonucleic acid (ssDNA) for multiple detections in an early phase of screening for cervical cancer in the E6 region and became a fundamental evolution of detection electrochemical HPV biosensor. Gene profiling of the virus ssDNA sequences has been carried by high-end bioinformatics tools such as GenBank, Basic Local Alignment Searching Tools (BLAST), and Clustal OMEGA in a row. The output from bioinformatics tools resulted in 100% of similarities between our virus ssDNA probe and HPV complete genome in the databases. The cross-validation between HPV genome and our designed virus ssDNA provided high specificity and selectivity during screening methods compared with Pap smear. The DNA probe for HPV 18, 5' COOH-GAT CCA GAA GGT ACA GAC GGG GAG GGC ACG 3', while 5'COOH-GGG CGC TGT GCA GTG TGT TGG AGA CCC CGA3' as DNA probe for HPV 58 designed with 66.77% guanine (G) and cytosine (C) content for both. Our virus ssDNA probe for the HPV biosensor promises high sensitivity, specificity, selectivity, repeatability, low fluid consumption, and will be useful in mini-size diagnostic devices for cervical cancer detection. |
| first_indexed | 2024-03-06T11:04:08Z |
| format | Article |
| id | upm.eprints-96625 |
| institution | Universiti Putra Malaysia |
| last_indexed | 2024-03-06T11:04:08Z |
| publishDate | 2021 |
| publisher | Wiley |
| record_format | dspace |
| spelling | upm.eprints-966252023-02-01T07:45:50Z http://psasir.upm.edu.my/id/eprint/96625/ Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles Jaapar, F. Nadhirah Parmin, Nor Azizah A. Halim, N. Hamidah Hashim, Uda Gopinath, Subash Chandra Bose Halim, F. Syakirah A. Rahim, Ruslinda Voon, C. H. M. N., Afnan Uda Sharifah Nadzirah Rejali, Zulida Mohd Jamil, Amilia Afzan Zakaria, Iffah Izzati The E6 region has higher protuberant probability annealing than consensus probe focusing on another region in the human papillomavirus (HPV) genome in terms of detection and screening method. Here, we designed the first multiple virus single-stranded deoxyribonucleic acid (ssDNA) for multiple detections in an early phase of screening for cervical cancer in the E6 region and became a fundamental evolution of detection electrochemical HPV biosensor. Gene profiling of the virus ssDNA sequences has been carried by high-end bioinformatics tools such as GenBank, Basic Local Alignment Searching Tools (BLAST), and Clustal OMEGA in a row. The output from bioinformatics tools resulted in 100% of similarities between our virus ssDNA probe and HPV complete genome in the databases. The cross-validation between HPV genome and our designed virus ssDNA provided high specificity and selectivity during screening methods compared with Pap smear. The DNA probe for HPV 18, 5' COOH-GAT CCA GAA GGT ACA GAC GGG GAG GGC ACG 3', while 5'COOH-GGG CGC TGT GCA GTG TGT TGG AGA CCC CGA3' as DNA probe for HPV 58 designed with 66.77% guanine (G) and cytosine (C) content for both. Our virus ssDNA probe for the HPV biosensor promises high sensitivity, specificity, selectivity, repeatability, low fluid consumption, and will be useful in mini-size diagnostic devices for cervical cancer detection. Wiley 2021 Article PeerReviewed Jaapar, F. Nadhirah and Parmin, Nor Azizah and A. Halim, N. Hamidah and Hashim, Uda and Gopinath, Subash Chandra Bose and Halim, F. Syakirah and A. Rahim, Ruslinda and Voon, C. H. and M. N., Afnan Uda and Sharifah Nadzirah and Rejali, Zulida and Mohd Jamil, Amilia Afzan and Zakaria, Iffah Izzati (2021) Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles. Biotechnology and Applied Biochemistry, 69 (5). pp. 1966-1983. ISSN 0885-4513; ESSN: 1470-8744 https://iubmb.onlinelibrary.wiley.com/doi/10.1002/bab.2260 10.1002/bab.2260 |
| spellingShingle | Jaapar, F. Nadhirah Parmin, Nor Azizah A. Halim, N. Hamidah Hashim, Uda Gopinath, Subash Chandra Bose Halim, F. Syakirah A. Rahim, Ruslinda Voon, C. H. M. N., Afnan Uda Sharifah Nadzirah Rejali, Zulida Mohd Jamil, Amilia Afzan Zakaria, Iffah Izzati Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles |
| title | Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles |
| title_full | Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles |
| title_fullStr | Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles |
| title_full_unstemmed | Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles |
| title_short | Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles |
| title_sort | designing dna probe from hpv 18 and 58 in the e6 region for sensing element in the development of genosensor based gold nanoparticles |
| work_keys_str_mv | AT jaaparfnadhirah designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT parminnorazizah designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT ahalimnhamidah designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT hashimuda designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT gopinathsubashchandrabose designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT halimfsyakirah designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT arahimruslinda designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT voonch designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT mnafnanuda designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT sharifahnadzirah designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT rejalizulida designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT mohdjamilamiliaafzan designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles AT zakariaiffahizzati designingdnaprobefromhpv18and58inthee6regionforsensingelementinthedevelopmentofgenosensorbasedgoldnanoparticles |