{"id":38660,"date":"2025-06-26T11:32:47","date_gmt":"2025-06-26T11:32:47","guid":{"rendered":"https:\/\/gaviki.com\/blog\/?p=38660"},"modified":"2025-06-26T11:32:49","modified_gmt":"2025-06-26T11:32:49","slug":"please-consider-the-restriction-enzymes-apai-and-pspomi-omg-who-thinks-of-these-names","status":"publish","type":"post","link":"https:\/\/gaviki.com\/blog\/please-consider-the-restriction-enzymes-apai-and-pspomi-omg-who-thinks-of-these-names\/","title":{"rendered":"Please consider the restriction enzymes ApaI and PspOMI (OMG, who THINKS of these names"},"content":{"rendered":"\n

Please consider the restriction enzymes ApaI and PspOMI (OMG, who THINKS of these names???). Anyway, these enzymes have the following recognition\/cut sequences, with the * indicating the cut site: ApaI: 5\u00e2\u20ac\u2122GGCCC3\u00e2\u20ac\u2122 3\u00e2\u20ac\u2122CCGGG<\/em>G5\u00e2\u20ac\u2122 PspOMI: 5\u00e2\u20ac\u2122GGGCCC3\u00e2\u20ac\u2122 3\u00e2\u20ac\u2122CCCGGG<\/em>G5\u00e2\u20ac\u2122 For each of these, please state whether the overhangs are 5\u00e2\u20ac\u2122 ends or 3\u00e2\u20ac\u2122 ends. Another enzyme, EagI, cuts at the sequence: 5\u00e2\u20ac\u2122CGGCCG3\u00e2\u20ac\u2122 3\u00e2\u20ac\u2122GCCGGC5\u00e2\u20ac\u2122 Can a molecule that has been cut with EagI be annealed for one that is cut with ApaI, PspOMI, neither, or both? Please demonstrate or explain verbally.<\/p>\n\n\n\n

The Correct Answer and Explanation is:<\/mark><\/strong><\/p>\n\n\n\n

1. ApaI:<\/strong><\/h3>\n\n\n\n

Recognition site:<\/strong><\/p>\n\n\n\n

    \n
  • 5\u2019\u202fGGCC*C\u202f3\u2019<\/li>\n\n\n\n
  • 3\u2019\u202fC\u202f*CCGGG\u202f5\u2019<\/li>\n<\/ul>\n\n\n\n

    Cutting pattern:<\/strong>
    ApaI cuts after the C<\/strong> on the top strand and before the C<\/strong> on the bottom strand. This leaves a 3\u2019 overhang<\/strong> of the sequence C<\/strong>.<\/p>\n\n\n\n

    Resulting ends:<\/strong><\/p>\n\n\n\n

      \n
    • 5\u2019 GGCC<\/li>\n\n\n\n
    • 3\u2019 CCGGG (with a 3′ overhang of “GGG”)<\/li>\n<\/ul>\n\n\n\n

      Therefore, ApaI produces a 3\u2019 overhang<\/strong>.<\/h3>\n\n\n\n
      \n\n\n\n

      2. PspOMI:<\/strong><\/h3>\n\n\n\n

      Recognition site:<\/strong><\/p>\n\n\n\n

        \n
      • 5\u2019\u202fG*GGCCC\u202f3\u2019<\/li>\n\n\n\n
      • 3\u2019\u202fCCCGGG*\u202f5\u2019<\/li>\n<\/ul>\n\n\n\n

        Cutting pattern:<\/strong>
        PspOMI cuts before the G<\/strong> on the top strand and after the G<\/strong> on the bottom strand, leaving a 5\u2019 overhang<\/strong>.<\/p>\n\n\n\n

        Resulting ends:<\/strong><\/p>\n\n\n\n

          \n
        • 5\u2019 G (overhang)<\/li>\n\n\n\n
        • 3\u2019 CCCGGG<\/li>\n<\/ul>\n\n\n\n

