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DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.
Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. Pham TM, et al. Among authors: zhu m. bioRxiv [Preprint]. 2023 Jun 8:2023.06.06.543917. doi: 10.1101/2023.06.06.543917. bioRxiv. 2023. Update in: ACS Synth Biol. 2023 Sep 15;12(9):2750-2763. doi: 10.1021/acssynbio.3c00358 PMID: 37333404 Free PMC article. Updated. Preprint.
Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.
Hedaya OM, Subbaiah KCV, Jiang F, Xie LH, Wu J, Khor E, Zhu M, Mathews DH, Proschel C, Yao P. Hedaya OM, et al. Among authors: zhu m. bioRxiv [Preprint]. 2023 Jun 15:2023.06.15.545153. doi: 10.1101/2023.06.15.545153. bioRxiv. 2023. Update in: Nat Commun. 2023 Oct 3;14(1):6166. doi: 10.1038/s41467-023-41799-1 PMID: 37397986 Free PMC article. Updated. Preprint.
Sequence Design Using RNAstructure.
Zhu M, Mathews DH. Zhu M, et al. Methods Mol Biol. 2025;2847:17-31. doi: 10.1007/978-1-0716-4079-1_2. Methods Mol Biol. 2025. PMID: 39312134
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