{"id":175,"date":"2023-01-31T09:35:20","date_gmt":"2023-01-31T14:35:20","guid":{"rendered":"https:\/\/www.yorku.ca\/science\/research\/pjohnsondev\/?page_id=175"},"modified":"2023-01-31T16:14:26","modified_gmt":"2023-01-31T21:14:26","slug":"assembly-pcr-oligo-maker","status":"publish","type":"page","link":"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/","title":{"rendered":"Assembly PCR Oligo Maker"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">A Tool For Designing Oligodeoxynucleotides For Constructing Long DNA Molecules<\/h2>\n\n\n\n<div style=\"height:24px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>Assembly PCR Oligo Maker is created to automate the design of oligodeoxynucleotides for the PCR based construction of long DNA molecules. This application is designed specifically to aid in the design of DNA molecules that are to be used for the production of RNA molecules by in vitro synthesis with T7 RNA polymerase.<\/p>\n\n\n\n<p>The input for Assembly PCR Oligo Maker is either the desired DNA sequence to be made, or an RNA sequence. If RNA is the input the program first determines the DNA sequence necessary to produce the desired RNA molecule. The program then determines the sequences of all the oligodeoxynucleotides necessary for a two-step assembly PCR-based synthesis of the desired DNA molecule.<\/p>\n\n\n\n<p>The output oligodeoxynucleoide sequences are designed to have a uniform melt temperature and are checked for regions of overlap outside of the desired priming regions necessary for the PCR.<\/p>\n\n\n\n<div style=\"height:24px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker-browser-requirements\/\" target=\"_blank\" rel=\"noreferrer noopener\">Mac Users please note<\/a><\/li><li><a href=\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/wp-content\/uploads\/sites\/749\/2023\/01\/manual.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">User manual (requires a pdf viewer)<\/a><\/li><li><a href=\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/protocol-for-assembly-pcr-reaction\/\" target=\"_blank\" rel=\"noreferrer noopener\">Protocol for assembly PCR reaction<\/a><\/li><li><a href=\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/wp-content\/uploads\/sites\/749\/2023\/01\/PCR-oligomaker.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Article from Nucleic Acids Res. (2005) 33: W521-W525 (requires a pdf viewer) - please cite this article<\/a><\/li><li><a href=\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/contact\/\" target=\"_blank\" rel=\"noreferrer noopener\">Feedback<\/a><\/li><\/ul>\n\n\n\n<div style=\"height:32px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p class=\"has-vivid-red-color has-text-color\">Please note that depending on the security settings in your browser you may not be able to see the button below to start the program. You may also see a red box or get an error message. To get the program started you need to select \"trust this site\" if a message pops up or click \"Allow\" to let www.yorku.ca run \"Java Applet\". You may also need to add this site to the trusted sites settings in your browser preferences (security then manage website settings for Java) and\/or Java preference panel or control panel (security setting, edit site list). It does work with the right settings!<\/p>\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n","protected":false},"excerpt":{"rendered":"<p>A Tool For Designing Oligodeoxynucleotides For Constructing Long DNA Molecules Assembly PCR Oligo Maker is created to automate the design of oligodeoxynucleotides for the PCR based construction of long DNA molecules. This application is designed specifically to aid in the design of DNA molecules that are to be used for the production of RNA molecules [&hellip;]<\/p>\n","protected":false},"author":45,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","footnotes":""},"tags":[],"class_list":["post-175","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.0 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Assembly PCR Oligo Maker - The Johnson Lab<\/title>\n<meta name=\"robots\" content=\"noindex, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Assembly PCR Oligo Maker - The Johnson Lab\" \/>\n<meta property=\"og:description\" content=\"A Tool For Designing Oligodeoxynucleotides For Constructing Long DNA Molecules Assembly PCR Oligo Maker is created to automate the design of oligodeoxynucleotides for the PCR based construction of long DNA molecules. This application is designed specifically to aid in the design of DNA molecules that are to be used for the production of RNA molecules [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/\" \/>\n<meta property=\"og:site_name\" content=\"The Johnson Lab\" \/>\n<meta property=\"article:modified_time\" content=\"2023-01-31T21:14:26+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/\",\"url\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/\",\"name\":\"Assembly PCR Oligo Maker - The Johnson Lab\",\"isPartOf\":{\"@id\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/#website\"},\"datePublished\":\"2023-01-31T14:35:20+00:00\",\"dateModified\":\"2023-01-31T21:14:26+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/#breadcrumb\"},\"inLanguage\":\"en-CA\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/assembly-pcr-oligo-maker\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Assembly PCR Oligo Maker\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/#website\",\"url\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/\",\"name\":\"The Johnson Lab\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/www.yorku.ca\/science\/research\/pjohnson\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-CA\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Assembly PCR Oligo Maker - The Johnson Lab","robots":{"index":"noindex","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"og_locale":"en_US","og_type":"article","og_title":"Assembly PCR Oligo Maker - The Johnson Lab","og_description":"A Tool For Designing Oligodeoxynucleotides For Constructing Long DNA Molecules Assembly PCR Oligo Maker is created to automate the design of oligodeoxynucleotides for the PCR based construction of long DNA molecules. 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