Organic additives stabilize RNA aptamer binding of malachite green
Aptamer-ligand binding has been utilized for biological applications due to its specific binding and synthetic nature. However, the applications will be limited if the binding or the ligand is unstable. Malachite green aptamer (MGA) and its labile ligand malachite green (MG) were found to have incre...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
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2017
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| Online Access: | https://hdl.handle.net/10356/80594 http://hdl.handle.net/10220/42176 |
| _version_ | 1811681324340084736 |
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| author | Zhou, Yubin Chi, Hong Wu, Yuanyuan Marks, Robert S. Steele, Terry W. J. |
| author2 | School of Materials Science & Engineering |
| author_facet | School of Materials Science & Engineering Zhou, Yubin Chi, Hong Wu, Yuanyuan Marks, Robert S. Steele, Terry W. J. |
| author_sort | Zhou, Yubin |
| collection | NTU |
| description | Aptamer-ligand binding has been utilized for biological applications due to its specific binding and synthetic nature. However, the applications will be limited if the binding or the ligand is unstable. Malachite green aptamer (MGA) and its labile ligand malachite green (MG) were found to have increasing apparent dissociation constants (Kd) as determined through the first order rate loss of emission intensity of the MGA-MG fluorescent complex. The fluorescent intensity loss was hypothesized to be from the hydrolysis of MG into malachite green carbinol base (MGOH). Random screening organic additives were found to reduce or retain the fluorescence emission and the calculated apparent Kd of MGA-MG binding. The protective effect became more apparent as the percentage of organic additives increased up to 10% v/v. The mechanism behind the organic additive protective effects was primarily from a ~5X increase in first order rate kinetics of MGOH→MG (kMGOH→MG), which significantly changed the equilibrium constant (Keq), favoring the generation of MG, versus MGOH without organic additives. A simple way has been developed to stabilize the apparent Kd of MGA-MG binding over 24 h, which may be beneficial in stabilizing other triphenylmethane or carbocation ligand-aptamer interactions that are susceptible to SN1 hydrolysis. |
| first_indexed | 2024-10-01T03:39:08Z |
| format | Journal Article |
| id | ntu-10356/80594 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T03:39:08Z |
| publishDate | 2017 |
| record_format | dspace |
| spelling | ntu-10356/805942023-07-14T15:49:40Z Organic additives stabilize RNA aptamer binding of malachite green Zhou, Yubin Chi, Hong Wu, Yuanyuan Marks, Robert S. Steele, Terry W. J. School of Materials Science & Engineering Malachite green aptamer Malachite green Aptamer-ligand binding has been utilized for biological applications due to its specific binding and synthetic nature. However, the applications will be limited if the binding or the ligand is unstable. Malachite green aptamer (MGA) and its labile ligand malachite green (MG) were found to have increasing apparent dissociation constants (Kd) as determined through the first order rate loss of emission intensity of the MGA-MG fluorescent complex. The fluorescent intensity loss was hypothesized to be from the hydrolysis of MG into malachite green carbinol base (MGOH). Random screening organic additives were found to reduce or retain the fluorescence emission and the calculated apparent Kd of MGA-MG binding. The protective effect became more apparent as the percentage of organic additives increased up to 10% v/v. The mechanism behind the organic additive protective effects was primarily from a ~5X increase in first order rate kinetics of MGOH→MG (kMGOH→MG), which significantly changed the equilibrium constant (Keq), favoring the generation of MG, versus MGOH without organic additives. A simple way has been developed to stabilize the apparent Kd of MGA-MG binding over 24 h, which may be beneficial in stabilizing other triphenylmethane or carbocation ligand-aptamer interactions that are susceptible to SN1 hydrolysis. NRF (Natl Research Foundation, S’pore) MOE (Min. of Education, S’pore) Accepted version 2017-03-16T05:06:58Z 2019-12-06T13:52:53Z 2017-03-16T05:06:58Z 2019-12-06T13:52:53Z 2016 Journal Article Zhou, Y., Chi, H., Wu, Y., Marks, R. S., & Steele, T. W. J. (2016). Organic additives stabilize RNA aptamer binding of malachite green. Talanta, 160, 172-182. 0039-9140 https://hdl.handle.net/10356/80594 http://hdl.handle.net/10220/42176 10.1016/j.talanta.2016.06.067 en Talanta © 2016 Elsevier. This is the author created version of a work that has been peer reviewed and accepted for publication by Talanta, Elsevier. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [http://dx.doi.org/10.1016/j.talanta.2016.06.067]. 36 p. application/pdf |
| spellingShingle | Malachite green aptamer Malachite green Zhou, Yubin Chi, Hong Wu, Yuanyuan Marks, Robert S. Steele, Terry W. J. Organic additives stabilize RNA aptamer binding of malachite green |
| title | Organic additives stabilize RNA aptamer binding of malachite green |
| title_full | Organic additives stabilize RNA aptamer binding of malachite green |
| title_fullStr | Organic additives stabilize RNA aptamer binding of malachite green |
| title_full_unstemmed | Organic additives stabilize RNA aptamer binding of malachite green |
| title_short | Organic additives stabilize RNA aptamer binding of malachite green |
| title_sort | organic additives stabilize rna aptamer binding of malachite green |
| topic | Malachite green aptamer Malachite green |
| url | https://hdl.handle.net/10356/80594 http://hdl.handle.net/10220/42176 |
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