{"id":83,"date":"2020-08-02T17:12:38","date_gmt":"2020-08-02T21:12:38","guid":{"rendered":"https:\/\/pressbooks.bccampus.ca\/kathleef\/?post_type=chapter&#038;p=83"},"modified":"2025-06-16T16:19:51","modified_gmt":"2025-06-16T20:19:51","slug":"chapter-14-alternative-cloning-methods-2-user-and-golden-gate","status":"publish","type":"chapter","link":"https:\/\/pressbooks.bccampus.ca\/kathleef\/chapter\/chapter-14-alternative-cloning-methods-2-user-and-golden-gate\/","title":{"raw":"Alternative Cloning Methods 2 - Golden Gate Cloning and BioBRICKS","rendered":"Alternative Cloning Methods 2 &#8211; Golden Gate Cloning and BioBRICKS"},"content":{"raw":"<h1 style=\"text-align: left\">Introduction<\/h1>\r\nIn this section we are going to look at the use of restriction enzymes that cut to one side of the recognition sequence rather than inside it. This type of enzyme is called type IIS. This means that <em>the overhang generated will be different for different DNA molecules<\/em>. The value of this is that you can design primers to amplify an insert that has the restriction enzyme sequence, followed by the sequence that will generate your desired overhang.\u00a0 You can do directional cloning easily. You still rely on restriction digest and ligation however, so the lower efficiency of this approach (compared to Gateway) is a potential drawback.\r\n\r\nBIO Bricks is the result of a non-profit organization's attempt to produce a set of components: promoters, coding sequences, and others (like ribosome binding sites) that can be assembled in various combinations to produce novel constructs.\r\n<div class=\"textbox shaded\">\r\n<h2 style=\"margin-top: 0em\">Contents<\/h2>\r\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 0em;text-align: left\"><a href=\"#Learning_Outcomes\">Learning Outcomes<\/a>\r\n<a href=\"#A_golden\">A. Golden Gate Cloning<\/a><\/p>\r\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 2em;text-align: left\"><a href=\"#A1_typeIIS\">A-1. Type IIS Restriction Enzymes<\/a>\r\n<a href=\"#A2_primer\">A-2. Primer design for Golden Gate Cloning<\/a><\/p>\r\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 0em;text-align: left\"><a href=\"#B_biobricks\">B. BioBricks<\/a><\/p>\r\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 2em;text-align: left\"><a href=\"#B1_igem\">B-1. IGEM (this information comes from Labster)<\/a>\r\n<a href=\"#B2_biobricks\">B-2. Bio BRICKS<\/a><\/p>\r\n<p style=\"text-align: left\"><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/back-matter\/recorded-lecture-videos\/#13\">List of lecture videos (excluding supplemental videos)<\/a><\/p>\r\n\r\n<\/div>\r\n\r\n<hr style=\"height: 5px;border-top: solid black\" \/>\r\n\r\n<div class=\"textbox textbox--learning-objectives\"><header class=\"textbox__header\">\r\n<h2 class=\"textbox__title\" style=\"margin-top: 0em;margin-bottom: 0em;text-align: center\"><a id=\"Learning_Outcomes\"><\/a>Learning Outcomes<\/h2>\r\n<\/header>\r\n<div class=\"textbox__content\">\r\n<ul>\r\n \t<li>Be able to <span style=\"text-decoration: underline\">design primers<\/span> to generate a desired overhang for cloning an insert into a vector using this method<\/li>\r\n \t<li><span style=\"text-decoration: underline\">Outline a cloning strategy<\/span> to add an insert to a Golden Gate vector<\/li>\r\n \t<li><span style=\"text-decoration: underline\">Outline a cloning strategy<\/span> using Bio Bricks and the 3A method (as done in the simulation)<\/li>\r\n \t<li>For the cloning strategies, <span style=\"text-decoration: underline\">include enough sequence<\/span> to show how the cloning works to join the fragments<\/li>\r\n<\/ul>\r\n<\/div>\r\n<\/div>\r\n\r\n<hr style=\"height: 5px;border-top: solid black\" \/>\r\n\r\n<h2><a id=\"A_golden\"><\/a>A. Golden Gate Cloning:<\/h2>\r\n<h3><a id=\"A1_typeIIS\"><\/a>A-1. Type IIS Restriction Enzymes<\/h3>\r\nType IIS restriction enzymes differ from the types of enzymes we've been using so far. They do not recognize palindromic sequences. They do not cut inside the recognition sequence but to one side of it. The ones we will be focussing on generate 4 base pair 5' overhangs.