User Manual
Contents
1. GS Laboratory of Natural Information Processing DA IICT Gandhinagar 3DNA 2 0 User Manual JDN DOD 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 1 3DNA 2 0 User Manual 2014 Manish K Gupta Laboratory of Natural Information Processing DA IICT Gandhinagar Gujarat 382007 http www guptalab oro 3dna The software described in this book is furnished under an open source license agreement and may be used only in accordance with the terms of the agreement Any selling or distribution of the program or its parts original or modified is prohibited without a written permission from Manish K Gupta Documentation version 2 0 Credits amp Team Principle Investigator India Dr Manish K Gupta Principle Investigator Germany Dr David M Smith Graduate Mentor India Dixita Limbachiya Graduate Mentor Germany Martin Sajfutdinow Developers Shikhar Kumar Gupta Foram Meghal Joshi Software Logo Foram Meghal Joshi Acknowledgements The authors would like to thank Dr David M Smith Head DNA Nanodevices and Martin Sajfutdinow PhD student at Fraunhofer Institute for Cell Therapy and Immunology for their valuable discussions and feedback The authors would also like to thank Bruno Lowagie http itexpdf com whose free open source libraries have been used for generating bar codes and PDF 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http gupt2. Open the 3DNA dmg file and mount it on your disk b Open the 3DNA pkg file and follow the instructions to install the software c Once the installation is complete you can run the software from your Applications folder C On Linux a Extract the file 3DNA zip on your disk b Open your system terminal c Type java jar 3DNA jar and press return to run 3DNA on your linux desktop 3 4 Uninstalling A On Windows Open the control panel and go to Add Remove programs Locate 3DNA in the list of applications and click on uninstall to remove the 3DNA from your system B On Mac OS X C On Linux Simply delete the directory where 3DNA has been installed 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 6 4 Using 3DNA 4 1 3D Molecular Canvas Molecular brick canvas is one of the most integral parts of the software The canvas is a cuboidal figure composed of individual molecular voxels The dimensions of the canvas can be specified as an input by the user gt bm NG eg ee 3DNA Dimens Canvas Height EM canvas width GJ Canvas Depth Eo ox Height in DNA Helices 3 Width in DNA Helices Depth in BP a multiple of 8 Figure 3 Input box for dimensions of molecular canvas Once the dimensions of the canvas are entered you will be redirected to the actual canvas interface Figure 4 3D molecular canvas of dimensions 6H by 6H by 48bp and its corresponding DNA hel
3. a lightweight version of full canvas visualization individual plane visualization allows the user to focus on all the DNA bricks present on a single plane or z coordinate The module loads comparatively faster than the full canvas visualization and is ideal for use on canvases with dimensions higher than 6H x 6H x 48BP 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 13 F Half Brick Domain 1 2 d Half Brick Domain 3 4 9 Full Brick North E Full Brick west P Full Brick East Sf Full Brick South Figure 16 visualization of DNA Bricks for west plane from a Figure 15 color encoding for visualization of Planes structure of dimensions 6H x 6H C Elementary visualization Elementary visualization uses an arrow like notation to denote DNA sequences rather than using a template strand This module is easier for preliminary analysis of the whole canvas and can be used to check for cavities or crystal shapes Figure 17 elementary visualization of a 5H x 10H x 80bp structure 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 14 4 8 Import and Export To provide flexibility and ability to open and edit an existing project the user may export a current project By availing the Export button the current project is saved as a 3dna file An existing project which has been exported previously can be opened and modified viewed
4. through the Import functionality by clicking on the Import button An existing project with 3dna extension can be imported 5 Legal Stuff 5 1 Copyright Distribution 3DNA License for use and distribution C 2013 Manish K Gupta Laboratory of Natural Information Processing DA IICT Gandhinagar Gujarat 382007 http www guptalab org 3dna Email 3dna guptalab org This software is available as an open source approval pending from Open Source Initiatives to academic non profit institutions etc under an open soutce license agreement and may be used only in accordance with the terms of the agreement Any selling or distribution of the program or its parts original or modified is prohibited without a written permission from Manish K Gupta Team Principle Investigator India Dr Manish K Gupta Principle Investigator Germany Dr David M Smith Graduate Mentor India Dixita Limbachiya Graduate Mentor Germany Martin Sajfutdinow Key Developers Shikhar Kumar Gupta Foram Meghal Joshi Software Logo Foram Meghal Joshi Note You can use 3DNA Pen on any computer including a computer in a commercial organization You don t need to register or pay for 3DNA 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 15 5 2 Warranty Licensor provides the Work and each Contributor provides its Contributions on an AS IS BASIS WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND either expr
