DNA Nanotechnology-Empowered Fluorescence Imaging of APE1 Activity

Round 1

Reviewer 1 Report

Reviewer’s Comments:

The manuscript “DNA Nanotechnology-Empowered Fluorescence Imaging of APE1 Activity” is very interesting work. In this study, apurinic/apyrimidinic endonuclease 1 (APE1), also known as redox factor-1 (Ref-1), is a multifunctional protein which is widely existing in living organisms. It can specifically recognize and cleave the DNA in apurinic/apyrimidinic (AP) site in the base excision repair (BER) pathway, as well as regulate the expression of genes to activate some transcription factors. The abnormal ex-pression and disruptions in the biological functions of APE1 are linked to a number of diseases, including inflammation, immunodeficiency, and cancer. Hence, it is extremely desired to monitor the activity of APE1, acquiring a thorough understanding of the healing process of damaged DNA and making clinical diagnoses. Thanks to the advent of DNA nanotechnology, some nanodevices are used to image the activity of APE1 with great sensitivity and simplicity. I believe this topic is of great interest to our reader, I think it needs minor revision before it is ready for publishing. So, I strongly recommend this manuscript for publication in this Journal with major revisions.

1. In this manuscript, the authors did not explain the importance of Fluorescence Imaging in the introduction part. The authors should explain the importance of Fluorescence Imaging.

2. The author should provide reason about this statement with recent references “In this review, we will summarize DNA nanotechnology-empowered fluorescence imaging in the past years for APE1 activity according to the types of DNA probe, which are classified into linear DNA probes, composite DNA nanomaterials and three-dimensional (3D) DNA nanostructures. We also highlight the future research directions in the field of APE1 activity imaging”.

3. Introduction part is not impressive and systematic. 

4. The authors should justify the following statement “Studies have shown that increased APE1 levels lead to migration, drug resistance of tumor cells and reduced patient survival”.

5. The authors should explain regarding the recent literature why “This strategy featured rapidity and high simplicity, which could be easily adaptable to alternative DNA repair enzymes”.

6. The authors should explain the statement with reference to the literature. “The DNA nanomachine was powered by the toehold-mediated strand displacement reaction, which provided enough fuel for the walker to travel continuously along each track”.

7. Comparison of the present results with other similar findings in the literature should be discussed in more detail. This is necessary in order to place this work together with other work in the field and to give more credibility to the present results.

8. The conclusion part is very weak. Improve by adding the results of your studies.

9. The authors should pay more attention to the English grammar, and the abbreviation of journal names in Ref.

Minor editing of English language required

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The manuscript-review titled “DNA Nanotechnology-Empowered Fluorescence Imaging of APE1 Activity” is reviewed.

Hui He et al summarize DNA nanotechnology for fluorescence imaging of APE1 activity. Linear DNA probes, composite DNA nanomaterials and 3D DNA nanostructures are carefully described and considered.

This manuscript content is very interesting and well written. However, there is one point that could be improved as it is an important aspect of fluorescent imaging - APE1 probes intracellular localization. APE1 is a multifunctional cellular protein that functions not only as a DNA repair enzyme, but also as a redox regulator of transcription factor activation. Given its critical role in cell function and survival, the cytoplasmic/nuclear distribution of APE1 is just as important. Therefore, it is interesting to touch upon the point of possible quantitative subcellular APE1 activity measurements.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

The authors delivered a very detail-oriented and well organized summary of recent advances in the field of APE1 imaging using DNA nanotechnology. However, I would really appreciate the authors to put some emphasis on the following parts:

1. The significance of APE1 imaging. In other words, it would be great if the authors can provide some clinical applications using the DNA nanotechnology for APE1 imaging. And are there any in vivo applications using the DNA nanotechnology for APE1 imaging?

2. Is there any limitations using the DNA nanotechnology for APE1 imaging. For examples, does the DNA nanoprobe have the ability to enter the nucleus?

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

The authors answered all my questions. I have no further comment. I fully support publication in the present form.