{"data":{"labs":[{"nid":"9040343","body":"(...)","title":"ATP\/MG Exclusion","status":"1","created":"15 Oct, 2018","founder_uid":"217870","founder":"mgotrik","founder_picture":"","cloud_round":null,"last_round":"0","date":null,"num_synth":"1000","affiliation":null,"selection":null,"cover_image":null,"round":1},{"nid":"8061654","body":"(...)","title":"CRISPR\/Cas9 - FMN 1b-ng - Same State","status":"1","created":"19 Aug, 2017","founder_uid":"49507","founder":"ElNando888","founder_picture":"sites\/default\/files\/pictures\/picture-49507.png","cloud_round":null,"last_round":"0","date":"05\/22\/2013 11:59 PM","num_synth":"2800","affiliation":null,"selection":null,"cover_image":"\/render\/img\/c96adfa03c4a5cf9737a7993d2362926fd0b2bc6.png","round":1},{"nid":"8060783","body":"(...)","title":"CRISPR\/Cas9 - FMN 1a-ng - Same State","status":"1","created":"18 Aug, 2017","founder_uid":"49507","founder":"ElNando888","founder_picture":"sites\/default\/files\/pictures\/picture-49507.png","cloud_round":null,"last_round":"0","date":"05\/22\/2013 11:59 PM","num_synth":"2800","affiliation":null,"selection":null,"cover_image":"\/render\/img\/c96adfa03c4a5cf9737a7993d2362926fd0b2bc6.png","round":1},{"nid":"5489438","body":"","title":"Sensor v2, turn-off variant 2","status":"1","created":"14 Jan, 2015","founder_uid":"48166","founder":"jnicol","founder_picture":"sites\/default\/files\/pictures\/picture-48166.gif","cloud_round":null,"last_round":"0","date":"05\/22\/2013 11:59 PM","num_synth":"1000","affiliation":null,"selection":null,"cover_image":"\/render\/img\/c0f73e32f8e68502acd0ffb60f549b9258c02b32.png","round":1},{"nid":"5489436","body":"","title":"Sensor for hsa-mir-208a","status":"1","created":"14 Jan, 2015","founder_uid":"48166","founder":"jnicol","founder_picture":"sites\/default\/files\/pictures\/picture-48166.gif","cloud_round":null,"last_round":"0","date":"05\/22\/2013 11:59 PM","num_synth":"1000","affiliation":null,"selection":null,"cover_image":"\/render\/img\/61693e7950c42fb228e8d9ac825bcb871fedb780.png","round":1},{"nid":"3381842","body":"There are two ways to approach the problem I'm presenting this time.\r\n\r\nThe first is simply to try to solve the structure the way it is actually presented in the lab (see picture below), and get the best possible score. To those who will follow this path, I wish good luck. \r\n\r\n\r\n(the color coding is simply blue\/yellow = paired\/unpaired)<\/i>\r\n\r\nThe other path is (for my money) a little smarter. If you guys manage to create a so-called \"kissing hairpin\", which is another form of pseudoknot that we haven't played with until now, well, you may reach a 100 score, or very close, and given the outline below and our recent successes with pseudoknots, this seems to be easier.\r\n\r\n\r\n\r\nHave fun! :)","title":"New Frontier 3","status":"1","created":"28 Sep, 2013","founder_uid":"49507","founder":"ElNando888","founder_picture":"sites\/default\/files\/pictures\/picture-49507.png","cloud_round":null,"last_round":"0","date":"05\/22\/2013 11:59 PM","num_synth":"60","affiliation":null,"selection":"user_vote","cover_image":"\/render\/img\/99180a26770df4099cd1dd9972097ded5f8642e7.png","round":1},{"nid":"3352869","body":"The G-quadruplex is a structure that appears both in nature and in the lab. It is formed by 4 separate G-rich strands. These strands can come either from different molecules or different segments of the same molecule. \r\n\r\nIn the 2012 review article 5\u2032-UTR RNA G-quadruplexes: translation regulation and targeting<\/a>, the authors say \"... The application and refinement of such approaches and other methods, including SHAPE<\/b> and CLIP-SEQ (138,139), could shed light on the existence and nature of RNA G-quadruplexes in cells.\"\r\n\r\nIn this lab, I propose we do this. The target structure here is referred to as a 3-loop intramolecular G-quadraplex. It has been created in vitro<\/i>, and in fact you can look at Figure 1 in A Sequence-Independent Analysis of the Loop Length Dependence of Intramolecular RNA G-Quadruplex Stability and Topology<\/a> for suggestions on how to fill out your sequence.\r\n\r\nThis is an \"impossible folding\" only in the sense that the Eterna energy model will completely fall on its face and tell you that your design won't fold into the target structure (or as is often expressed by players, \"isn't stable\"). Don't believe it.","title":"Impossible Folding II - The Intramolecular G-quadruplex","status":"1","created":"20 Sep, 2013","founder_uid":"57675","founder":"Omei","founder_picture":"sites\/default\/files\/pictures\/picture-57675.png","cloud_round":null,"last_round":"0","date":"05\/22\/2013 11:59 PM","num_synth":"40","affiliation":null,"selection":"user_vote","cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1379635939.png","round":1},{"nid":"3260302","body":"A test to see how SHAPE data relates to Kd values of hexaloops.\r\n\r\nTwo hexaloops are fixed with two remaining for you to play with. These have the highest and lowest Kd values in my tables. Get creative and colorful!\r\n\r\nA fully stable solution is possible and preferred.","title":"Hexaloop Kd and SHAPE test","status":"1","created":"23 Aug, 2013","founder_uid":"55836","founder":"eternacac","founder_picture":"sites\/default\/files\/pictures\/picture-55836.gif","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"40","affiliation":null,"selection":"user_vote","cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377287222.png","round":1},{"nid":"3252175","body":"Does strength in the neck area stabilize the rest of the puzzle. This lab will\r\ncompare 3 configurations to see how the neck area affects the rest of the puzzle.\r\nThe hypothesis is that a stronger more stable neck will stabilize the rest of the puzzle, resulting in higher scoring synthesis results.\r\n30 lab slots are requested per lab.","title":"Neck strength analysis 3 of 3 - Weak - AUs + GUs.","status":"1","created":"20 Aug, 2013","founder_uid":"42833","founder":"JR","founder_picture":"sites\/default\/files\/pictures\/picture-42833.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"30","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3249774","body":"I want to analyze the behaviour of large GU stacks, which are considered stable by eteRNA, in nature.\r\n\r\nYour task is to change the stacks and loops at the ends of the GU stack, so many possible influences by other bases\/pairs can be studied.