\u00a0 The recognition sequences are shown with the cut site indicated in brackets beside the sequence, like this: 5'-GGTCTC-3' (1,5). This is the recognition sequence for <em>Bsa<\/em>I. The first number tells you how far from the recognition sequence the enzyme cuts on the top strand, and the second number indicates the cut site on the lower strand. In this case the enzyme cuts one nucleotide 3' to the final C of the sequence on the top strand and 5 nucleotides 5' to the first G of the bottom strand. It looks like this:\r\n\r\n<img class=\"alignnone wp-image-971\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-300x91.png\" alt=\"\" width=\"531\" height=\"161\" \/>\r\n\r\nThis shows the recognition sequence and the results of the cut.\r\n\r\nThe Ns indicate that the 5' overhang could be any sequence.\r\n\r\nThis is an example of\u00a0 another Type IIS enzyme called <em>Bpi<\/em>I.\u00a0 The recognition sequence for this enzyme is listed as: 5'-GAAGAC-3' (2,6)\r\n\r\n<img class=\"alignnone size-full wp-image-902\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example.png\" alt=\"\" width=\"535\" height=\"204\" \/>\r\n\r\n<span style=\"background-color: #ffff00\">(where is the attribution for this image?)<\/span>\r\n\r\nHere is some practice in determining the overhang generated by this type of enzyme:\r\n\r\n[h5p id=\"56\"]\r\n\r\n[h5p id=\"57\"]\r\n\r\n<hr \/>\r\n\r\n<h3><a id=\"A2_primer\"><\/a>A-2. Primer design for Golden Gate Cloning<\/h3>\r\nIn order to do cloning with the Golden Gate method it is best to start by visualizing the product you want to generate.\r\n<ol>\r\n \t<li>Draw out the sequence at the positions where the \"joins\" will be.<\/li>\r\n \t<li>Determine the overlaps that will be needed to join the sequences.<\/li>\r\n \t<li>Figure out where the<em> Bsa<\/em>I (or other) restriction sites need to be placed.<\/li>\r\n \t<li>Draw out the ends ofthe PCR fragment you would get with the primers you've designed<\/li>\r\n \t<li>Draw what the ends will look like after the restriction digest.<\/li>\r\n \t<li>Join the ends and confirm that the ligation product matches the desired fragment.<\/li>\r\n<\/ol>\r\n<a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning.pptx\">Click h<\/a><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning.pptx\">e<\/a><a style=\"text-align: initial;font-size: 1em\" href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning.pptx\">re for the powerpoint slides presented in the video below<\/a><span style=\"text-align: initial;font-size: 1em\">\u00a0(note: there are errors on slide 5 &amp; 8 which have been corrected).<\/span>\r\n\r\n[embed]https:\/\/www.youtube.com\/watch?v=W0AnwBCn920&amp;feature=youtu.be&amp;hd=1[\/embed]\r\n\r\n&nbsp;\r\n\r\nHere is a qui<span style=\"text-align: initial;font-size: 1em\">ck (I hope) practice in oligo design for golden gate cloning.\u00a0 Here are the oligo sequences (A); these will be annealed by the same process we are using for our CRISPR oligos.\u00a0 The annealed sequences are shown in B.<\/span>\r\n\r\nA.\r\n\r\n<img class=\"alignnone wp-image-1120\" style=\"font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Oligos.png\" alt=\"\" width=\"288\" height=\"58\" \/>\r\n\r\nB.\r\n\r\n<img class=\"alignnone wp-image-1122\" style=\"font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Annealed.png\" alt=\"\" width=\"217\" height=\"106\" \/>\r\n\r\nWe want to clone the annealed oligos into a vector cut with a type IIS restriction enzyme. The schematic of what we are trying to do is shown in C. Note that we want the orientation as shown, with the forward oligo on the top strand and the reverse on the bottom strand. The blue squiggles drawn in represent the sequences we need to add to the oligos so that the desirded overhang is generate after annealing. The cloning site of the vector and the restriction enzyme will use to cut the vector is shown in D. Your job is to determine what overhangs are generated by the restriction enzyme,<em> Bsp<\/em>MI, to select the sequence that should be added to each oligo, and to determine which end it should be added to, with the aim being to clone the oligos into the vector as shown in the schematic in C.\r\n\r\nC.\r\n\r\n<img class=\"alignnone size-large wp-image-1123\" style=\"font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic.png\" alt=\"\" width=\"414\" height=\"48\" \/>\r\n\r\n&nbsp;\r\n\r\nD.