uSER MANUAL
Contents
1. Tools gt Estimator a small pop up window opens up where the user can enter the cost per base of DNA This will give you total cost of the DNA sequences used to generate DNA sequences in US dollar USD 8 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visit us ath ttp www guptalab org DNA Pen Free Hand Molecular Canvas B File Edit Tools Help Social Media Pen Eraser Select a dimension for the Brick Wall 1050nm x 699 525nm x 348nm 350nm x 231nm 259 174nm 210 138 175 114nm 147 99 126nm 87nm 3 02 8 29 2013 ogg 2 Figure 5 Dimensions for the free grid molecular canvas 10 Capture the screenshot This will take the screenshot of the canvas It is available in Tools menu This will ask user to save the screenshot at user choice destination 11 Clear This will clear your shapes drawn on the molecular canvas 12 Social Media This provides links to follow us on the social media websites You can follow DNA Pen at Facebook Twitter Quora and You tube Output Once you save the draw data the output generated 15 in the excel format The destination place which you have selected to save the draw data contains the excel file Double click on the file to open it It gives the information about the base sequences required for the shape designed Also it includes the sequences for each domain in the DNA bricks n2. Introduction Overview Product Scope Product Perspective System Summary Getting Started Free hand Molecular Canvas Digitized Molecular Canvas Save Detailed DNA Data Save DNA Sequence Save PDF Create Latex file View Draw Image Edit Dimension Estimator Capture Canvas Screenshot Clear Social Media Help Support and Feedback References 03 04 04 05 06 07 09 10 11 11 2 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitusathttp www guptalab org General Information 1 Introduction DNA is a fundamental unit of any organism which makes it the most intriguing and exciting option available for construction of nanostructure Due to its specificity of the base pairing it weaves itself in to the target structures at nano level DNA origami 1 is a simple method used to construct complex two dimensional 2D and three dimensional 3D structures by DNA self assembly 2 However conducting random experiments for constructing such structures is exhaustive and expensive hence there is need to develop the software for such nanoscale construction DNA Pen is one such tool for creation of two dimensional DNA nanostructures which employs the idea of DNA Bricks 3 4 Desired shapes are created on the molecular canvas and the respective sequences required for the building of the shapes is generated as output It generates error free DNA sequence with the error correction and stability
3. Free hand Molecular Canvas e Work on Digitized Molecular Canvas e Save Detailed DNA Data e Save DNA Sequence e Save PDF e Create Latex file e View Draw Image e Edit Dimension e Estimator e Capture Canvas Screenshot e Clear e Social Media 4 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visit us ath ttp www guptalab org 1 Free Hand Molecular Canvas This option is available under the tools menu of the menu bar When the user clicks on Tools gt Free Hand Molecular Canvas the display area on the DNA Pen s home window where user can draw the 2D structure he wants to create Using this molecular canvas is very easy a simple mechanism is to be followed The user has to click and drag the mouse simultaneously on the canvas in accordance with the shape that he wants to create It works just like drawing tool Paint where you can draw any shape If you want erase some you can select Erase button on right hand top corner of the screen To again start drawing select Pen mode by Pen button next to erase button Figure 1 is the example of the hindi letter OM created on the free hand molecular canvas User can draw any free hand shape he wishes to built at nano scale on this free hand molecular canvas File Edit Tools Help Social Media Pen Eraser zi 10 55 AM ESSE DE d 8 29 2013 Figure 1 Free Hand Molecular Canvas 2 Digitized Molecular Canvas This option is available u
