How global DNA unwinding causes non-uniform stress distribution and melting of DNA

Korbinian Liebl; Martin Zacharias

doi:10.1371/journal.pone.0232976

Peer Review History

Original SubmissionFebruary 26, 2020
1 Apr 2020 Decision Letter - Claudio M. Soares, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-20-05578 How global DNA unwinding causes non-uniform stress distribution and melting of DNA PLOS ONE Dear Dr. Zacharias, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the all the points raised by both reviewers. We would appreciate receiving your revised manuscript by May 16 2020 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Claudio M. Soares, Ph.D Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.plosone.org/attachments/PLOSOne_formatting_sample_main_body.pdf and http://www.plosone.org/attachments/PLOSOne_formatting_sample_title_authors_affiliations.pdf [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: In this paper the authors present a Molecular Dynamics (MD) work to characterize the structural changes and energetics during the unwinding and melting of DNA duplexes containing a TATA-box transcription start sequence. The authors find that the elastic deformation of two DNA constructs is distributed non-uniformly during unwinding and results in the local melting of the TATA-box, which also absorbs the deformation energy of the duplex while the rest of the sequence relaxes to B-form. The authors find good agreement between the free-energy profile reconstructed along the degree of unwinding from fully-atomistic MD and from an Ising model based on experimental parameters, thus corroborating the use of MD simulations to study the molecular details and energetics of global DNA unwinding processes. Overall the study is interesting, clearly written, and should be published after the authors have addressed the following minor issues noticed: 1) Can the authors demonstrate that, or at least argue on, the local melting of the TATA-box during global unwinding is independent on its positioning along the duplex? What if the TATA-box is positioned, for example, between base pairs 10-15 or 20-25 ? Would the TATA-box continue to absorb the majority of the deformation energy and locally melt (and not other regions) at sigma around 0.073 ? 2) It is now evident that local base-pair melting is a step-wise asymmetric process with one of the two Watson-Crick bases having higher probability to fray than the complementary one (PNAS 100, 13922–13927 (2003); J Phys Chem B 113, 2614–2623 (2009); J Comput Chem 32, 3354–3361 (2011); PNAS 113, 116–121 (2016); J Mol Model. 23, 226 (2017); PNAS 116, 22471-22477 (2019)). In this context, it would be interesting for the authors to comment on the molecular details governing the melting of the TATA-box from such perspective. Did they observe, for instance, preferential fraying of Thymine(T) leading to melting of the TATA-box ? Reviewer #2: This well-written manuscript describes a computational study of double stranded DNA under torsional stress. Specifically, the authors performed all-atom molecular dynamics simulations of two 50-basepair DNA fragments different in their CG content but featuring the same TATA box, a fragment of DNA that is frequently present at the start of DNA transcription sites. The under-twisting of DNA was realized by means of torsional restraints. Gradual increase of the restraints allowed the authors to observe redistribution of the mechanical energy at the bp level, melting of the TATA box, and, impressively, obtain the free-energy costs associated with the above transitions. The authors rationalize the results of the simulations using an Ising model. This is a very impressive study that has the potential to become a classic paper in the field of computational DNA mechanics. The observations of TATA box melting and redistribution of mechanical deformation energy are particularly valuable. The manuscript is clearly written and can be followed by a person familiar with the subject. The manuscript can be published in its present form, though it would be nice if the authors could split the very long first paragraph of the Conclusions into several shorter paragraphs. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: Aleksei Aksimentiev [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0232976.r001
Revision 1
22 Apr 2020 Author Response Garching, 12.4.2020 Dear Dr. Soares Thank you for returning our manuscript entitled “How global DNA unwinding causes non-uniform stress distribution and melting of DNA" by K. Liebl and M. Zacharias and the comments of the reviewers. In the following we like to comment on the concerns of the reviewers and indicate the changes and additions we have made to the manuscript. We also provide a version of the manuscript with all changes marked red. Referee: 1 Reviewer #1: In this paper the authors present a Molecular Dynamics (MD) work to characterize the structural changes and energetics during the unwinding and melting of DNA duplexes containing a TATA-box transcription start sequence. The authors find that the elastic deformation of two DNA constructs is distributed non-uniformly during unwinding and results in the local melting of the TATA-box, which also absorbs the deformation energy of the duplex while the rest of the sequence relaxes to B-form. The authors find good agreement between the free-energy profile reconstructed along the degree of unwinding from fully-atomistic MD and from an Ising model based on experimental parameters, thus corroborating the use of MD simulations to study the molecular details and energetics of global DNA unwinding processes. Overall the study is interesting, clearly written, and should be published after the authors have addressed the following minor issues noticed: Response: We thank the reviewer for the encouraging comment. 