Here is the abstract:. Sophisticated analysis and simplified visualization are crucial for understanding complicated structures of biomacromolecules. The program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options.
In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR -enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious.
These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the web application, and the web application programming interface. The supplemental PDF serves as a practical guide, with complete and reproducible examples. The idea of representing bases and WC-pairs as rectangular blocks came from the pioneering work of Calladine et al. Indeed, the base block schematics have continuously evolved for over two decades, as appreciated in the acknowledgements:.
I would like to thank Christopher A. Hunter, Christopher R. Calladine, Helen M. Berman, Catherine L. Lawson, Zukang Feng, Wilma K. Olson and Harmen J. Bussemaker for their helpful input on the block schematic during its continuous evolution for over two decades. I also thank Jessalyn Lu and Yin Yin Lu for proofreading the manuscript, and the user community for feedback. Notably, the supplemental PDF has been diligently written to serve as a practical guide, with complete and reproducible examples.
In fact, the paper concludes with the following two sentences:. Finally, all results reported here are completely reproduceable see the supplemental PDF. Please do not forget to visit back for more 3DNA-related information.
Search What's new? Methods : Databases with G4-related data Currently, there exist 16 databases, which store information concerning quadruplexes. Methods : Tools that analyze and visualize 2D and 3D structure Currently, four tools can analyze and visualize G4 structures. Conclusion DSSR comprehensively examines the G4 structure, determines a variety of its parameters and provides the schematic 3D view.
Nucleic Acids Res. Nucleic Acids Res, 37, W Nucleic Acids Res 46 : — EMBO J 37 : e Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun 10 : Class I PreQ1 riboswitch regulates downstream gene expression in response to its cognate ligand PreQ1 7-aminomethyldeazaguanine. Hatchet ribozyme structure and implications for cleavage mechanism. Proc Natl Acad Sci : — This crystal structure of the hatchet ribozyme product features a compact symmetric dimer. Crystal structure of an adenovirus virus-associated RNA.
Acutely bent viral RNA fragment is a protein kinase R inhibitor and features an unusually structured apical loop, a wobble-enriched, coaxially stacked apical and tetra-stems, and a central domain pseudoknot that resembles codon-anticodon interactions.
RNA 25 : 60— Participants track their heritable traits down through the tree and find which combination of traits they have out of a possible 16 options. Track participant responses throughout the day by having them add a small object bean, marble, microcentrifuge tube to one of 16 mason jars aligned with possible trait combinations.
Encourage people to revisit the booth to see how common or uncommon their combination of traits is among the group at the fair. For another spin on the activity: A Tree of Genetic Traits. In Lesson 2, students examine three different situations where DNA typing was used to carry out justice.
Students also identify and evaluate different uses of DNA typing techniques and its possible benefits and misuses. Epigenetics Resources from GSLC This series of resources about epigenetics by the Genetic Science Learning Center GSLC at the University of Utah includes an introductory video called "The Epigenome at a Glance," a number of interactive tools demonstrating key epigenetics concepts, and other great resources exploring the relationship between epigenetics and nutrition, the brain, inheritance and more.
Informational Videos from Stated Clearly These engaging animated videos by Stated Clearly, accurately explain the basics of genetics and evolution. Together they act as an introductory course to these fields of study, with videos including "What Exactly Is a Gene?
These resources also include information about specific inheritance of gene examples, and ten straightforward, printable activities to learn about traits with your family or class.
Or just the young at heart? Enjoy Cell Press' Coloring with Cell: coloring book pages exploring the world of cellular biology. These color-in comics are graphical representations of a bioscientific process, left black and white for your coloring pleasure! Map-Ed Genetics from pgEd Map-Ed is an interactive learning website from the Personal Genetics Education Project pgEd featuring short quizzes focused on a variety of genetics-related topics.
After completing each quiz, students can "pin" their location on a world map and - over time - watch participants and knowledge spread across the world! Map-Ed is designed to raise public awareness and knowledge about personal genetics using means that everyone can access. These resources for each molecue include interactive exploration tools, explanations of core topics, and applications and examples.
Lesson Plans from pgEd This lesson plan database from the Personal Genetics Education Project pgEd includes interactive lessons for high school and college educators to engage their students in discussions of ethics and personal genetics. The lessons are relevant to multiple subjects, including biology, health, social studies, law, physical education and psychology.
All contain background reading for teachers and students, a selection of classroom activities, discussion points, in some cases a slide presentation or video clip, and an evaluation. Topics include "Introduction to personal genetics", "Direct-to-consumer genetic testing", "History, eugenics and genetics" and many more.
These animations can be helpful for visualizing complex biological concepts. Also, articipants can make their own karyotype in an interactive exploration activity. Your Genome and You gives information on how the science of genetics and genomics impacts what a person looks like physical traits and their health risk for disease. USA , E—E Barnes, R.
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Zivanov, J. Elife 7 , e Rohou, A. Terwilliger, T. Improvement of cryo-EM maps by density modification. Methods 17 , — Pettersen, E. UCSF chimera—a visualization system for exploratory research and analysis. Emsley, P. Features and development of Coot. Comparative protein structure modeling of genes and genomes. Eswar, N. Comparative protein structure modeling using Modeller. Chapter 5 , Unit Google Scholar. Piana, S. Development of a force field for the simulation of single-chain proteins and protein-protein complexes.
Theory Comput. Lemkul, J. Living J. Van Der Spoel, D. Lindahl, E. Abraham, M. SoftwareX 1—2 , 19—25 McGibbon, R. MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Pedregosa, F. Scikit-learn: machine learning in Python. Hunter, J. Matplotlib: a 2D graphics environment. Article Google Scholar. Tiberti, M. PLoS Comput.
Humphrey, W. VMD: visual molecular dynamics. Lilkova, E. Piotto, M. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. NMR 2 , — Lee, W. Bioinformatics 31 , — Williamson, R. Mapping the binding site for matrix metalloproteinase on the N-terminal domain of the tissue inhibitor of metalloproteinases-2 by NMR chemical shift perturbation.
Biochemistry 36 , — Farmer, B. Ishida, T. PrDOS: prediction of disordered protein regions from amino acid sequence. Soding, J. The HHpred interactive server for protein homology detection and structure prediction. Download references. Muskett, Timothy J. Sobhy, Vlad S. Raducanu, Samir M. You can also search for this author in PubMed Google Scholar. Takahashi, M. All authors discussed the results and commented on the manuscript.
Correspondence to Samir M. Hamdan or Alfredo De Biasio. Peer review information Nature Communications thanks Huilin Li and the other, anonymous, reviewer s for their contribution to the peer review of this work. Peer reviewer reports are available. Reprints and Permissions. Nat Commun 12, Download citation. Received : 23 July Accepted : 22 September Published : 19 October Anyone you share the following link with will be able to read this content:.
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Download PDF. Subjects Cryoelectron microscopy DNA. Introduction Cells are continuously subjected to DNA damage caused by environmental mutagens and reactive metabolites, which threaten the stability of the cell genome 1 , 2. Full size image. Data availability The data that support this study are available from the corresponding authors upon reasonable request. References 1. PubMed Article Google Scholar Google Scholar Article Google Scholar View author publications.
Ethics declarations Competing interests The authors declare no competing interests. Additional information Peer review information Nature Communications thanks Huilin Li and the other, anonymous, reviewer s for their contribution to the peer review of this work.
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