4. modules 5 By the designing of the structures visualizing the structure the software increase the efficiency and productivity of the nano scale construction 2 Overview DNA Pen has been primarily developed to facilitate the construction of nanostructures by DNA Brick The software encourages the users to first visualize the structures draw them accordingly on a virtual sheet and then generates the required DNA strand sequence By this we not only achieve automation but also minimize the need for repetitive experimentation for developing one structure The reduction in exhaustion is because of two processes that the software undertakes The software is able to give infinite number of DNA strand sequences for the same shape It allows user to choose to variety of DNA strands for the experiments 3 Product Scope This software provides the user with e Visualization and list of DNA strand sequences for DNA Bricks of different dimensions e Visualization and list of DNA Brick sequences for 2D structures drawn on a free hand draw grid e Visualization and list of DNA strand sequences for 2D structures drawn on digital grid Each cell in the grid represents one tile of DNA Brick e DNA Pen checks for the thermal stability of the DNA strand sequences generated Also it makes sure that there are no possibilities for any kind of secondary structures being formed The strings then go through a refined process to ensure that they satisfy the
5. 8 292 11 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitus ath ttp www guptalab org
6. C Coordinate 45 Y Coordinate 56 d1GTAGACGTGT 2 TAGTGATACCT 3 TGCATATGTCG 4 AACTTCACAG X Coordinate 45 Y Coordinate 58 d1 ATACATCGAT d2 TGAGAGCATIT d3TGTCATTGTAG d4 AGCAAGGTGA Coordinate 41 Y Coordinate 76 91 AGATGTGAAA d2 CTCTAACACIT d3 GCGTTGGTGAG 44 AGATATCGTA X Coordinate 44 Y Coordinate 78 91 GTCAGTCTCT d2 GATGTCGAGGT d3TCACCGTGGTG 44 AGCTTAACAC X Coordinate 46 Y Coordinate 78 91 TCAGGTGTGA d2 d3 GATAGATCTCG d4 ATGAACCGAG X Coordinate 47 Y Coordinate 78 d1 AGTCAGCGCG 2 TTATAGAAGGT 43 GTGAAGCGCGG 44 AGTCTGACTA X Coordinate 48 Y Coordinate 78 d1 TCCTGTATGC d2 AGATCCGTCIT d3ATCTACAGCGG dd AGGACAGCGC Coordinate 49 Y Coordinate 78 d1 CGCTCGCTAA d2 CTCTGGAGAAT 3 ACACCTACCAG 44 AGATCGATGT Coordinate 53 Y Coordinate 64 91 TAACTGCGCC d2 GCTGATAGAGT d3TATCGAATGCG d4 AATGACACGT X Coordinate 51 Y Coordinate 60 91 TACGTCGAAC d2 ATAGCAGCGTT d3 TGCGGAAGAGG 44 ATTCCACTTA X Coordinate 48 Y Coordinate 54 41 CGATTCCTGA d2 ATGGACTTICGT d3CTAGCTCTAGG 44 AGGTCGTATA X Coordinate 47 Y Coordinate 54 d1 TGTATAAGTG d2 GGAGTACTGAT d3AGTCTCAGGCG 44 ACGCAGTGGA X Coordinate 46 Y Coordinate 54 d1 AGGTAGACCG d2GCTGCCATGTT 3 CGTATCTATCG 4 ATCTAGTGAG Coordinate 45 Y Coordinate 55 d1 CACTCAGTGTG d2CTGATGCGGT 3 CGGTCTACCT d4 ATCATACGGCG Coordinate 44 Y Coordinate 57 91 CCTCTCATGTG d2CAGTGTCGAT d3 ACACGTCTAC d4 ATCAGCCACTT Coordinate 42 Y Coordinate 57 d1 CATCTCTTGCT d2 TCACCTTGCT d3 AACTTGGTGC d4 AGG
7. CCTAGCGG IX Coordinate 41 Y Coordinate 56 91 TCTCGCGCCT d2CGCGAGCTCTT d3CGACACTCTGG d4 AGATGCCATC Coordinate 39 Y Coordinate 55 d1 CCAGAGTGTCG d2 CTGCCTCTIT d3 GGCATGACGC 4 AGTCAGATAGC X Coordinate 39 Y Coordinate 53 d1 CGACGTAGTGC d2 TCTATGTGAT d3 CTATCATGTC d4 ATAGGAGATCA X Coordinate 38 Y Coordinate 51 91 CGCCGTGTGTC 42 3 GGTCTACTCA d4 AAGATACTGCC X Coordinate 38 Y Coordinate 50 91 TAGACGACCA 2 GGCAGTATCTT 3 CGTACAACCAG d4 ACACGTATAC Coordinate 38 Y Coordinate 49 d1 CGTTACTTACG 42 d3 ACTCAGGCGC 4 AGATATGCCAG Coordinate 38 Y Coordinate 48 d1 AGGCAGGCAT 02 CTGGCATATCT d3ATGCCGATGAG 04 ACTATCGAAG 4 gt Sheet lt gt l Default JLsto l Sum 0 o e 100 Sheet 1 1 I war A Figure 6 Sample DNA detailed output file Help Menu 3 21 PM B gt Cha 5 1 3 tie el CP cn Help menu which is very common in any software There are four options in the Help Menu 1 User Manual 2 Product Demo 3 Product Feedback 4 About First option user manual should open this user manual in the default PDF reader of uset s system Second option product demo will open the homepage of DNA Pen where the demo is available Third option will open the feedback form where you can give feedback for the software Finally about option recognize the contributors in this project There is a dialog box that opens up as shown b
8. Laboratory of Natural Information Processing DA IICT Gandhinagar DNA Pen User Manual 0 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitusathttp www guptalab org DNA Pen User Manual O 2013 Manish K Gupta Laboratory of Natural Information Processing DA IICT Gandhinagar Gujarat 382007 http www guptalab org dnapen 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 1 0 This file was last modified on August 29 2013 Credits amp Team Principle Investigator Manish K Gupta PhD Graduate Mentor Dixita Limbachiya Developers Arnav Goyal Shikhar Kumar Gupta Foram Joshi Sushant Pritmani amp Akshita Sahai Software Logo Foram Joshi Acknowledgments The authors would like to thank Priyanka Shukla and Sonam Jain for providing the module to generate error free DNA sequences and Bruno Lowagie http itextpdf com whose free open source libraries have been used for generating bar codes and PDF We thanks GLYPHICONS free for providing us icons http glyphicons com 1 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitusathtt p w w w guptalab org gt m Table of contents General Information
