Nature Structural & Molecular Biology, Published online: 12 September 2025; doi:10.1038/s41594-025-01669-4The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammalian cells for transcriptional regulation.

The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammali...

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The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammali...

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Abstract. Identification of DNA-binding proteins (DBPs) is a crucial task in genome annotation, as it aids in understanding gene regulation, DNA replicatio

Nature Structural & Molecular Biology, Published online: 12 September 2025; doi:10.1038/s41594-025-01669-4The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammalian cells for transcriptional regulation.

Iodinated disinfection byproducts (I-DBPs) pose significant health concerns due to their high toxicity. Current approaches to recognize unknown I-DBPs in mass spectrometry (MS) analysis rely on negative ionization mode, in which the characteristic I– fragment can be observed in tandem mass spectra (MS/MS). Still, many I-DBPs ionize exclusively in positive ionization mode, where the I– fragment is absent. To address this gap, this work developed a machine learning-based strategy to recognize iodinated compounds (I-compounds) from their MS/MS in both electrospray positive (ESI+) and negative ionization (ESI−) modes. Investigating over 6000 MS/MS spectra of 381 I-compounds, we first identified five characteristic I-containing neutral losses and one diagnostic I– fragment in ESI+ and ESI– modes, respectively. We then trained Random Forest models and integrated them into IodoFinder, a Python program, to streamline the recognition of I-compounds from raw LC-MS data. IodoFinder accurately recognized over 96% of the 161 I-compound standards in both ionization modes. In its application to DBP mixtures, IodoFinder discovered 19 I-DBPs with annotated structures and an additional 17 with assigned formulas, including 12 novel and 3 confirmed I-DBPs. We envision that IodoFinder will advance the identification of both known and unknown I-compounds in exposome studies.

Brominated disinfection byproducts (Br-DBPs) generated during water treatment pose significant health risks due to their high toxicity. This study conducted a comparative nontargeted analysis of Br-DBPs generated during chlorination and chloramination using ultra-performance liquid chromatography (UPLC) coupled with high-resolution (HR) mass spectrometry (MS), including MS and tandem MS experiments. An advanced halogen extraction code identified halogenated compounds via isotopic patterns of chlorine (Cl) and bromine (Br), with MFAssignR assigning molecular formulas. Chlorination resulted in a total of 154 Br-DBPs, most containing carbon, hydrogen, oxygen, and bromine (CHOBr), whereas chloramination generated 79 Br-DBPs, predominantly nitrogenous Br-DBPs (CHONBr), including 57 CHOBr and 22 CHONBr, effectively preserving aromatic structures within natural organic matter (NOM). Several Br-DBPs with strong instrument responses, including brominated aliphatic carboxylic acids and aromatic phenolic acids formed primarily during chlorination, were identified, whereas nitrogenous Br-DBPs were exclusive to chloramination. In silico toxicity assessments indicate that many Br-DBPs identified in this study, particularly those with multiple bromine substitutions and functional groups such as nitro and carboxylic acids in aromatic structures, exhibit substantially higher acute toxicity and mutagenic potential compared to regulated DBPs like bromoform and dibromacetic acid. These findings highlight the need to prioritize polybrominated, aromatic, and nitrogenous Br-DBPs in water treatment research and regulation.

The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and…