\r\n\r\n<img class=\" wp-image-1121 alignleft\" style=\"margin-bottom: 4.44444em;text-align: center;font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/vector-cloning-site.png\" alt=\"\" width=\"414\" height=\"83\" \/>\r\n\r\n&nbsp;\r\n\r\n&nbsp;\r\n\r\n&nbsp;\r\n\r\n&nbsp;\r\n\r\n[h5p id=\"58\"]\r\n\r\n[h5p id=\"59\"]\r\n\r\n[h5p id=\"60\"]\r\n\r\n[h5p id=\"61\"]\r\n\r\n[h5p id=\"62\"]\r\n\r\n&nbsp;\r\n\r\n<hr style=\"height: 5px;border-top: solid black\" \/>\r\n\r\n<h2><a id=\"B_biobricks\"><\/a>B. BioBricks:<\/h2>\r\n<h3><a id=\"B1_igem\"><\/a>B-1. IGEM (this information comes from Labster)<\/h3>\r\n<div class=\"container main-body\">\r\n<div id=\"article-container\">\r\n<div class=\"wiki-article\">\r\n\r\n\"The International Genetically Engineered Machine (iGEM) Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology and the development of an open community and collaboration.\"\r\n\r\niGEM has three main activities\r\n<ul>\r\n \t<li>iGEM Competition - this is an international competition for students interested in the field of synthetic biology. The aim is for them to design a novel molecular machine that will address a real world problem. Teams of undergraduate students as well as high school students can enter these competitions.<\/li>\r\n \t<li>Labs Program - a program for academic labs to use the same resources as the competition teams.<\/li>\r\n \t<li>Registry of Standard Biological Parts - the group maintains a database listing a growing collection of genetic parts used for building biological devices and systems.<\/li>\r\n<\/ul>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<div id=\"footer-container\"><footer id=\"wiki-footer\">\r\n<div class=\"colophon\"><\/div>\r\n<\/footer><\/div>\r\n&nbsp;\r\n\r\n<hr \/>\r\n\r\n<h3><a id=\"B2_biobricks\"><\/a>B-2. Bio BRICKS<\/h3>\r\nThe genetic parts mentioned above are the Bio BRICKs. As the name suggests, the parts can be combined to build novel constructs with unique combinations of promoter and coding sequences, somewhat like building a structure with Lego bricks. They can be used to make genetically engineered biological \"machines\".\u00a0 <span style=\"background-color: #ffff00\">[Insert examples of such constructs, what they are used for]<\/span>\r\n\r\nEach \"part\" comes in a plasmid, with an origin of replication, an antibiotic resistance gene, and the unique sequence, or \"part\".\u00a0 Each part (coding sequence or promoter)\u00a0 is flanked by the same Prefix (set of restriction sites) before it and Suffix (a different set of restriction sites) after it. In the prefix is <em>Eco<\/em>RI, <em>Not<\/em>1 and <em>Xba<\/em>I.\u00a0 In the suffix is <em>Spe<\/em>I, <em>Not<\/em>I and <em>Pst<\/em>I.\r\n\r\nThe picture below comes from Labster and shows the prefix and suffix relative to the \"part\".\r\n<h3><img class=\"alignnone wp-image-890 \" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences.jpg\" alt=\"\" width=\"570\" height=\"308\" \/><\/h3>\r\nThe key to being able to join different parts to assemble a novel construct is that the <em>Xba<\/em>I and <em>Spe<\/em>I restriction sites are different but leave compatible overhangs. Therefore if one part is cut with <em>Xba<\/em>I and the other with <em>Spe<\/em>I, the two pieces can be joined by ligation. When they are, the same Prefix and Suffix now flank the joined pieces. The place where the sequences are joined is now neither an <em>Xba<\/em>I nor an <em>Spe<\/em>I site, and is referred to as a \"scar\".\r\n\r\nI've drawn it below. Note the prefix and suffix sequences to either side of the parts, the promoter shown in blue and the coding sequence in red. When the promotor piece is cut with <em>Spe<\/em>I and the coding piece with <em>Xba<\/em>I compatible ends are formed and these can be ligated together. Notice also that the 8 nucleotides between the two pieces is the scar. One drawback to this method is that because the \"join\" between the two pieces is 8 nucleotides long, it will disrupt the reading frame between two coding pieces so making gene fusions is not possible. The joined pieces are now flanked by the same suffix and prefix pieces, which can be used to ligate these pieces into a vector backbone. This vector will have the <em>ccdB<\/em> gene in it and it will be cut with <em>EcoR<\/em>I and <em>Pst<\/em>I. The promoter piece was cut with <em>Eco<\/em>RI and the coding piece with <em>Pst<\/em>I so that the whole thing assembles into the vector backbone to make your construct. The promoter construct, the coding construct and the \"backbone\" construct all have different antibiotic resistance. The transformed cells are plated on the antibiotic that selects for the \"backbone\" or destination vector. Any of the destination vectors that were not cut and did not undergo ligation will not allow transformed cells to grow because of the <em>ccdB<\/em> gene.