9. constraints for error correcting codes 3 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitusathttp www guptalab org 4 Product Perspective This product s main aim is to make the process of making the computerization and computation of DNA Origami structure user friendly System Summary Operating Systems Windows 7 Mac OS X This software requires the system to have specifications similar to 2 4 GHz Core 2 Duo 100 MB Hard Disk 2GB Random Access Memory and Basic peripherals like keyboard mouse etc Getting Started Once you have successfully installed the software open DNA pen by double clicking on the icon available on your desktop screen a window with four menu options on the menu bar will appear The dialogue box generating the random tips will appear that will guide the user about the software utility It includes the button for creating the new project User can click on this button or can select the option Create a new project from the file menu This will open the dialogue box that will ask to enter the name of the project Once user specifies the name select the path to save the project at specific location and click on create button Once you save the project folder at specified location this folder consists of all the output files of your project The main features that the software provides the user with and which are spanned across these four options on the menu bar are e Work on
10. elow which contains information like logo of the software version of the software name of the software Credits button and URL of the software On pressing Credits it opens a PDF document in user s default PDF reader 10 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitus ath ttp www guptalab org Support and Feedback Users ate requested to contact team at the email dnapen guptalab org for feedback and any other issues with the software Two platform specific installers Windows and Mac are available on the project home page along with source code with open source license agreement References 1 Rothemund Paul WK Design of DNA origami Proceedings of the 2005 IEEE ACM International conference on Computer aided design IEEE Computer Society 2005 2 Carlos Ernesto Castro Fabian Kilchherr Do Nyun Kim Enrique Lin Shiao Tobias Wauer Philipp Wortmann Mark Bathe and Hendrik Dietz A Primer to Scaffolded DNA Origami Nature Methods 2011 vol 8 3 pages 221 229 3 Bryan Wei Mingjie Dai and Peng Yin Complex Shaped Self Assembled from Single Stranded DNA Tiles Nature 2012 vol 485 pages 623 626 4 Yonggang Ke Luvena L Ong Willam M Shih and Peng Yin Three Dimensional Structures Self Assembled from DNA Bricks Science 2012 vol 338 pages 1177 1183 5 Olgica Milenkovic and Navin Kashyap DNA Codes that Avoid Secondary Structures International Symposium on Information Theory ISIT 2005 pages 28
11. he output in one PDF Once you draw the shape on the canvas click on this option It will include the barcode number which is unique to all the shapes drawn by the user This will help to identify the shapes drawn by him uniquely It will include image of the structure designed in the canvas dimension of the brick and brick image This all are the output in one page which will help user to understand it better A pop up window is generated that confirms that file is saved successfully at specified location with the FreeGridData_filename If user had drawn on freehand molecular canvas and DigitizedGridData_filename 6 Create Latex File This option includes all the latex file of the DNA sequence and its related information like total number of half tile and full tiles and total DNA sequences generated in one PDF Once you save the DNA sequences click on this option This will create the latex folder which include image of the shape and PDF that includes all the DNA sequences in well organized tabular format All are the output in one folder which will help user to understand it better 7 View Draw Image This option will generate the image of the shape drawn It will display the tiles arranged in specific manner according to the shape drawn on the molecular canvas This will allow the 7 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visit us ath ttp www guptalab org user to understand how the specific shape ge