5. 3D structures B Complex scripts for determining DNA sequences for each new structure C Integration of the scripts and DNA strand lists with experimental setup in laboratories The aforementioned ad hoc approach could be error prone and cumbersome to work with Scripts that are used to generate DNA sequences vary with their developers thus creating documentation conflicts and poor communication across different labs Finally using proprietary licensed software to visualize 3D structures could be a challenge in itself Although most of the 3D rendering engines are capable of rendering shapes with more than hundreds of sequences it becomes confusing for the user to analyze and draw observations when the visualization is too cluttered 3DNA as a software suite helps in providing solutions to such challenges in the following way Lightweight open source application Intuitive and user friendly Easy to work with even with minimal in depth knowledge GOW gt Provides different visualization modules customized specifically for viewing analyzing DNA sequences 1 2 Organization Efforts have been made to make the usage of the software intuitive and user friendly The diagram below depicts the basic workflow of 3DNA 3DNA Import 3dna Create new file canvas Sculpt canvas Visualize shape SVE DAN Estimate cost sequence data Figure 2 Software workflow Export 3dna file 3DNA 2 0 User Manual Last updated on Jan 29 2015 Vi
6. ails of the model Each brick is 32nt long and composed of 4 domains of equal length Each of these 8nt domains interacts with a local neighboring domain containing the complementary strand Such an interaction for a single domain measures 2 5 by 2 5 by 2 7 nm and can be seen as a voxel in the molecular canvas As seen in fig 1 each two brick assembly forms a 90 dihedral angle via hybridization of two complementary 8 nt domains By deselecting voxels from the molecular canvas of user defined dimensions various shapes can be sculpted Figure 1 Self assembly of DNA brick sequences in Lego like fashion Each domain is represented by an and its complementary domain by alphabet Four different types of DNA sequences are used to fully model a structure these include A half bricks or 16 nt sequences B full bricks or 32 nt sequences C Protector bricks full and half bricks which are partially poly 1T strands at the front and back faces of the 3D structure They prevent unwanted hybridization of the DNA strands D boundary bricks 48 nt sequences formed by the concatenation of a full and a half brick found at the boundary surfaces of the structure 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 4 2 Why to use 3DNA 1 1 How 3DNA helps you The general setup for designing and modeling 3D shapes using DNA Bricks mostly includes A Use of heavy licensed software for designing and visualizing
7. alab org 3dna Page 2 Table of Contents 1 Basics of DNA Lego Modeling 1 1 Introduction Keywords 1 2 Technique and details of the model 2 Why to use 3DNA 2 1 How 3DNA helps you 2 2 Software Organization 3 Installation and download 3 1 Where to find it 3 2 System requirements 3 3 Setup and Installation 3 4 Uninstalling 4 Using 3DNA 4 1 3D Molecular Canvas 4 2 Modeling Sculpting Shapes 4 3 DNA Sequence format 4 4 Advanced Panel 4 5 Saving options 4 6 Cost Estimator 4 7 Visualization 4 8 Import and Export 5 Legal Stuff 5 1 Copyright Distribution 5 2 Warranty 6 References and Feedback 7 Glossary 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 3 1 Basics of DNA Lego Modelling 1 1 Introduction Sculpting has a long history and is often considered as one of the oldest art forms In this era of DNA Nanotechnology it is now possible to create nano sized sculptures out of blocks of DNA DNA Lego modeling is a robust technique for constructing 3D DNA nano structures by the combination of distinct single stranded DNA strands called DNA bricks in a fashion similar to that of Lego bricks This manual assumes that the user is familiar with the basics of base pairing of DNA bricks The reader should refer to Three Dimensional Structures Self Assembled from DNA Bricks for further technical details on the language semantics 1 2 Technique and det