\r\n\r\n&nbsp;\r\n\r\n<img class=\"alignnone size-large wp-image-891\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-1024x443.jpg\" alt=\"\" width=\"1024\" height=\"443\" \/>\r\n\r\n<a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13B-Biobricks.pptx\">Click here for the powerpoint slides presented in the video below<\/a>.\r\n\r\n[embed]https:\/\/www.youtube.com\/watch?v=dL-qds01Fxc&amp;feature=youtu.be&amp;hd=1[\/embed]\r\n\r\n<hr \/>\r\n<p style=\"text-align: left\"><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/chapter\/chapter-13-alternative-cloning-methods-1-gateway-cloning\/\">Previous (Chapter 13)<\/a><span style=\"float: right\"><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/chapter\/chapter-15-alternative-methods-of-cloning-3-slic\/\">Next (Chapter 15)<\/a><\/span><\/p>","rendered":"<h1 style=\"text-align: left\">Introduction<\/h1>\n<p>In this section we are going to look at the use of restriction enzymes that cut to one side of the recognition sequence rather than inside it. This type of enzyme is called type IIS. This means that <em>the overhang generated will be different for different DNA molecules<\/em>. The value of this is that you can design primers to amplify an insert that has the restriction enzyme sequence, followed by the sequence that will generate your desired overhang.\u00a0 You can do directional cloning easily. You still rely on restriction digest and ligation however, so the lower efficiency of this approach (compared to Gateway) is a potential drawback.<\/p>\n<p>BIO Bricks is the result of a non-profit organization&#8217;s attempt to produce a set of components: promoters, coding sequences, and others (like ribosome binding sites) that can be assembled in various combinations to produce novel constructs.<\/p>\n<div class=\"textbox shaded\">\n<h2 style=\"margin-top: 0em\">Contents<\/h2>\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 0em;text-align: left\"><a href=\"#Learning_Outcomes\">Learning Outcomes<\/a><br \/>\n<a href=\"#A_golden\">A. Golden Gate Cloning<\/a><\/p>\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 2em;text-align: left\"><a href=\"#A1_typeIIS\">A-1. Type IIS Restriction Enzymes<\/a><br \/>\n<a href=\"#A2_primer\">A-2. Primer design for Golden Gate Cloning<\/a><\/p>\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 0em;text-align: left\"><a href=\"#B_biobricks\">B. BioBricks<\/a><\/p>\n<p style=\"margin-top: 0em;margin-bottom: 0em;margin-left: 2em;text-align: left\"><a href=\"#B1_igem\">B-1. IGEM (this information comes from Labster)<\/a><br \/>\n<a href=\"#B2_biobricks\">B-2. Bio BRICKS<\/a><\/p>\n<p style=\"text-align: left\"><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/back-matter\/recorded-lecture-videos\/#13\">List of lecture videos (excluding supplemental videos)<\/a><\/p>\n<\/div>\n<hr style=\"height: 5px;border-top: solid black\" \/>\n<div class=\"textbox textbox--learning-objectives\">\n<header class=\"textbox__header\">\n<h2 class=\"textbox__title\" style=\"margin-top: 0em;margin-bottom: 0em;text-align: center\"><a id=\"Learning_Outcomes\"><\/a>Learning Outcomes<\/h2>\n<\/header>\n<div class=\"textbox__content\">\n<ul>\n<li>Be able to <span style=\"text-decoration: underline\">design primers<\/span> to generate a desired overhang for cloning an insert into a vector using this method<\/li>\n<li><span style=\"text-decoration: underline\">Outline a cloning strategy<\/span> to add an insert to a Golden Gate vector<\/li>\n<li><span style=\"text-decoration: underline\">Outline a cloning strategy<\/span> using Bio Bricks and the 3A method (as done in the simulation)<\/li>\n<li>For the cloning strategies, <span style=\"text-decoration: underline\">include enough sequence<\/span> to show how the cloning works to join the fragments<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<hr style=\"height: 5px;border-top: solid black\" \/>\n<h2><a id=\"A_golden\"><\/a>A. Golden Gate Cloning:<\/h2>\n<h3><a id=\"A1_typeIIS\"><\/a>A-1. Type IIS Restriction Enzymes<\/h3>\n<p>Type IIS restriction enzymes differ from the types of enzymes we&#8217;ve been using so far. They do not recognize palindromic sequences. They do not cut inside the recognition sequence but to one side of it. The ones we will be focussing on generate 4 base pair 5&#8242; overhangs.