\r\n\r\nThe submitted designs needn't fit the given outline, if the GU stack is not interrupted by unpaired bases.","title":"Large GU stack","status":"1","created":"19 Aug, 2013","founder_uid":"112053","founder":"player4596","founder_picture":"","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"35","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3231043","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the C-C mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - C-C Mismatch - Pilot Run","status":"1","created":"11 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3229428","body":"While sitting at puzzlemaker, I was playing with two adjacent 1-3 Loops, and realized that it's impossible to make them stable if there's only a A-U or G-U in between. So here it is, Lab which will test and answer an important question: \r\n Will it Fold?\r\nJust remember - use A-U or G-U between 1-3's. ","title":"Double 1-3 Loop","status":"1","created":"10 Aug, 2013","founder_uid":"55082","founder":"RedSpah","founder_picture":"sites\/default\/files\/pictures\/picture-55082.gif","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"60","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3228873","body":"I think the length of the non-hairpin stem matter and that can affect how hard an adjacent multi loop is. Before we couldn't make the shorter designs, so I gave them long stems knowing that I wanted short stems. Now we can decide what length to make our RNA - from 1-89 nucleotides of length. Since I found the some of the results from Janderson and mine Motor protein and Chicken\/Frog leg experiments to be different from what I expected, eg. that the labs with non-hairpins 2 times adjacently attached actually looked easier than those with less adjacent attachment, which was the opposite of what I expected. Basically I wish to see if turning the table - making the non hairpin stem short and prolonging the other stems - to take the pressure of them, changes what type of adjacent multi loop that is easier? I\u2019m intrigued to see if changing the length of the non-hairpin stem, will change the outcome. Welcome to join the experiment. ","title":"Reversed motor - step 1","status":"1","created":"10 Aug, 2013","founder_uid":"8627","founder":"Eli Fisker","founder_picture":"sites\/default\/files\/pictures\/picture-8627.jpg","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"40","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3228095","body":"This is a mod of JandersonLee's Chicken Leg and a continuation of the Chicken\/Frog leg series. Adjacent stemmed multiloops did turn out to be hard, especially in the Motor protein series. However some of the results from the experiments with non hairpin stems in connection with adjacent multiloops, made me wonder about if it matter what side of the non hairpin stem, the multiloop is adjacently attached. Does it matter what side is adjacent? Does chirality plays a role here? ","title":"Chicken Leg - Reversed","status":"1","created":"10 Aug, 2013","founder_uid":"8627","founder":"Eli Fisker","founder_picture":"sites\/default\/files\/pictures\/picture-8627.jpg","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"40","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3223711","body":"I'm interested in why the transcribed sequences of tRNA don't seem to fold (in natural mode) into the familiar \"clover-leaf\" secondary structure. The failure to fold might be due to the relatively high percentage of modified bases in tRNA. That is, the modifications might be necessary to stabilize the normal tRNA structure. I'd like to propose one or more lab puzzles based on some specific tRNA sequence: one in which selected unmodified bases of the natural tRNA, the anticodon (34-36) and a few other conserved regions are locked (as shown for the human serine tRNA here), and perhaps another in which there are different restrictions. In this puzzle, I have left off the terminal CCA which would be added to the 3' end of the sequence, because in the Teeny tRNA puzzle I posted earlier this sequence interacts strongly with the GG at the beginning of the published puzzle. The structures are stabilizable, at least in silico eterna, by making changes to some of the bases. \r\n\r\nMy question is, can an RNA sequence with no modified bases fold into a functional tRNA? There are two layers to this question, only one of which can probably be addressed here. First, can a synthesized RNA sequence with no modified bases fold like a typical tRNA? The second question would be whether an unmodified RNA sequence could WORK like a real tRNA. The second question seems to go well beyond the bounds of the Eterna project, but would be interesting to think about. ","title":"Unmodified tRNA sequences","status":"1","created":"09 Aug, 2013","founder_uid":"44631","founder":"macclark52","founder_picture":"sites\/default\/files\/pictures\/picture-44631.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"40","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3215810","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the A-G mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - A-G Mismatch - Pilot Run","status":"1","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3215647","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the G-A mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - G-A Mismatch - Pilot Run","status":"1","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3215631","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the A-C mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - A-C Mismatch - Pilot Run","status":"1","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3215568","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the C-A mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - C-A Mismatch - Pilot Run","status":"1","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3215559","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the U-C mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - U-C Mismatch - Pilot Run","status":"1","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1},{"nid":"3215466","body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the C-U mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.","title":"SHAPE Profile - C-U Mismatch - Pilot Run","status":"1","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","founder_picture":"sites\/default\/files\/pictures\/picture-24263.png","cloud_round":"9","last_round":"0","date":"06\/23\/2013 11:59 PM","num_synth":"25","affiliation":null,"selection":"user_vote","cover_image":null,"round":1}],"num_labs":"29","num_slots":"9513"},"memcache":true}