Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method
T7 RNA polymerase is the most widely used enzyme in RNA synthesis, and it is also used for RNA labeling in position-selective labeling of RNA (PLOR). PLOR is a liquid–solid hybrid phase method that has been developed to introduce labels to specific positions of RNA. Here, we applied PLOR as a single...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/5/4934 |
| _version_ | 1797615071621283840 |
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| author | Ping-Yi Chien Lingzhi Gao Yu Liu |
| author_facet | Ping-Yi Chien Lingzhi Gao Yu Liu |
| author_sort | Ping-Yi Chien |
| collection | DOAJ |
| description | T7 RNA polymerase is the most widely used enzyme in RNA synthesis, and it is also used for RNA labeling in position-selective labeling of RNA (PLOR). PLOR is a liquid–solid hybrid phase method that has been developed to introduce labels to specific positions of RNA. Here, we applied PLOR as a single-round transcription method to quantify the terminated and read-through products in transcription for the first time. Various factors, including pausing strategies, Mg<sup>2+</sup>, ligand and the NTP concentration at the transcriptional termination of adenine riboswitch RNA have been characterized. This helps to understand transcription termination, which is one of the least understood processes in transcription. Additionally, our strategy can potentially be used to study the co-transcription behavior of general RNA, especially when continuous transcription is not desired. |
| first_indexed | 2024-03-11T07:21:18Z |
| format | Article |
| id | doaj.art-216f34fbab5344408411b8d828369be3 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T07:21:18Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-216f34fbab5344408411b8d828369be32023-11-17T07:55:29ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01245493410.3390/ijms24054934Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) MethodPing-Yi Chien0Lingzhi Gao1Yu Liu2State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, ChinaState Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, ChinaState Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, ChinaT7 RNA polymerase is the most widely used enzyme in RNA synthesis, and it is also used for RNA labeling in position-selective labeling of RNA (PLOR). PLOR is a liquid–solid hybrid phase method that has been developed to introduce labels to specific positions of RNA. Here, we applied PLOR as a single-round transcription method to quantify the terminated and read-through products in transcription for the first time. Various factors, including pausing strategies, Mg<sup>2+</sup>, ligand and the NTP concentration at the transcriptional termination of adenine riboswitch RNA have been characterized. This helps to understand transcription termination, which is one of the least understood processes in transcription. Additionally, our strategy can potentially be used to study the co-transcription behavior of general RNA, especially when continuous transcription is not desired.https://www.mdpi.com/1422-0067/24/5/4934transcription terminationsingle-round transcriptionPLORriboswitch RNA |
| spellingShingle | Ping-Yi Chien Lingzhi Gao Yu Liu Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method International Journal of Molecular Sciences transcription termination single-round transcription PLOR riboswitch RNA |
| title | Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method |
| title_full | Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method |
| title_fullStr | Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method |
| title_full_unstemmed | Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method |
| title_short | Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method |
| title_sort | quantitative analysis of transcription termination via position selective labeling of rna plor method |
| topic | transcription termination single-round transcription PLOR riboswitch RNA |
| url | https://www.mdpi.com/1422-0067/24/5/4934 |
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