\u00a0 The recognition sequences are shown with the cut site indicated in brackets beside the sequence, like this: 5&#8242;-GGTCTC-3&#8242; (1,5). This is the recognition sequence for <em>Bsa<\/em>I. The first number tells you how far from the recognition sequence the enzyme cuts on the top strand, and the second number indicates the cut site on the lower strand. In this case the enzyme cuts one nucleotide 3&#8242; to the final C of the sequence on the top strand and 5 nucleotides 5&#8242; to the first G of the bottom strand. It looks like this:<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-971\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-300x91.png\" alt=\"\" width=\"531\" height=\"161\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-300x91.png 300w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-1024x312.png 1024w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-768x234.png 768w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-65x20.png 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-225x68.png 225w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135-350x107.png 350w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning-1-e1606335607135.png 1518w\" sizes=\"auto, (max-width: 531px) 100vw, 531px\" \/><\/p>\n<p>This shows the recognition sequence and the results of the cut.<\/p>\n<p>The Ns indicate that the 5&#8242; overhang could be any sequence.<\/p>\n<p>This is an example of\u00a0 another Type IIS enzyme called <em>Bpi<\/em>I.\u00a0 The recognition sequence for this enzyme is listed as: 5&#8242;-GAAGAC-3&#8242; (2,6)<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-902\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example.png\" alt=\"\" width=\"535\" height=\"204\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example.png 535w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example-300x114.png 300w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example-65x25.png 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example-225x86.png 225w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Example-350x133.png 350w\" sizes=\"auto, (max-width: 535px) 100vw, 535px\" \/><\/p>\n<p><span style=\"background-color: #ffff00\">(where is the attribution for this image?)<\/span><\/p>\n<p>Here is some practice in determining the overhang generated by this type of enzyme:<\/p>\n<div id=\"h5p-56\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-56\" class=\"h5p-iframe\" data-content-id=\"56\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Type IIS RE OH1\"><\/iframe><\/div>\n<\/div>\n<div id=\"h5p-57\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-57\" class=\"h5p-iframe\" data-content-id=\"57\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Type IIS RE OH2\"><\/iframe><\/div>\n<\/div>\n<hr \/>\n<h3><a id=\"A2_primer\"><\/a>A-2. Primer design for Golden Gate Cloning<\/h3>\n<p>In order to do cloning with the Golden Gate method it is best to start by visualizing the product you want to generate.<\/p>\n<ol>\n<li>Draw out the sequence at the positions where the &#8220;joins&#8221; will be.<\/li>\n<li>Determine the overlaps that will be needed to join the sequences.<\/li>\n<li>Figure out where the<em> Bsa<\/em>I (or other) restriction sites need to be placed.<\/li>\n<li>Draw out the ends ofthe PCR fragment you would get with the primers you&#8217;ve designed<\/li>\n<li>Draw what the ends will look like after the restriction digest.<\/li>\n<li>Join the ends and confirm that the ligation product matches the desired fragment.<\/li>\n<\/ol>\n<p><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning.pptx\">Click h<\/a><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning.pptx\">e<\/a><a style=\"text-align: initial;font-size: 1em\" href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13A-Golden-gate-cloning.pptx\">re for the powerpoint slides presented in the video below<\/a><span style=\"text-align: initial;font-size: 1em\">\u00a0(note: there are errors on slide 5 &amp; 8 which have been corrected).