{"id":3304,"date":"2019-04-16T09:51:01","date_gmt":"2019-04-16T00:51:01","guid":{"rendered":"http:\/\/163.180.4.222\/lab\/?p=3304"},"modified":"2019-04-16T09:51:01","modified_gmt":"2019-04-16T00:51:01","slug":"structure-and-functional-reselection-of-the-mango-iii-fluorogenic-rna-aptamer","status":"publish","type":"post","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=3304","title":{"rendered":"Structure and functional reselection of the Mango-III fluorogenic RNA aptamer"},"content":{"rendered":"<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p class=\"js-section-title section-title strong position-relative tighten-line-height background-gray-light pt20 pb6 pl0 pr20 standard-space-below small-space-above mq640-pt10 mq640-pb10 mq640-pl20 mq640-mt0 mq640-ml-20 mq640-mr-20 extend-left\"><strong>Abstract<\/strong><\/p>\n<p>&nbsp;<\/p>\n<div id=\"Abs1-content\" class=\"pl20 mq875-pl0 js-collapsible-section\">\n<p>Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant\u00a0<i>i<\/i>Mango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range\u00a0<i>trans<\/i>\u00a0Watson\u2013Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved\u00a0<i>i<\/i>Mango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.<\/p>\n<\/div>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>(\uc6d0\ubb38: <a href=\"https:\/\/www.nature.com\/articles\/s41589-019-0267-9?utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%3A+nchembio%2Frss%2Fcurrent+%28Nature+Chemical+Biology+-+Issue%29\">\uc5ec\uae30<\/a>\ub97c \ud074\ub9ad\ud558\uc138\uc694~)<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>&nbsp; &nbsp; Abstract &nbsp; Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable<a href=\"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=3304\" class=\"more-link\">(more&#8230;)<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[34,29,30],"tags":[],"class_list":["post-3304","post","type-post","status-publish","format-standard","hentry","category-lets-do-chemistry","category-lets-do-science","category-recent-science-news"],"aioseo_notices":[],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack-related-posts":[{"id":2099,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=2099","url_meta":{"origin":3304,"position":0},"title":"Aptamers and Clinical Applications","author":"biochemistry","date":"October 23, 2018","format":false,"excerpt":"\u00a0 \u00a0 Gov Lists 28 Clinical Studies, Mostly Ocular, for Aptamers Only 3 On This List Are Currently Active Studies NOXXON Pharma\u2019s Mirror-Image L-RNA Aptamer is in the Clinic for Cancers \u00a0 Devoted readers of\u00a0Zone In With Zon\u00a0who have photographic memories\u2014or anyone who simply uses this blog\u2019s search engine\u2014will know\u2026","rel":"","context":"In &quot;Essays on Science&quot;","block_context":{"text":"Essays on Science","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=32"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/zon.trilinkbiotech.com\/wp-content\/uploads\/2018\/02\/aptamer-300x242.png?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3261,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=3261","url_meta":{"origin":3304,"position":1},"title":"Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts","author":"biochemistry","date":"April 9, 2019","format":false,"excerpt":"\u00a0 \u00a0 Abstract \u00a0 RNA aptamers and RNA aptamer-based devices can be genetically encoded and expressed in cells to probe and manipulate cellular function. However, their usefulness in the mammalian cell is limited by low expression and rapid degradation. Here we describe the Tornado (Twister-optimized RNA for durable overexpression) expression\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":4481,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=4481","url_meta":{"origin":3304,"position":2},"title":"RNA therapies explained","author":"biochemistry","date":"October 18, 2019","format":false,"excerpt":"\u00a0 Treatments that target RNA or deliver it to cells fall into three broad categories, with hybrid approaches also emerging. \u00a0 \u00a0 Illustration of messenger RNA (red) produced from a DNA strand (purple).