12. nder the tools menu of the menu bar When the user clicks on the Tools gt Digitized Molecular Canvas the display area on the DNA Pen s home window would be filled up with a gridded canvas Here the canvas would be filled with cells which are bigger in size as compared to the cells available in Free Hand Molecular Canvas The user simply needs to click on the cell that he wants to be a part of his structure The cell gets highlighted as the user clicks on it Figure 2 is the example of the nano shape of Cross designed on the 5 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visit us ath ttp www guptalab org digitized canvas There is an undo option available in the tools which enable the user to undo the designed once built Also by clicking twice on the cell it will de highlight the cell amp x File Edit Tools Help Social Media Pen Eraser 10 56 AM 8 29 2013 Ie 18 3 Figure 2 Digitized Molecular Canvas 3 Save Detailed DNA Data This option is available under the File menu of the menu bar When the user clicks on File gt Save Detailed DNA Data DNA Pen checks whether the user has created a design on either of the two molecular canvases available The software saves an excel file which c
13. ontains an ordered list of the DNA strand sequences required to make such a structure experimentally and cootdinates of the tile used to generate the shape A pop up window is generated that confirms that file is saved successfully at specified location with the name DNAData filename Figure 3 shows the way to save the designed shape which will generate the sequence to for the designed shape 4 Save Sequence This option is available under the File menu of the menu bar When the user clicks on File gt Save DNA Sequence DNA Pen checks whether the user has created a new Brick and changed the dimensions from the default values The software saves an excel file which contains an ordered list of the DNA strand sequences used to make the Brick A pop up window is generated that confirms that file is saved successfully at specified location with the name DNAData_filename 6 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visit us ath ttp www guptalab org m Create a new Project 4 Save DNA Sequences d Create Latex File View Draw Image Save PDF Edit Tools Help Social Media Exit Figure 3 Save detailed DNA option generate DNA sequences 5 Save PDE This option includes all t
14. ts arranged according the design of the single stranded tiles Figure 4 displays the arrangement of the SST for the shape in figure 3 Output Value Generated 5 fel ATGATATGGT Brick 27 X 3 Y 10 DNA Sequence Brick 28 X 2 7 DNA Sequence ee TTTTTTTTTTTGTCTTATCTTGCCGATGAATTTTTTTTTTTT Brick 29 X 2 omm Y 9 DNA Sequence TITTTTTTTTTACGTGTGTATCAACACTCGATTTTTTTTTTT EM X 1 04 PM 8 29 2013 FeO g Figure 4 SST arrange in specific manner by view draw image option 8 Edit Dimensions This option is available on the menu bar under the Edit menu When the user clicks on Edit gt Edit Dimensions small pop up window opens up where the user can select any dimensions from dropdown options The pop up has 2 buttons at the bottom of the window the Save and the Cancel button The Save button saves the dimensions of the brick created and now if the user wotks on the molecular canvas the bricks used in the backend would be of the dimensions as specified by the user Figure 5 shows the dialouge box appear when uset wish to change the brick dimension 9 Estimator This option is available on the menu bar under the Tools menu When the user clicks on
15. umber of full and half tile for each domain and number of stick ends It generates the coordinates for each base in the sequence on the basis of shape constructed on the molecular canvas Figure 6 show the sample output file for the above shape mentioned in the digitized molecular canvas This output helps the researcher to design the shape with respect to atrangement of bricks DNA and the stick ends 9 Page DNA Pen User Manual 1 0 Last updated on August 29 2013 Visitusathttp www guptalab org File Edit View Insert Format Tools Data Window Help EM Gal asas vro mm vy BJ Arial v 10 EF U Jh 3 ez Ta A p Al v fx XCordinate A c D Cordinate Domain 1 Domain 2 Domain 3 Domain 4 IX Coordinate 43 Coordinate 57 d1 CTACAATGACA d2 GCTCTGTCCT d3 GATGACCAAT d4 AATGATATAGC X Coordinate 39 Y Coordinate 32 41 TCGCGTATAT d2 ATGTATGCGGT d3GTCGGCTGGCG d4 AGTACTGCCG X Coordinate 45 Y Coordinate 24 d1 ACTGTGTACG d2 GCATGGCGTGT d3CTGCCGCTCTG d4 AGATTGGCAG X Coordinate 46 Y Coordinate 24 d1 ACCTACACCA 2 TCGCGGCGTGT 43 CGACCATAGCG 44 ATGTCGATAT X Coordinate 49 Y Coordinate 52 91 TGCGAGCTGT d2 ATGGTCATGCT d3CTGTACCGCTG 4 AGGTCATGCG Coordinate 47 Y Coordinate 55 d1CATCTGTGCTC 2 3 4 ATCAGTACTCC X Coordinate 46 Y Coordinate 55 d1 CGTACCGTGCT d2GCCGCTTCGT d3 CACTTATACA d4 AACATGGCAG
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