Content of review 1, reviewed on July 15, 2024

The authors report a small molecule aldehyde for labelling lysines (and potentially other nucleophiles) on proteins. Upon conjugation of this aldehyde to lysines, the reagent undergoes a cascade of rearrangement to produce a fluorescent molecule (6-dimethylamino 3-methyleneisoindolin-1-one) covalently attached to the lysines.

This new molecule is inspired by existing dimethylamino phthalimide. However, the authors show that it is significantly more stable between pH 6 and 8, ideal for bioconjugation reactions.

The authors report the labelling for model reactions, oligo-oligo conjugation, and oligo-protein conjugation. I am generally satisfied with the experiments and I suggest accepting the paper after the authors address the following minor comments.

  1. For reference number 2, the authors should consider including the work from Chris Chang and Vishal Rai's lab. They have developed small molecules for labelling specific amino acids on proteins for bioconjugation. I personally would also refrain from citing works from MDPI journals due to their non-stringent and non-ideal review process and kind of predatory behaviour.

  2. Please add a hypothesized mechanism for dehydration/tautomerisation to generate compound 2/5 from ODN 1/6. I am having difficulty understanding this mechanism.

  3. What is the reason for including fluorescence spectra at two different excitation wavelengths in Fig 1?

  4. For Fig 2b and 2c, please colour code the triangles for compound 4b instead of using the black triangles. Otherwise, it is difficult to compare the two molecules (4a and 4b).

  5. For Figure 1 and 2 (and the SI), please put the letter numbering (a, b,c, d) on the left instead of the right. It was difficult to read as letter labels are generally always put on the left for papers.

  6. Please add the brightness values in different solvents for compound 7 and 4b. This does not require any experiments. Brightness = quantum yield of fluorescence x extinction coefficient. This will allow readers to judge whether the new molecule 7 is brighter than 4b. The authors claim that 7 has a higher fluorescence intensity.

  7. Please include information in the SI about how the quantum yields were obtained.

  8. For Figure 4, please indicate the identity fo compound at 10 mins in the sample "4 h after hv"

  9. Please include the power of the LED source, as it is critical for uncaging experiments.

For Supporting Information:

  1. Please make the NMR of compounds consistent in terms of colour, integration and placement of chemical shifts on the spectra.

  2. Many NMR spectra have incorrect integrations (for example compound 7, compound 12). Please check for all the compounds.

  3. Some NMR spectra are green, and some are black. Please make them consistent.

  4. Some NMRs have chemical shifts, while others don't. Please make them consistent.

Source

    © 2024 the Reviewer.

References

    Mariko, A., Chiyoe, O., Yixuan, L., Kaori, S., Yukiko, A., Chiemi, G., Yichun, W., Yang, P., Guosheng, G., Tsutomu, K., Yosuke, T., Shigeki, S. 2024. Design and synthesis of an environment-sensitive 3-methyleneisoindolin-1-one fluorophore for labeling DNA-interacting proteins. Organic & Biomolecular Chemistry.