\u00a0Credit: Juan Gaertner\/SPL \u00a0 \u00a0 The conventional view of RNA casts the molecule in a supporting role \u2014\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2732,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=2732","url_meta":{"origin":3304,"position":3},"title":"\uc9c0\uad6c \uc0dd\ubb3c DNA\uc640 \ub2e4\ub978 \uc720\uc804 \uc815\ubcf4 \ubd84\uc790\uc2dc\uc2a4\ud15c \ud569\uc131 &#038; Four new DNA letters double life\u2019s alphabet","author":"biochemistry","date":"February 23, 2019","format":false,"excerpt":"\u00a0 \u00a0 \"\ub73b\ubc16\uc758\" \uc678\uacc4\uc0dd\uba85\uccb4 \uac00\ub2a5 \uc785\uc99d\u2026\ud0d0\uc0c9 \ubc29\uc2dd \uc7ac\uac80\ud1a0 \ud544\uc694\uc131 \uc81c\uae30\ub3fc \u00a0 \uc0c8\ub85c \ud569\uc131\ub41c '\ud558\uce58\ubaa8\uc9c0\u00a0DNA'\uae30\uc874 4\uac1c \uc694\uc18c(\uc801\uc0c9\u00b7\ub179\uc0c9\u00b7\uccad\uc0c9\u00b7\ud669\uc0c9 )\uc5d0\ub2e4 \uc0c8\ub85c 4\uac1c(\ubd84\ud64d\uc0c9, \ubcf4\ub77c\uc0c9, \uc624\ub80c\uc9c0\uc0c9, \uccad\ub85d\uc0c9)\uac00 \ucd94\uac00\ub410\ub2e4. [\uc778\ub514\uc560\ub098 \uc758\uacfc\ub300\ud559\uc6d0 \uc81c\uacf5] \u00a0 \uacfc\ud559\uc790\ub4e4\uc774 \ub514\uc625\uc2dc\ub9ac\ubcf4\ud575\uc0b0(DNA)\ucc98\ub7fc \uc720\uc804 \uc815\ubcf4\ub97c \uc800\uc7a5\ud558\uace0 \uc804\ub2ec\ud560 \uc218 \uc788\ub294 \ubd84\uc790\uc2dc\uc2a4\ud15c\uc744 \ud569\uc131\ud574 \ub0c8\ub2e4. \uc774\ub294 \uc0c8\ub85c\uc6b4 \uc0dd\uba85\uccb4 \ud615\ud0dc\ub294 \uc544\ub2c8\uc9c0\ub9cc\u00a0DNA\uc5d0 \uae30\ubc18\ud55c \uc9c0\uad6c \uc0dd\uba85\uccb4\uc640\ub294 \uc804\ud600 \ub2e4\ub978 \uc678\uacc4 \uc0dd\uba85\uccb4\uac00\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1550,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=1550","url_meta":{"origin":3304,"position":4},"title":"DNA tags used to image sugar-bearing proteins on cells","author":"biochemistry","date":"September 4, 2018","format":false,"excerpt":"\u00a0 \u00a0 (\uc6d0\ubb38) \u00a0 \u00a0 Methods for imaging sugars attached to proteins \u2014 the protein glycoforms \u2014 are of interest because glycoforms affect protein movement and localization in cells. A versatile approach is now reported that uses DNA as molecular identity tags. \u00a0 \u00a0 The attachment of sugar molecules to\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3018,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=3018","url_meta":{"origin":3304,"position":5},"title":"\uadf9\uc800\uc628\uc804\uc790\ud604\ubbf8\uacbd\uc73c\ub85c \uad00\ucc30\ud55c RNA \uc911\ud569 \ud6a8\uc18c\uc758 \ubaa8\uc2b5","author":"biochemistry","date":"March 29, 2019","format":false,"excerpt":"\u00a0 \u00a0 2013\ub144 \uc0c8\ub85c\uc6b4 \uc804\uc790\ud0d0\uc9c0\uae30\uc758 \ub3c4\uc785\uc73c\ub85c \uadf9\uc800\uc628\uc804\uc790\ud604\ubbf8\uacbd(Cryo-EM)\uc774 \uc644\uc131\ub418\uba74\uc11c \uc0dd\ud654\ud559 \ubd84\uc57c\uc5d0\uc11c\ub294 \uadf8\uc57c\ub9d0\ub85c \u2018\uadf9\uc800\uc628\uc804\uc790\ud604\ubbf8\uacbd\u2019 \uc2dc\ub300\uac00 \uc5f4\ub838\ub2e4. \uc0dd\uccb4\ub9ac\ub4ec\uc744 \uc870\uc808\ud558\ub294 \ub2e8\ubc31\uc9c8\uc774\ub098, \uadc0\uc5d0\uc11c \uc555\ub825 \ubcc0\ud654\ub97c \ub290\uaef4 \uc77d\uace0 \ub4e3\uac8c \ub3c4\uc640\uc8fc\ub294 \uc13c\uc11c \ubd84\uc790, \uc9c0\uce74 \ubc14\uc774\ub7ec\uc2a4 \ub4f1\uc758 \uad6c\uc870\uac00 \uadf9\uc800\uc628\uc804\uc790\ud604\ubbf8\uacbd \uae30\uc220 \ub355\ubd84\uc5d0 \ubc1d\ud600\uc84c\ub2e4. \uc720\uba85\ud55c \uad6d\uc81c\ud559\uc220\uc9c0 \ud45c\uc9c0 \uc5ed\uc2dc \uc790\uc8fc \uadf9\uc800\uc628\uc804\uc790\ud604\ubbf8\uacbd\uc73c\ub85c \uad00\ucc30\ud55c \u25cb\u25cb\u25cb\uc758 \ubaa8\uc2b5\uc774 \uc790\uc8fc \uc7a5\uc2dd\ud558\uace0 \uc788\ub2e4. \uc774\ubc88 \uc8fc \ub124\uc774\ucc98\uc758 \ud45c\uc9c0\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_sharing_enabled":false,"jetpack_shortlink":"https:\/\/wp.me\/p9Xo1j-Ri","_links":{"self":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts\/3304","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=3304"}],"version-history":[{"count":1,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts\/3304\/revisions"}],"predecessor-version":[{"id":3305,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts\/3304\/revisions\/3305"}],"wp:attachment":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3304"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3304"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3304"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}