8. an 29 2015 Visit us at http guptalab org 3dna Page 9 a 16nt file A csv file containing all the half brick sequences required for completing the molecular canvas The general format of this file is strand number plate number position on plate domainl 3 DNA sequence domain2 4 DNA sequence helix 1 helix 3 z1 z3 coordinate helix 2 helix 4 z2 z4 coordinate b 32nt file A csv file containing all the full brick sequences required for completing the molecular canvas The general format of this file is strand number plate number position on plate domaint DNA sequence domain2 DNA sequence domain3 DNA sequence domain4 DNA sequence helix 1 z1 coordinate helix 2 z2 coordinate helix 3 z3 coordinate helix 4 z4 coordinate check1 check2 check3 check4 c 48nt file A csv file containing all the boundary brick sequences required for completing the molecular canvas The general format of this file is strand number plate number position on plate domaint DNA sequence domain2 DNA sequence domain3 DNA sequence domain4 DNA sequence domain5 DNA sequence domain6 DNA sequence helix 1 z1 coordinate helix 2 z2 coordinate helix 3 z3 coordinate helix 4 z4 coordinate helix 5 z5 coordinate helix 6 z6 coordinate check1 check2 check3 check4 check5 check6 Check x is a binary value 1 if domain x DNA sequence is a poly 1T TTTTTTTT sequence and 0 if domain x DNA sequence is not a poly 1T seq
9. back faces along Z coordinate of the 3D structure 14 Strand number A unique number associated with each strand 15 Tail Domains 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 17 Domains present at the minimum z coordinate for a given structure 16 Voxels Each 8 base pair domain interaction between bricks defines a voxel with dimensions of 2 5 by 2 5 by 2 7 nanometers 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 18
10. ess or implied including without limitation any warranties or conditions of TITLE NON INFRINGEMENT MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE 6 References and Feedback Users are requested to contact team at the feedback page on the website www guptalab org 3dna for any issue with the software or they can also mail at 3dna guptalab org Two platform specific installers Windows and Mac are available on the project home page along with source code 7 Glossary 1 Boundary bricks These are short 16nt bricks which can be found on the boundary surfaces along the X and Y direction Except for the boundary bricks at the front end of the structure all of the short 16nt bricks can be connected with the 32nt bricks on their left Z direction to form 48nt boundary bricks See figure 2 Crystal It is continuous DNA bricks structure composed by the concatenation o f similar building blocks of smaller size The X crystal is formed by growth of the structure along the X axis Similarly the Y crystal grows along the Y axis and Z crystal along the Z axis It is also possible to design two dimensional crystals which simultaneously grow along two axes See figure 3 DNA brick A single stranded DNA sequence which is synthetic in nature It is the main building block of the molecular canvas and is of 2 types full brick 32nt half brick 16nt 4 Domain Each DNA brick is composed of segments of equal length 8nt called d
11. he desired direction of rotation B Translation User can translate move around the molecular canvas by long pressing the right mouse button and moving the pointer in the desire direction of translation C Zoom User can zoom in and zoom out of the canvas scene by long pressing the mouse scroll wheel and zoom in by moving the pointer upward or zoom out by moving the pointer downward Alternatively for pointer devices without the scroll wheel a similar feature can be accessed by long pressing the Alt key on the keyboard along with the left mouse button Toolbar Navigation These features can also be used by clicking on the buttons present in the navigation bar on the left side of the main software interface These buttons can be used to navigate the canvas scene to zoom in out move left right up down for resetting the molecular canvas to its original position and to undo any unwanted selection of a voxel ORO i a Ate Figure 5 Navigation toolbar 4 3 DNA Sequence Formats Using the molecular canvas various shapes can be created The assembly process of the structure can be achieved using a set of random yet unique sequences or a fixed set of sequences which may be uploaded by clicking on the es Change List button under the Choose DNA sequences list option on the advanced panel 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 8 A Random sequences DNA bricks offers a s
