Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex
We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found tha...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2016-01-01
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| Series: | Science and Technology of Advanced Materials |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/14686996.2016.1243000 |
| _version_ | 1818658440561557504 |
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| author | Yu-mi Ueda Yu-ki Zouzumi Atsushi Maruyama Shu-ichi Nakano Naoki Sugimoto Daisuke Miyoshi |
| author_facet | Yu-mi Ueda Yu-ki Zouzumi Atsushi Maruyama Shu-ichi Nakano Naoki Sugimoto Daisuke Miyoshi |
| author_sort | Yu-mi Ueda |
| collection | DOAJ |
| description | We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences. |
| first_indexed | 2024-12-17T03:57:25Z |
| format | Article |
| id | doaj.art-fc1de7c2f3fc40deb9b85c5294a18065 |
| institution | Directory Open Access Journal |
| issn | 1468-6996 1878-5514 |
| language | English |
| last_indexed | 2024-12-17T03:57:25Z |
| publishDate | 2016-01-01 |
| publisher | Taylor & Francis Group |
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| series | Science and Technology of Advanced Materials |
| spelling | doaj.art-fc1de7c2f3fc40deb9b85c5294a180652022-12-21T22:04:35ZengTaylor & Francis GroupScience and Technology of Advanced Materials1468-69961878-55142016-01-0117175375910.1080/14686996.2016.12430001243000Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplexYu-mi Ueda0Yu-ki Zouzumi1Atsushi Maruyama2Shu-ichi Nakano3Naoki Sugimoto4Daisuke Miyoshi5Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan UniversityFaculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan UniversityDepartment of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of TechnologyFaculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan UniversityFaculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan UniversityFaculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan UniversityWe systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences.http://dx.doi.org/10.1080/14686996.2016.1243000dnag-quadruplexduplexmolecular crowdingosomolyte |
| spellingShingle | Yu-mi Ueda Yu-ki Zouzumi Atsushi Maruyama Shu-ichi Nakano Naoki Sugimoto Daisuke Miyoshi Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex Science and Technology of Advanced Materials dna g-quadruplex duplex molecular crowding osomolyte |
| title | Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex |
| title_full | Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex |
| title_fullStr | Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex |
| title_full_unstemmed | Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex |
| title_short | Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex |
| title_sort | effects of trimethylamine n oxide and urea on dna duplex and g quadruplex |
| topic | dna g-quadruplex duplex molecular crowding osomolyte |
| url | http://dx.doi.org/10.1080/14686996.2016.1243000 |
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