Minelise’s comment on: Synthesis and Direct Observation of Thermoresponsive DNA Copolymers

By Minelise E. Rivera

MER blog image 18-05

In this paper, Li and Schroeder use single molecule techniques to have a direct observation on DNA-PNIPAM copolymers. First, they synthetized DNA-PNIPAM copolymers using a two-step strategy based on polymerase chain reaction (PCR) for generating linear DNA backbones containing dibenzocyclooctyne-dUTP, then grafted thermoresponsive side branches (PNIPAM) onto DNA backbones using copper-free click chemistry. Subsequent single molecule fluorescence spectroscopy studies unveiled more clearly the molecular heterogeneity association with the stretching and relaxing of the polymer above and below their LCST. Their results showed that intramolecular conformational dynamics of DNA-PNIPAM copolymers are affected by properties of the branches like molecular weight, density, leading to a change in transition temperatures. In other words, the single molecule technique provided a better understanding in a molecular perspective of chemically heterogeneous and stimuli-response polymers.

As I read this paper and looked for information to better understand it, I was amazed by the details with which they worked with throughout their study. I would have thought of working better with a bunch of them instead of just single molecules. It didn’t cross my mind that someone was going to, not only synthesized the molecule, but also study its characteristics. It was very interesting to learn about the methods that they used for characterization and synthesis. It got me wondering if those methods were the only ones that would work in this case and why. But, what I think that was very useful for me is that I got to understand better the importance of the LCST and the role that it played in their system. It reminded me of our project in which the SGQ self-assembles into the SHS and how it is to study it and understand its influence in the SHS as it was important for the copolymers with which it was worked with in the paper.

9 thoughts on “Minelise’s comment on: Synthesis and Direct Observation of Thermoresponsive DNA Copolymers

  1. Rating (synopsis): 3/5
    Rating (figure): 3/5

    The vocabulary used in the synopsis is very elegant, though I’m not sure if all of the words really are correctly used. At least I found it hard to understand. For example, despite re-reading the phrase several times, I’m still not sure what the following sentence should mean: single molecule fluorescence spectroscopy studies unveiled more clearly the molecular heterogeneity association with the stretching and relaxing of the polymer above and below their LCST. However, overall the synopsis is ok and includes the main aspects of the paper.
    About the figure, I can’t remember what SPACC is supposed to mean. If wasn’t important enough to include in the synopsis, it probably isn’t necessary to include in the figure, but if it did need to be included, a little more explanation should be provided. Also, I feel the figure fails to show a very important aspect of the paper: the fact that it is single molecule studies.

  2. Rating (synopsis): 4/5
    Rating (figure): 4/5

    I liked that the first paragraph of the narrative, straight to the point and very concise. Regarding the second paragraph, the last sentence confused me since it is too wordy for the point she is trying to make. Overall, I like that the narrative shows us the science of the article and the impact it had on Minelise.

    The image is very simple and definitely contains the essence of the paper. The image could have highlighted, like the comment, the collapse of a single molecule of DNA upon a change in temperature by single-molecule fluorescence microscopy. Maybe she could have included some modified version of figure 4a in the image.

  3. Rating (synopsis): 4/5
    Rating (figure): 4/5

    The synopsis that minelis provided seemed clear to me because she used an easy vocabulary. To put the paragraph as events of what the authors of the scientific article talked about seemed to me an easier way to understand the article. It is interesting how they could verify the behavior of the LCST by changing properties of the polymer that was studying which is the DNA-PNIPAM. Also, I agree with her by saying that I could understand the LCST theme since it seemed a complicated concept at first. I consider the LCST an important and key factor for our investigation.

    The image was clear and simple, it helped me to see in a general way what the scientific article was about. Although I would have highlighted more in the image what the scientists wanted to reach in the article.

  4. Rating (synopsis) 4/5
    Rating (figure) 4/5

    In my opinion, Minelise’s synopsis was straight-forward explaining the key components of the paper and how they synthesized PNIPAM copolymers and the important results. I liked that she included a more broad opinion of what she captured most from the paper, expressing the true idea of reading more papers throughout our undergraduate studies, to grasp new ideas and integrate them into future works.

    The figure was a good one explaining the main points in the synopsis but I would have labeled SPACC completely, as Diana commented, so that the reader doesn’t have to go back to the paper if he/she doesn’t remember some initials.

  5. Rating Synopsis 4/5
    Rating Figure 4/5

    I think that Minelise explain really well the main idea of the article, what they did and the results that they obtain. I like the simplicity of the first paragraph. Also I like that she give her opinion about the article and how she incorporate some elements of the article with what we perform in the lab (the importance of an LCST event).
    The figure, I think is good, maybe I would include an image of results.

  6. Rating (synopsis): 4/5
    Rating (figure): 3/5

    Taking in consideration that Minelise is a student on her first year of research I believe her take on the article is fairly to the point. Not necessarily taking in consideration all the aspects of the paper but bringing the general idea of the article in a simple manner. As for her comment, seems she has too many ideas without a necessarily a coherent line. As for her image, what is SPACC?

  7. Rating (synopsis): 4/5
    Rating (figure): 4/5

    I really enjoyed how Minelise explained the paper in a brief and concise manner. The way she explains the single molecule technique is good, maybe she could have explained it better because in the paper they show an image of the ”microfluidic flow cell and surface-tethered DNA-PNIPAM copolymers” which are a very interesting part of the research showing the technique.

    As for the image, it covers the idea of the paper, although I wanted to see the single molecule technique images from the paper. Also, I think that by ”SPACC”, she meant ”SPAAC” which stands for ”Strain-Promoted Alkyne-Azide Cycloadditions” used for the synthesis of the thermoresponsive DNA copolymers.

  8. Rating (Synopsis): 3/5
    Rating (Figure): 4/5

    I liked how Minelise divided her synopsis into two sections/paragraphs: paragraph 1 includes the experimental details and more of the science and the idea behind the paper, while paragraph 2 includes Minelise’s opinion and take on the paper. Paragraph 1 provides a brief overview of what was done in the paper, which I think is useful in an exercise like this, where the person who presented the paper is supposed to teach the rest of the lab members about the article’s research and findings in a summarized and simplified manner. I think that Minelise managed to do that, even if some details were missed.

    I like Minelise’s figure because it conveys most of the main idea of the article efficiently. However, it doesn’t include a representation of the single-molecule imaging technique used in the paper, and it also includes the term “SPACC”, which is not mentioned in the synopsis but is mentioned in the paper as SPACC-the procedure used to covalently link the PNIPAM branches to the DNA backbone.

  9. Rating (Synopsis): 4/5
    Rating (Figure): 5/5

    This synopsis was very much of my liking since it was short, precise and was easy to follow. Nevertheless, it had some minor details. For example, as mentioned in some of the other comments of our colleagues, you do not mention the SPACC that is seen in the figure, which I guess is the copper free click reaction that you mentioned. Also, it would have been nice if you mentioned some of the possible applications or uses, if any.

    Regarding the picture, it was an excellent image. Like your synopsis, your figure is precise and easy to follow.

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