12. imple and robust method for the self assembly of shapes with respect to sequence composition 3 DNA chooses DNA sequences from a set of random unique sequences with GC content 40 60 and Hamming distance less than or equal to 6 per domain This is the default option B Fixed sequences A set of fixed sequences with coordinates can be imported as csv files This feature is explained in more detail in 4 B Import DNA Sequences 4 4 Advanced Panel Advanced panel can be invoked by clicking the RS auiron from the taskbar Advanced panel comprises of various different functionalities which can either be used to further model the canvas or can be used to implement constraints and features to the 3D shape DNA sequences These include A Delete multiple voxels a Delete canvas plane b Delete canvas row column along a particular axis B Import DNA Sequences User can import their own set of DNA sequences to create shapes based on the sequences that they already have Import sequence module supported by 3DNA only takes csv as an input with a specific format The 3 csv file one each for half brick full brick and boundary bricks has a separate format for each The software takes 3 different files in its import framework Selected file for 16nt i16ntFile csv Selected file for 32nt 32ntFile csv Selected file for 48nt 48ntFile csv Ali files selected Figure 6 Import sequence framework 3DNA 2 0 User Manual Last updated on J
13. ix model Each individual molecular voxel in the molecular canvas represents an interaction of a domain with its complementary strand A voxel measures 2 5 by 2 5 by 2 7 nanometers A collection of all such voxels forms the molecular canvas The six faces of the molecular canvas are characterized with different colors to distinguish one from another the XY plane is green in color the YZ plane is grey and the XZ plane is yellow Molecular axis originates from the top left corner of the first face 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 7 denoting that point as origin and its associated voxel as the first brick with coordinates 0 0 1 One key information to note here is that the first Z Axis plane has the plane number 1 as compared to X and Y Axis plane number which start with 0 Z Axis plane O is reserved for protector bricks poly 1T which can be enabled disabled separately explained in detail in 5 4 2 Modeling Sculpting Shapes The molecular canvas has been designed to make the modeling and navigation as intuitive as possible Individual molecular voxels can be deselected by simply clicking on them User can interact with the molecular canvas either by mouse movements or by clicking the various buttons in the Left toolbar Mouse Navigation A Rotation Molecular canvas can be rotated canvas across its origin by long pressing the left mouse button and moving the pointer in t
14. l Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 11 Figure 12 y crystal indicating growth along the y axis Figure 13 xy crystal indicating growth along the x and y axes D Implement advanced constraints on DNA Sequences 4 5 a Enable cavity boundary bricks This function when enabled identifies and creates boundary bricks surrounding the internal cavity This is an option to explore how the stability and formation is affected with the presence or absence of longer strands in different parts of the 3D structure Enable poly 1T domains In the case when coordinates sequences cannot be mapped from an imported csv file section 4 B they are considered as removed deleted voxels In this situation the corresponding domains of single stranded DNA which were to be complementary to these removed deleted voxels can be replaced by poly 1T domains if this function is enabled If not enabled the complementary strands remain in their original State Saving options Output DNA sequences obtained from the software can be saved on the local storage in 2 different formats viz pdf and csv By default the name of these files are named as a derivative of the current project name The output files contain all the data for the prescribed structure including the DNa sequence coordinates in two formats x y z coordinates and helix z coordinate for each domain Thus for example if a full bricks is taken in
15. omains Full bricks have 4 domains and half bricks have 2 5 Full Bricks These are 32 nucleotide single stranded DNA sequences These full brick strands serve as building blocks of the 3D molecular canvas 6 Half Bricks These are 16 nucleotide single stranded DNA sequences found usually at the boundary surfaces of the 3D structure 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 16 7 Head Domains Domains present at the minimum z coordinate for a given structure 8 Helix numbers Similar to the caDNAno design 3DNA assigns the coordinates in the form of a combination of helix numbers and Z coordinate numbers See figure 9 Molecular Canvas A master brick collection of voxels is a molecular canvas Its dimensions can be defined by the user 10 Plate number The number associated with the plate for pipetting in the experimental setup 11 Poly 1T domains A domain which is entirely made up of Thymine i e the sequence TTTITTTTT These domains can be found in protector bricks or as domains which were complementary to the removed voxels in order to prevent unwanted hybridization 12 Position on plate The number associated with the position on a plate for pipetting in the experimental setup 13 Protector bricks These are 32 nt bricks with a special purpose They contain poly 1T domains in order to prevent unwanted hybridization of DNA strands at the front and