<\/span><\/p>\n<p><iframe loading=\"lazy\" id=\"oembed-1\" title=\"Chapter 13 Golden Gate cloning\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/W0AnwBCn920?feature=oembed&#38;rel=0\" frameborder=\"0\" allowfullscreen=\"allowfullscreen\"><\/iframe><\/p>\n<p>&nbsp;<\/p>\n<p>Here is a qui<span style=\"text-align: initial;font-size: 1em\">ck (I hope) practice in oligo design for golden gate cloning.\u00a0 Here are the oligo sequences (A); these will be annealed by the same process we are using for our CRISPR oligos.\u00a0 The annealed sequences are shown in B.<\/span><\/p>\n<p>A.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-1120\" style=\"font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Oligos.png\" alt=\"\" width=\"288\" height=\"58\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Oligos.png 238w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Oligos-65x13.png 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Oligos-225x45.png 225w\" sizes=\"auto, (max-width: 288px) 100vw, 288px\" \/><\/p>\n<p>B.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-1122\" style=\"font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Annealed.png\" alt=\"\" width=\"217\" height=\"106\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Annealed.png 186w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Annealed-65x32.png 65w\" sizes=\"auto, (max-width: 217px) 100vw, 217px\" \/><\/p>\n<p>We want to clone the annealed oligos into a vector cut with a type IIS restriction enzyme. The schematic of what we are trying to do is shown in C. Note that we want the orientation as shown, with the forward oligo on the top strand and the reverse on the bottom strand. The blue squiggles drawn in represent the sequences we need to add to the oligos so that the desirded overhang is generate after annealing. The cloning site of the vector and the restriction enzyme will use to cut the vector is shown in D. Your job is to determine what overhangs are generated by the restriction enzyme,<em> Bsp<\/em>MI, to select the sequence that should be added to each oligo, and to determine which end it should be added to, with the aim being to clone the oligos into the vector as shown in the schematic in C.<\/p>\n<p>C.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-1123\" style=\"font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic.png\" alt=\"\" width=\"414\" height=\"48\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic.png 414w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic-300x35.png 300w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic-65x8.png 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic-225x26.png 225w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/cloning-schematic-350x41.png 350w\" sizes=\"auto, (max-width: 414px) 100vw, 414px\" \/><\/p>\n<p>&nbsp;<\/p>\n<p>D.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-1121 alignleft\" style=\"margin-bottom: 4.44444em;text-align: center;font-size: 1em\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/vector-cloning-site.png\" alt=\"\" width=\"414\" height=\"83\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/vector-cloning-site.png 329w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/vector-cloning-site-300x60.png 300w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/vector-cloning-site-65x13.png 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/vector-cloning-site-225x45.png 225w\" sizes=\"auto, (max-width: 414px) 100vw, 414px\" \/><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<div id=\"h5p-58\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-58\" class=\"h5p-iframe\" data-content-id=\"58\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Golden gate practice 1\"><\/iframe><\/div>\n<\/div>\n<div id=\"h5p-59\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-59\" class=\"h5p-iframe\" data-content-id=\"59\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Golden gate practice 2.