          Therefore, PspOMI produces a 5\u2019 overhang<\/strong>.<\/h3>\n\n\n\n
          \n\n\n\n

          3. EagI:<\/strong><\/h3>\n\n\n\n

          Recognition site:<\/strong><\/p>\n\n\n\n

            \n
          • 5\u2019\u202fC*GGCCG\u202f3\u2019<\/li>\n\n\n\n
          • 3\u2019\u202fGCCGG*C\u202f5\u2019<\/li>\n<\/ul>\n\n\n\n

            Cutting pattern:<\/strong>
            EagI cuts between C and G<\/strong> on both strands symmetrically, producing the overhang GGCC<\/strong> on the 5\u2019 end<\/strong>.<\/p>\n\n\n\n

            Resulting ends:<\/strong><\/p>\n\n\n\n

              \n
            • 5\u2019 CGGCC<\/li>\n\n\n\n
            • 3\u2019 GCCGG
              (Leaving a 5\u2019 overhang<\/strong> of “GGCC”)<\/li>\n<\/ul>\n\n\n\n

              Therefore, EagI produces a 5\u2019 overhang<\/strong>.<\/h3>\n\n\n\n
              \n\n\n\n

              Can a molecule cut with EagI anneal with ApaI or PspOMI?<\/h3>\n\n\n\n

              Let\u2019s compare the sticky ends:<\/p>\n\n\n\n

                \n
              • EagI sticky end:<\/strong> 5\u2019 overhang of GGCC<\/strong><\/li>\n\n\n\n
              • ApaI sticky end:<\/strong> 3\u2019 overhang, not complementary<\/strong> to GGCC<\/li>\n\n\n\n
              • PspOMI sticky end:<\/strong> 5\u2019 overhang, but G<\/strong> (single base), not complementary to GGCC<\/li>\n<\/ul>\n\n\n\n

                Conclusion:<\/strong>
                The sticky ends from EagI are not compatible with either ApaI or PspOMI<\/strong>, because the sequences and overhang types (length and base sequence) do not match. For sticky ends to anneal, the overhangs must be complementary and of the same type (both 5\u2019 or both 3\u2019).<\/p>\n\n\n\n

                \n\n\n\n

                Final Answers:<\/h3>\n\n\n\n
                  \n
                • ApaI:<\/strong> 3\u2019 overhang<\/li>\n\n\n\n
                • PspOMI:<\/strong> 5\u2019 overhang<\/li>\n\n\n\n
                • EagI’s product can anneal with:<\/strong> neither<\/strong> ApaI nor PspOMI<\/li>\n<\/ul>\n\n\n\n
                  \"\"<\/figure>\n","protected":false},"excerpt":{"rendered":"

                  Please consider the restriction enzymes ApaI and PspOMI (OMG, who THINKS of these names???). Anyway, these enzymes have the following recognition\/cut sequences, with the * indicating the cut site: ApaI: 5\u00e2\u20ac\u2122GGCCC3\u00e2\u20ac\u2122 3\u00e2\u20ac\u2122CCGGGG5\u00e2\u20ac\u2122 PspOMI: 5\u00e2\u20ac\u2122GGGCCC3\u00e2\u20ac\u2122 3\u00e2\u20ac\u2122CCCGGGG5\u00e2\u20ac\u2122 For each of these, please state whether the overhangs are 5\u00e2\u20ac\u2122 ends or 3\u00e2\u20ac\u2122 ends. Another enzyme, EagI, cuts at […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-38660","post","type-post","status-publish","format-standard","hentry","category-quiz-questions"],"_links":{"self":[{"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/posts\/38660","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/comments?post=38660"}],"version-history":[{"count":1,"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/posts\/38660\/revisions"}],"predecessor-version":[{"id":38672,"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/posts\/38660\/revisions\/38672"}],"wp:attachment":[{"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/media?parent=38660"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/categories?post=38660"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/gaviki.com\/blog\/wp-json\/wp\/v2\/tags?post=38660"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}