Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing
Round 1
Reviewer 1 Report
In this short communication-type article, Funck et al. present a method to detect thrombin using chiral plasmonic metamolecules. The similar metamolecules - but with different opening and closing mechanisms (strand-displacement, light, pH) - have already been presented several times in the literature. Recently, the same authors published a RNA-sensor based on these same chiral plasmonic metamolecules. Therefore, this manuscript can be considered as a follow-up study to their recently published article (Funck et al. Angew. Chem. Int. Ed. 2018, 57,13495) as the system is nearly the same and therefore, it also lacks a bit of novelty. Nevertheless, the implementation is promising as the presented system allows detection of small amounts of thrombin via reliable binding to aptamers. The manuscript is technically sound, and I believe this manuscript is acceptable for publication in Applied Sciences after some minor concerns have been addressed. Please see my minor comments/suggestions below: - The authors should present the strand sequences in Section 2 rather in a Table than in the text. - In Figure 2a caption, please explain the red arrow there as well (now it is only explained in the text). It would also be good to mention that this 1 uM concentration (where the observed trend clearly changes) has not been used in the Hill fit, if that is the case (same for 100 nM?). Please explain those data points also in the figure caption (for Fig. 2b). - The authors cite a bunch of relevant research papers but they could deepen the discussion especially on dynamic DNA nanostructures by adding some recent literature to the introduction, at the moment there are only two papers on DNA origami devices implicitly included and not discussed (Refs. 25 and 26). The authors could cite for example H. Ijäs et al., Int J Mol Sci 2019, 19, 2114, and M. Endo & H. Sugiyama, Molecules 2018, 23, 1766 (both papers are about dynamic DNA machines and devices). Moreover, the authors have cited just one protocol/review about DNA origami fabrication, which is already partially outdated (from 2011), and therefore I would suggest them to add more recent reviews on structural DNA nanotechnology to their introduction.
Author Response
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Author Response.pdf
Reviewer 2 Report
1. What is the explaination of the peak arise at 790 nm, and why the fig 2b is non linear (behaves as enzyme reaction)? Why authors choose hill fit, any specific reasons?
2. Why the signal obtained in fig 1 a is bit noisy?
Author Response
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Author Response File: Author Response.pdf
Reviewer 3 Report
In this work dual aptamer-functionalized 3D plasmonic metamolecule for thrombin sensing was described. Authors demonstrated that the obtained metamolecule detects human alpha thrombin in solution at concentrations of 100 pM and above. This work is of interest because the method described here allows to one-step, high sensitivity optical detect of human thrombin proteins in solution. The article looks like a short communication and may be published after major revision.
Notes:
1. The authors should avoid any slangs in the article like “DNA oligos” (Section 2. Materials and Methods). It should be changed by “DNA oligomers”.
2. The “Preparing and measuring 3D plasmonic metamolecule” section is written not clear. The detailed description of absorbance measuring of metamolecules at longitudinal surface plasmon wavelength (Nanodrop, Thermo Fisher Scientific) should be added.
3. Why other methods are not carried out for confirmation of sensing of human thrombin protein by DNA-based plasmonic metamolecule? For example, the metamolecule interaction with thrombin could be studied by Dynamic Light Scattering method in solution.
4. Figure 2a. From these spectra is not clear the complex formation reaches or no the plateau?
5. What is the stability of the complex between metamolecule and thrombin? Is this process reversible or not?
Author Response
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Author Response File: Author Response.pdf
Round 2
Reviewer 3 Report
In this work authors demonstrate a DNA based plasmonic metamolecule capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods is used to provide optical read-out of thrombin binding. The work is of interest because the method developed allows one-step, high sensitivity optical detection of human thrombin proteins in solution. Also, there’s possibility for obtained structures work in physiological buffer conditions especially in the absence of magnesium chelator ethylenediaminetetraacetic acid.
Authors have corrected all comments in the paper and quite clearly answered to the questions. However, other methods for thrombin detection may be employed and discussed in the manuscript, but not only a new method described in this work. It is at the discretion of authors. I hope these corrections improved the paper and the revised version corresponds to high standards of Applied Sciences. After careful consideration, I think that this article may be published in this view.