\"><\/iframe><\/div>\n<\/div>\n<div id=\"h5p-60\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-60\" class=\"h5p-iframe\" data-content-id=\"60\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Golden gate practice 3\"><\/iframe><\/div>\n<\/div>\n<div id=\"h5p-61\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-61\" class=\"h5p-iframe\" data-content-id=\"61\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Golden gate practice 4\"><\/iframe><\/div>\n<\/div>\n<div id=\"h5p-62\">\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-62\" class=\"h5p-iframe\" data-content-id=\"62\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"Golden gate practice 5\"><\/iframe><\/div>\n<\/div>\n<p>&nbsp;<\/p>\n<hr style=\"height: 5px;border-top: solid black\" \/>\n<h2><a id=\"B_biobricks\"><\/a>B. BioBricks:<\/h2>\n<h3><a id=\"B1_igem\"><\/a>B-1. IGEM (this information comes from Labster)<\/h3>\n<div class=\"container main-body\">\n<div id=\"article-container\">\n<div class=\"wiki-article\">\n<p>&#8220;The International Genetically Engineered Machine (iGEM) Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology and the development of an open community and collaboration.&#8221;<\/p>\n<p>iGEM has three main activities<\/p>\n<ul>\n<li>iGEM Competition &#8211; this is an international competition for students interested in the field of synthetic biology. The aim is for them to design a novel molecular machine that will address a real world problem. Teams of undergraduate students as well as high school students can enter these competitions.<\/li>\n<li>Labs Program &#8211; a program for academic labs to use the same resources as the competition teams.<\/li>\n<li>Registry of Standard Biological Parts &#8211; the group maintains a database listing a growing collection of genetic parts used for building biological devices and systems.<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"footer-container\">\n<footer id=\"wiki-footer\">\n<div class=\"colophon\"><\/div>\n<\/footer>\n<\/div>\n<p>&nbsp;<\/p>\n<hr \/>\n<h3><a id=\"B2_biobricks\"><\/a>B-2. Bio BRICKS<\/h3>\n<p>The genetic parts mentioned above are the Bio BRICKs. As the name suggests, the parts can be combined to build novel constructs with unique combinations of promoter and coding sequences, somewhat like building a structure with Lego bricks. They can be used to make genetically engineered biological &#8220;machines&#8221;.\u00a0 <span style=\"background-color: #ffff00\">[Insert examples of such constructs, what they are used for]<\/span><\/p>\n<p>Each &#8220;part&#8221; comes in a plasmid, with an origin of replication, an antibiotic resistance gene, and the unique sequence, or &#8220;part&#8221;.\u00a0 Each part (coding sequence or promoter)\u00a0 is flanked by the same Prefix (set of restriction sites) before it and Suffix (a different set of restriction sites) after it. In the prefix is <em>Eco<\/em>RI, <em>Not<\/em>1 and <em>Xba<\/em>I.\u00a0 In the suffix is <em>Spe<\/em>I, <em>Not<\/em>I and <em>Pst<\/em>I.<\/p>\n<p>The picture below comes from Labster and shows the prefix and suffix relative to the &#8220;part&#8221;.<\/p>\n<h3><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-890\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences.jpg\" alt=\"\" width=\"570\" height=\"308\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences.jpg 853w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences-300x162.jpg 300w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences-768x414.jpg 768w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences-65x35.jpg 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences-225x121.jpg 225w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/BioBrick-Prefix-and-Suffix-sequences-350x189.jpg 350w\" sizes=\"auto, (max-width: 570px) 100vw, 570px\" \/><\/h3>\n<p>The key to being able to join different parts to assemble a novel construct is that the <em>Xba<\/em>I and <em>Spe<\/em>I restriction sites are different but leave compatible overhangs. Therefore if one part is cut with <em>Xba<\/em>I and the other with <em>Spe<\/em>I, the two pieces can be joined by ligation. When they are, the same Prefix and Suffix now flank the joined pieces. The place where the sequences are joined is now neither an <em>Xba<\/em>I nor an <em>Spe<\/em>I site, and is referred to as a &#8220;scar&#8221;.