1) Can the authors demonstrate that, or at least argue on, the local melting of the TATA-box during global unwinding is independent on its positioning along the duplex? What if the TATA-box is positioned, for example, between base pairs 10-15 or 20-25 ? Would the TATA-box continue to absorb the majority of the deformation energy and locally melt (and not other regions) at sigma around 0.073 ? Response: The torsional deformation on the DNA is introduced gradually in the simulations that are much longer than any prior simulations that introduce torsion stress in DNA. The fact that the calculated free energy change for the melting process is well converged indicates that sufficient time is given for the distribution of the stress along the DNA. Secondly, in both DNA sequences we used for the simulations the TATA-box segment was located off center. Nevertheless, melting occurred in both cases at the TATA-box. These two observations strongly suggest that the effect (as expected) is not depending on the position of the TATA-box in the DNA. 2) It is now evident that local base-pair melting is a step-wise asymmetric process with one of the two Watson-Crick bases having higher probability to fray than the complementary one (PNAS 100, 13922–13927 (2003); J Phys Chem B 113, 2614–2623 (2009); J Comput Chem 32, 3354–3361 (2011); PNAS 113, 116–121 (2016); J Mol Model. 23, 226 (2017); PNAS 116, 22471-22477 (2019)). In this context, it would be interesting for the authors to comment on the molecular details governing the melting of the TATA-box from such perspective. Did they observe, for instance, preferential fraying of Thymine(T) leading to melting of the TATA-box ? Response: We checked the simulation trajectories for the step-wise asymmetry. We found indeed that upon melting thymine bases showed a higher tendency for fraying by a factor of 1.2 to 1.3 compared to adenine in the TATA-box. The paragraph on page 9 was modified accordingly and new references were added. Reviewer #2: This well-written manuscript describes a computational study of double stranded DNA under torsional stress. Specifically, the authors performed all-atom molecular dynamics simulations of two 50-basepair DNA fragments different in their CG content but featuring the same TATA box, a fragment of DNA that is frequently present at the start of DNA transcription sites. The under-twisting of DNA was realized by means of torsional restraints. Gradual increase of the restraints allowed the authors to observe redistribution of the mechanical energy at the bp level, melting of the TATA box, and, impressively, obtain the free-energy costs associated with the above transitions. The authors rationalize the results of the simulations using an Ising model. This is a very impressive study that has the potential to become a classic paper in the field of computational DNA mechanics. The observations of TATA box melting and redistribution of mechanical deformation energy are particularly valuable. The manuscript is clearly written and can be followed by a person familiar with the subject. The manuscript can be published in its present form, though it would be nice if the authors could split the very long first paragraph of the Conclusions into several shorter paragraphs. Response: We thank the reviewer for the encouraging statement. We followed the recommendation of the reviewer and split the Conclusion section into paragraphs to improve readability of this section. Finally, we like to thank the reviewers for the fair comments and hope that with the additions and changes we have made to the manuscript it is now acceptable for publication in PlosOne. Yours sincerely, Korbinian Liebl, Martin Zacharias Attachments Attachment Submitted filename: response_KL_MZ_PlosOne.pdf https://doi.org/10.1371/journal.pone.0232976.r002
27 Apr 2020 Decision Letter - Claudio M. Soares, Editor How global DNA unwinding causes non-uniform stress distribution and melting of DNA PONE-D-20-05578R1 Dear Dr. Zacharias, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. With kind regards, Claudio M. Soares, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: I am glad to confirm that the Authors have sufficiently addressed my concerns with their revisions. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No https://doi.org/10.1371/journal.pone.0232976.r003
Formally Accepted
1 May 2020 Acceptance Letter - Claudio M. Soares, Editor PONE-D-20-05578R1 How global DNA unwinding causes non-uniform stress distribution and melting of DNA Dear Dr. Zacharias: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Claudio M. Soares Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0232976.r004

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