A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers
The accurate, simple, and efficient measurement of the concentration of single-stranded DNA (ssDNA) is important for many analytical applications, such as DNA adsorption, biosensor design, and disease diagnosis, but it is still a challenge. Herein, we studied a cationic conjugated polymer (CCP)-base...
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| Format: | Article |
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MDPI AG
2023-01-01
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| Series: | Biosensors |
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| Online Access: | https://www.mdpi.com/2079-6374/13/1/122 |
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| author | Pengbo Zhang Mohamad Zandieh Yuzhe Ding Lyuyuan Wu Xiaoyu Wang Juewen Liu Zhengping Li |
| author_facet | Pengbo Zhang Mohamad Zandieh Yuzhe Ding Lyuyuan Wu Xiaoyu Wang Juewen Liu Zhengping Li |
| author_sort | Pengbo Zhang |
| collection | DOAJ |
| description | The accurate, simple, and efficient measurement of the concentration of single-stranded DNA (ssDNA) is important for many analytical applications, such as DNA adsorption, biosensor design, and disease diagnosis, but it is still a challenge. Herein, we studied a cationic conjugated polymer (CCP)-based ssDNA assay taking advantage of the obvious fluorescence change of CCPs upon binding ssDNA. Poly(3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene hydrochloride) (PMNT) achieved an apparent dissociation constant (<i>K</i><sub>d</sub>) of 57 ± 4 nM for ssDNA, indicating a very high binding affinity between PMNT and ssDNA. This allowed us to develop a CCP-based ssDNA biosensor with a detection limit of 0.6 nM, similar to the fluorescence-dye-based method using SYBR Green I and SYBR Gold. Our CCP-based biosensor produced smaller differences among ssDNA samples with different base compositions. In addition, the existence of double-stranded DNA (dsDNA) at different concentrations did not interfere with the fluorescence of PMNT, indicating that our CCP-based biosensor was more suitable for the measurement of ssDNA. Compared with fluorescence-intensity-based quantification, our CCP system allowed ratiometric quantification, which made the calibration easier and more robust. We then applied our method to the quantification of ssDNA on AuNPs using both unmodified and thiolated ssDNA, and the accurate quantification of ssDNA was achieved without any fluorophore modification. This method provides an alternative approach for the measurement of ssDNA. |
| first_indexed | 2024-03-09T13:24:17Z |
| format | Article |
| id | doaj.art-5adb35906a6f4c67bc7f3bbe0a083195 |
| institution | Directory Open Access Journal |
| issn | 2079-6374 |
| language | English |
| last_indexed | 2024-03-09T13:24:17Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biosensors |
| spelling | doaj.art-5adb35906a6f4c67bc7f3bbe0a0831952023-11-30T21:25:49ZengMDPI AGBiosensors2079-63742023-01-0113112210.3390/bios13010122A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated PolymersPengbo Zhang0Mohamad Zandieh1Yuzhe Ding2Lyuyuan Wu3Xiaoyu Wang4Juewen Liu5Zhengping Li6School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, ChinaDepartment of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, CanadaDepartment of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, CanadaDepartment of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, CanadaSchool of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, ChinaDepartment of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, CanadaSchool of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, ChinaThe accurate, simple, and efficient measurement of the concentration of single-stranded DNA (ssDNA) is important for many analytical applications, such as DNA adsorption, biosensor design, and disease diagnosis, but it is still a challenge. Herein, we studied a cationic conjugated polymer (CCP)-based ssDNA assay taking advantage of the obvious fluorescence change of CCPs upon binding ssDNA. Poly(3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene hydrochloride) (PMNT) achieved an apparent dissociation constant (<i>K</i><sub>d</sub>) of 57 ± 4 nM for ssDNA, indicating a very high binding affinity between PMNT and ssDNA. This allowed us to develop a CCP-based ssDNA biosensor with a detection limit of 0.6 nM, similar to the fluorescence-dye-based method using SYBR Green I and SYBR Gold. Our CCP-based biosensor produced smaller differences among ssDNA samples with different base compositions. In addition, the existence of double-stranded DNA (dsDNA) at different concentrations did not interfere with the fluorescence of PMNT, indicating that our CCP-based biosensor was more suitable for the measurement of ssDNA. Compared with fluorescence-intensity-based quantification, our CCP system allowed ratiometric quantification, which made the calibration easier and more robust. We then applied our method to the quantification of ssDNA on AuNPs using both unmodified and thiolated ssDNA, and the accurate quantification of ssDNA was achieved without any fluorophore modification. This method provides an alternative approach for the measurement of ssDNA.https://www.mdpi.com/2079-6374/13/1/122cationic conjugated polymerfluorescencelabel-freessDNAbiosensor |
| spellingShingle | Pengbo Zhang Mohamad Zandieh Yuzhe Ding Lyuyuan Wu Xiaoyu Wang Juewen Liu Zhengping Li A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers Biosensors cationic conjugated polymer fluorescence label-free ssDNA biosensor |
| title | A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers |
| title_full | A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers |
| title_fullStr | A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers |
| title_full_unstemmed | A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers |
| title_short | A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers |
| title_sort | label free mix and detect ssdna binding assay based on cationic conjugated polymers |
| topic | cationic conjugated polymer fluorescence label-free ssDNA biosensor |
| url | https://www.mdpi.com/2079-6374/13/1/122 |
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