Easy triplex: An online tool for predicting the formation of DNA-RNA 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 DNA-RNA 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 DNA-RNA 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/.