Easy triplex: An online tool for predicting the formation of DNARNA triple helices
Increasing evidence supports the idea that intranuclear noncoding RNAs interact with target DNA to regulate their expression. The structural basis of this process involves the formation of DNARNA triple helices without unwinding the DNA double helix. This triplex formation process relies on the bas...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037025001291 |
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| author | Lintao Xian Jianming Liu Shunshun Zhu Fan Liang Hao Luo Li Zhao Min Shi Cheng Gong Zhen Li Tao Guo |
| author_facet | Lintao Xian Jianming Liu Shunshun Zhu Fan Liang Hao Luo Li Zhao Min Shi Cheng Gong Zhen Li Tao Guo |
| author_sort | Lintao Xian |
| collection | DOAJ |
| description | Increasing evidence supports the idea that intranuclear noncoding RNAs interact with target DNA to regulate their expression. The structural basis of this process involves the formation of DNARNA triple helices without unwinding the DNA double helix. This triplex formation process relies on the base pairing of the triplex target site (TTS) and the triplex-forming oligonucleotide (TFO), making the prediction of their binding crucial for mechanistic investigations. Here, we propose an online tool called Easy Triplex for predicting the formation of DNARNA triplexes. Using the canonical Hoogsteen pairing rules, Easy Triplex matches and predicts the details and distribution of all TTSs and TFOs on the basis of the user-provided DNA and RNA sequences. Practical application has shown that Easy Triplex can efficiently and accurately predict known triplex information. Its flexible parameter settings and scientifically set default output thresholds make Easy Triplex suitable for predicting the TFOs of both long and short noncoding RNAs. Additionally, users can choose to export the distribution information of CpG islands on the DNA sequence for further TTS screening. Thus, Easy Triplex is a simple and convenient online tool for predicting triplex formation. Easy Triplex is publicly accessible at http://easy-triplex.com/. |
| format | Article |
| id | doaj-art-8e933f6f6a7c46f8a85a0957733cea08 |
| institution | OA Journals |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-8e933f6f6a7c46f8a85a0957733cea082025-08-20T02:16:05ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-01271550155810.1016/j.csbj.2025.04.008Easy triplex: An online tool for predicting the formation of DNARNA triple helicesLintao Xian0Jianming Liu1Shunshun Zhu2Fan Liang3Hao Luo4Li Zhao5Min Shi6Cheng Gong7Zhen Li8Tao Guo9Department of Intelligent Medical Engineering, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Intelligent Medical Engineering, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Pathophysiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Clinical Microbiology, School of Laboratory Medicine, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Pathophysiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, ChinaDepartment of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Correspondence to: Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan 430071, China.Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Correspondence to: Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan 430071, China.Department of Pathophysiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China; Correspondence to: Shandong Second Medical University, Baotong West Street 7166, Weifang 261053, China.Increasing evidence supports the idea that intranuclear noncoding RNAs interact with target DNA to regulate their expression. The structural basis of this process involves the formation of DNARNA triple helices without unwinding the DNA double helix. This triplex formation process relies on the base pairing of the triplex target site (TTS) and the triplex-forming oligonucleotide (TFO), making the prediction of their binding crucial for mechanistic investigations. Here, we propose an online tool called Easy Triplex for predicting the formation of DNARNA triplexes. Using the canonical Hoogsteen pairing rules, Easy Triplex matches and predicts the details and distribution of all TTSs and TFOs on the basis of the user-provided DNA and RNA sequences. Practical application has shown that Easy Triplex can efficiently and accurately predict known triplex information. Its flexible parameter settings and scientifically set default output thresholds make Easy Triplex suitable for predicting the TFOs of both long and short noncoding RNAs. Additionally, users can choose to export the distribution information of CpG islands on the DNA sequence for further TTS screening. Thus, Easy Triplex is a simple and convenient online tool for predicting triplex formation. Easy Triplex is publicly accessible at http://easy-triplex.com/.http://www.sciencedirect.com/science/article/pii/S2001037025001291Online toolNon-coding RNAHoogsteen pairingTriplex |
| spellingShingle | Lintao Xian Jianming Liu Shunshun Zhu Fan Liang Hao Luo Li Zhao Min Shi Cheng Gong Zhen Li Tao Guo Easy triplex: An online tool for predicting the formation of DNARNA triple helices Computational and Structural Biotechnology Journal Online tool Non-coding RNA Hoogsteen pairing Triplex |
| title | Easy triplex: An online tool for predicting the formation of DNARNA triple helices |
| title_full | Easy triplex: An online tool for predicting the formation of DNARNA triple helices |
| title_fullStr | Easy triplex: An online tool for predicting the formation of DNARNA triple helices |
| title_full_unstemmed | Easy triplex: An online tool for predicting the formation of DNARNA triple helices |
| title_short | Easy triplex: An online tool for predicting the formation of DNARNA triple helices |
| title_sort | easy triplex an online tool for predicting the formation of dnarna triple helices |
| topic | Online tool Non-coding RNA Hoogsteen pairing Triplex |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025001291 |
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