Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons
Round 1
Reviewer 1 Report
The peer-reviewed manuscript exactly corresponds to the scientific profile of the Symmetry journal, since it develops one of the topical areas of natural science and biophysics, according to which symmetry is one of the basic factors in the structure, functioning, and development of matter in living and non-living nature. The title of the manuscript and the abstract adequately reflect its content.
The author has carried out an original theoretical study, which shows the possibility of the existence of synchronous oscillations in the duplex B-DNA molecules with mirror-symmetric codons. Interference stretching and stacking radial oscillations of nucleotides pair around the helix axis is considered based on the approximations of the Peyrard-Dauxois-Bishop model.
The most significant and interesting result of the study is the conclusion about the possibility of the occurrence of coherent states, which have a mirror-symmetric arrangement of nucleotide pairs.
It should be noted that the theoretical and mathematical part of the work was done quite professionally, and does not cause any special comments. The result obtained, as the author himself notes, is interesting for interpreting the mechanisms of important molecular biological processes, such as transcription or micromechanical DNA unwinding initiation and the nucleation of denaturation bubbles (4 - 6 base pairs as a minimal cooperative construct).
A fundamental and intuitively natural result seems to be the idea that in the region of moderate temperatures it is the regular mirror-symmetric groups of base pairs in highly cooperative DNA that can serve as some kind of quasi-mechanical (electromechanical) "resonators".
At the same time, when considering the mechanisms of dynamic, oscillatory processes, it is fundamentally important to discuss the provisions based on which both the approach and the model are built. If we are talking about an oscillatory system, then the real studied macromolecular system, certainly, refers to dissipative ones. In DNA, we are dealing with a macroscopic dissipative system, where processes take place in a viscous medium, and nucleotides are hydrated. Therefore, I would like to see in the statement of the problem at least a preliminary discussion of the problem of "quality factor" and "losses" in this oscillatory system, as well as a brief consideration of the nature and resource of possible energy sources for the excitation of synchronous oscillations. For the discussed system, under conditions of thermodynamic equilibrium, it is unrealistic to assume that fluctuations can generate macroscopic coherent perturbations in it. And the direct mechanism of coherence, given by the author, seems to be quite adequate.
There is also a specific question. According to some reports, 4 - 8 water molecules can be associated with each nucleotide. There are also ions there. Altogether, they not only create a viscous dissipative medium but changes the real masses of structures involved in oscillatory processes. The author himself speaks about this, but I would like to see estimates of frequency deviations in the acoustic range when binding ligands and taking into account hydration. The reviewer has no right to demand an exact answer to the questions posed, but it would be undesirable to ignore them when constructing a model and discussing the results since the masses of molecular formations are essential for making estimates in a given physical system. The real system as a mechanical vibrational system is far from the idealized molecular structure in a vacuum.
In essence, as a reviewer, I highly appreciate this work and consider it desirable to publish it in the Symmetry journal. I also consider it desirable to briefly discuss the problem associated with the dissipation of energy in DNA as a mechanical oscillatory system.
Author Response
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Author Response File: 
Author Response.pdf
Reviewer 2 Report
It is with pleasure that I have reviewed this manuscript. I do believe that the author provided very good data in an area of high interest. I do hope that this study could continue in another manuscript and give insides about the temperature dependence of the system theoretically. I think that the manuscript it should be published as it is, although I would like to see from the author before that, a detailed experimental protocol in order for this work to be able to be used from other researchers and cited in high numbers as it deserves.
Best regards
Author Response
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Author Response File: Author Response.pdf