16. sit us at http guptalab org 3dna Page 5 3 Installation and download 3 1 Where to find it 3DNA can be downloaded from the downloads page of the software s official website at http euptalab ore 3dna You can also download supplementary data to get you started with the input and output formats of the software 3 2 System requirements 3DNA is a cross platform software which means it can be used on the majorly popular desktop environments i e Windows Mac OS X and on various flavors of Linux Usage of a mouse pointing device is recommended for modeling and analyzing 3D shapes 3 3 Setup Installation instructions for running 3DNA on a machine will vary from one operating system to another Bundled binary installer obtained from the website contains the relevant instructions required to build 3DNA on the system A compiled description on building 3DNA can be found below A On Windows a On executing the setup a dialog box should appear with a short description of the software Click on Next to proceed b By clicking on Next button the License agreement will appear Please accept the license and click on Next to proceed c A dialog box will appear asking the user to select the location for installing the software d In the next dialog box you will get an option to create desktop icon and start menu entry for the installation entry e Finally click on Install to install 3DNA software on your system B On Mac OS X a
17. to consideration it would consist of 4 domains The coordinates would be in the form x1 yl z1 k2 y2 z2 x3 y3 z3 x4 y4 z4 and helix1 z1 helix2 z2 helix3 z3 elix4 z4 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna_ Page 12 4 6 Cost Estimator 3DNA comes with an inbuilt estimator function which can be used to calculate the cost of conducting a specific experiment The module takes cost per DNA base in USD as the input variable and gives the total cost of DNA sequences in USD 4 7 Visualization 3DNA comes integrated with visualization modules to verify and analyze the shape drawn using the molecular canvas Considering the limitations of the graphic rendering hardware as well as the user s ability to clearly validate shapes 3DNA provides 3 different types of visualizations to the user these include Figure 14 DNA helix model for structure of dimensions 6H x 6H x 40bp A Full canvas visualization Helical representation of the interaction between individual single stranded DNA sequences and how they join in the Lego like fashion to make a full scaled DNA molecular canvas Note Full canvas visualization module renders individual DNA strands which might use large amount of CPU processing powers To visualize canvases of dimensions higher than 6Hx6Hx48BP one should choose Individual plane visualization for analysis B Individual plane visualization Built as
18. uence The imported files should also contain poly 1T domain protector strands if the user wants to have a structure with protector bricks The software will choose a subset of correct DNA strands from the given set of files to form the prescribed shape on the molecular canvas C Implementing advanced features on 3D structure a 48 nt Boundary bricks This function can be enabled on different canvas planes which will result in the concatenation of 16nt boundary bricks and 32nt bricks along the left Z coordinate to form 48nt boundary bricks G J 5 3 Enable Boundary Br E ss I Max X Plane E Max Y Plane Figure 7 Enable Boundary bricks option menu 3DNA 2 0 User Manual Last updated on Jan 29 2015 Visit us at http guptalab org 3dna Page 10 b Protector bricks The 32 nt bricks with poly 1T domains can be enabled disabled at the extreme left and right along Z axis by selecting the appropriate option Enable Protector Bri i i Sebect Canwas Plame E pin Plane fe Max 7 Plane Figure 8 Enable Protector bricks option menu c Enable crystal s 3DNA also boasts the functionality to create DNA brick crystals elongating in X Y and Z directions These can be enabled by selecting the appropriate buttons 7 Enable Crystals X Crystal Y Crystal Figure 10 z crystal indicating growth along the z axis Figure 11 x crystal indicating growth along the x axis 3DNA 2 0 User Manua
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