<\/p>\n<p>I&#8217;ve drawn it below. Note the prefix and suffix sequences to either side of the parts, the promoter shown in blue and the coding sequence in red. When the promotor piece is cut with <em>Spe<\/em>I and the coding piece with <em>Xba<\/em>I compatible ends are formed and these can be ligated together. Notice also that the 8 nucleotides between the two pieces is the scar. One drawback to this method is that because the &#8220;join&#8221; between the two pieces is 8 nucleotides long, it will disrupt the reading frame between two coding pieces so making gene fusions is not possible. The joined pieces are now flanked by the same suffix and prefix pieces, which can be used to ligate these pieces into a vector backbone. This vector will have the <em>ccdB<\/em> gene in it and it will be cut with <em>EcoR<\/em>I and <em>Pst<\/em>I. The promoter piece was cut with <em>Eco<\/em>RI and the coding piece with <em>Pst<\/em>I so that the whole thing assembles into the vector backbone to make your construct. The promoter construct, the coding construct and the &#8220;backbone&#8221; construct all have different antibiotic resistance. The transformed cells are plated on the antibiotic that selects for the &#8220;backbone&#8221; or destination vector. Any of the destination vectors that were not cut and did not undergo ligation will not allow transformed cells to grow because of the <em>ccdB<\/em> gene.<\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-891\" src=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-1024x443.jpg\" alt=\"\" width=\"1024\" height=\"443\" srcset=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-1024x443.jpg 1024w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-300x130.jpg 300w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-768x332.jpg 768w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-1536x664.jpg 1536w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-2048x885.jpg 2048w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-65x28.jpg 65w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-225x97.jpg 225w, https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/biobricks-ligation-350x151.jpg 350w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/p>\n<p><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-content\/uploads\/sites\/1093\/2020\/08\/Chapter-13B-Biobricks.pptx\">Click here for the powerpoint slides presented in the video below<\/a>.<\/p>\n<p><iframe loading=\"lazy\" id=\"oembed-2\" title=\"Chapter 13 Bio Bricks\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/dL-qds01Fxc?feature=oembed&#38;rel=0\" frameborder=\"0\" allowfullscreen=\"allowfullscreen\"><\/iframe><\/p>\n<hr \/>\n<p style=\"text-align: left\"><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/chapter\/chapter-13-alternative-cloning-methods-1-gateway-cloning\/\">Previous (Chapter 13)<\/a><span style=\"float: right\"><a href=\"https:\/\/pressbooks.bccampus.ca\/kathleef\/chapter\/chapter-15-alternative-methods-of-cloning-3-slic\/\">Next (Chapter 15)<\/a><\/span><\/p>\n","protected":false},"author":1046,"menu_order":17,"template":"","meta":{"pb_show_title":"on","pb_short_title":"Gateway Cloning","pb_subtitle":"Gateway Cloning","pb_authors":[],"pb_section_license":"cc-by"},"chapter-type":[47],"contributor":[],"license":[52],"class_list":["post-83","chapter","type-chapter","status-publish","hentry","chapter-type-standard","license-cc-by"],"part":3,"_links":{"self":[{"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/chapters\/83","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/wp\/v2\/users\/1046"}],"version-history":[{"count":25,"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/chapters\/83\/revisions"}],"predecessor-version":[{"id":1526,"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/chapters\/83\/revisions\/1526"}],"part":[{"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/parts\/3"}],"metadata":[{"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/chapters\/83\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/wp\/v2\/media?parent=83"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/pressbooks\/v2\/chapter-type?post=83"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/wp\/v2\/contributor?post=83"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/pressbooks.bccampus.ca\/kathleef\/wp-json\/wp\/v2\/license?post=83"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}