Computer modeling to optimize the sensitivity of an optical DNA nanosensor
This paper describes how the sensitivity of an optical DNA nanosensor based on MNPs and QDs was enhanced by using computer simulations including an innovative software, Grasshopper. The data used was derived from a previously constructed mechanism which, although successful in detecting target DNA q...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Published: |
Elsevier
2015
|
| Online Access: | http://psasir.upm.edu.my/id/eprint/44155/ |
| _version_ | 1848850405894651904 |
|---|---|
| author | Hushiarian, Roozbeh Yusof, Nor Azah Houshiarian, Negin Abdullah, Abdul Halim Alang Ahmad, Shahrul Ainliah |
| author_facet | Hushiarian, Roozbeh Yusof, Nor Azah Houshiarian, Negin Abdullah, Abdul Halim Alang Ahmad, Shahrul Ainliah |
| author_sort | Hushiarian, Roozbeh |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | This paper describes how the sensitivity of an optical DNA nanosensor based on MNPs and QDs was enhanced by using computer simulations including an innovative software, Grasshopper. The data used was derived from a previously constructed mechanism which, although successful in detecting target DNA qualitatively, raised some areas for further investigation.
By adjusting the relative proportions of DNA probes, MNPs and QDs in the model, we were able to simulate a range of different reactions in the sensor and to measure them quantitatively. We were able to observe MNPs and QDs binding to more than one strand of DNA and to better understand how they network in different concentrations of the solution. We found a direct correlation coefficient of 0.9666 between the fluorescent intensity of the CdSe/ZnS QDs and the concentration of tDNA within the range of 1 × 10−6–3.9 × 10−9 M.
To optimize the sensor further, we also modified the hybridization procedure, breaking it into two steps. This produced a very satisfactory LOD calculation of 1.75 × 10−9 M.
Finally, when we applied the 2 step hybridization procedure we were able to improve the sensitivity of the optical nanosensor up to 20% furthur. |
| first_indexed | 2025-11-15T10:05:46Z |
| format | Article |
| id | upm-44155 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T10:05:46Z |
| publishDate | 2015 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-441552023-12-25T12:12:14Z http://psasir.upm.edu.my/id/eprint/44155/ Computer modeling to optimize the sensitivity of an optical DNA nanosensor Hushiarian, Roozbeh Yusof, Nor Azah Houshiarian, Negin Abdullah, Abdul Halim Alang Ahmad, Shahrul Ainliah This paper describes how the sensitivity of an optical DNA nanosensor based on MNPs and QDs was enhanced by using computer simulations including an innovative software, Grasshopper. The data used was derived from a previously constructed mechanism which, although successful in detecting target DNA qualitatively, raised some areas for further investigation. By adjusting the relative proportions of DNA probes, MNPs and QDs in the model, we were able to simulate a range of different reactions in the sensor and to measure them quantitatively. We were able to observe MNPs and QDs binding to more than one strand of DNA and to better understand how they network in different concentrations of the solution. We found a direct correlation coefficient of 0.9666 between the fluorescent intensity of the CdSe/ZnS QDs and the concentration of tDNA within the range of 1 × 10−6–3.9 × 10−9 M. To optimize the sensor further, we also modified the hybridization procedure, breaking it into two steps. This produced a very satisfactory LOD calculation of 1.75 × 10−9 M. Finally, when we applied the 2 step hybridization procedure we were able to improve the sensitivity of the optical nanosensor up to 20% furthur. Elsevier 2015 Article PeerReviewed Hushiarian, Roozbeh and Yusof, Nor Azah and Houshiarian, Negin and Abdullah, Abdul Halim and Alang Ahmad, Shahrul Ainliah (2015) Computer modeling to optimize the sensitivity of an optical DNA nanosensor. Sensors and Actuators B: Chemical, 207 (pt. A). pp. 716-723. ISSN 0925-4005; ESSN: 1873-3077 https://www.sciencedirect.com/science/article/pii/S0925400514012295 10.1016/j.snb.2014.09.120 |
| spellingShingle | Hushiarian, Roozbeh Yusof, Nor Azah Houshiarian, Negin Abdullah, Abdul Halim Alang Ahmad, Shahrul Ainliah Computer modeling to optimize the sensitivity of an optical DNA nanosensor |
| title | Computer modeling to optimize the sensitivity of an optical DNA nanosensor |
| title_full | Computer modeling to optimize the sensitivity of an optical DNA nanosensor |
| title_fullStr | Computer modeling to optimize the sensitivity of an optical DNA nanosensor |
| title_full_unstemmed | Computer modeling to optimize the sensitivity of an optical DNA nanosensor |
| title_short | Computer modeling to optimize the sensitivity of an optical DNA nanosensor |
| title_sort | computer modeling to optimize the sensitivity of an optical dna nanosensor |
| url | http://psasir.upm.edu.my/id/eprint/44155/ http://psasir.upm.edu.my/id/eprint/44155/ http://psasir.upm.edu.my/id/eprint/44155/ |