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| | <!--- Basic Page Needs========================================================================= --> | | <!--- Basic Page Needs========================================================================= --> |
| − | <meta charset="utf-8"> | + | <meta charset="utf-8"/> |
| − | <title>Uranyl Adsorption</title>
| + | <title>Uranyl adsorption</title> |
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| − | <meta name="description" content="Wiki of Peking iGEM 2016" />
| + | <meta name="description" content="Wiki of Peking iGEM 2016" /> |
| − | <meta name="author" content="Li Jiamian & Wang Yuqing">
| + | <meta name="author" content="Li Jiamian & Wang Yuqing"/> |
| − | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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| − | <!-- Fix Overwrite the original iGEM style=================================================== -->
| + | <!-- Fix Overwrite the original iGEM style=================================================== --> |
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| | + | |
| | + | <!-- Navigation --> |
| | <div id="navigation" class="navbar navbar-fixed-top"> | | <div id="navigation" class="navbar navbar-fixed-top"> |
| | <div class="navbar-inner "> | | <div class="navbar-inner "> |
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| | <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#" > Achievements</a> | | <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#" > Achievements</a> |
| | <ul class="dropdown-menu"> | | <ul class="dropdown-menu"> |
| − | <li><a href="https://2016.igem.org/Team:Peking/Demonstrate" >Results</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/Results" >Results</a></li> |
| | <li><a href="https://2016.igem.org/Team:Peking/Basic_Part" >Parts</a></li> | | <li><a href="https://2016.igem.org/Team:Peking/Basic_Part" >Parts</a></li> |
| | <li><a href="https://2016.igem.org/Team:Peking/Collaborations" >Collaborations</a></li> | | <li><a href="https://2016.igem.org/Team:Peking/Collaborations" >Collaborations</a></li> |
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| | <li><a href="https://2016.igem.org/Team:Peking/Description" >Overview</a></li> | | <li><a href="https://2016.igem.org/Team:Peking/Description" >Overview</a></li> |
| | <li><a href="https://2016.igem.org/Team:Peking/Design" >Design</a></li> | | <li><a href="https://2016.igem.org/Team:Peking/Design" >Design</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/Cross-linking" >Cross-linking</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/Crosslinking" >Crosslinking</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/Uranyl-absorption" >Uranyl absorption</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/Uranyl-adsorption" >Uranyl adsorption</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/Retrievability" >Collection</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/Clearance" >Clearance</a></li> |
| | <li><a href="https://2016.igem.org/Team:Peking/Secretion" >Secretion</a></li> | | <li><a href="https://2016.igem.org/Team:Peking/Secretion" >Secretion</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/Proof" >Proof and speculation</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/Demonstrate" >Final Performance</a></li> |
| | </ul> | | </ul> |
| | </li> | | </li> |
| − | <li class="dropdown menu-4"><a class="colapse-menu1" href="#" >Modeling</a> | + | <li class="dropdown menu-4"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Modeling</a> |
| | <ul class="dropdown-menu"> | | <ul class="dropdown-menu"> |
| − | <li><a href="https://2016.igem.org/Team:Peking/Model" >Protein polymerization</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/Model/GelPoint" > Model of Gel Point </a></li> |
| | + | <li><a href="https://2016.igem.org/Team:Peking/Model/MassDistribution" > Model of Mass Distribution</a></li> |
| | + | <li><a href="https://2016.igem.org/Team:Peking/Software" >Software</a></li> |
| | </ul> | | </ul> |
| | </li> | | </li> |
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| | <ul class="dropdown-menu"> | | <ul class="dropdown-menu"> |
| | <li><a href="https://2016.igem.org/Team:Peking/HP/Gold" >Overview</a></li> | | <li><a href="https://2016.igem.org/Team:Peking/HP/Gold" >Overview</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/HP/Gold#311" >Field research</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/HP/311" >Field research</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/HP/Gold#questionnaire" >Questionnaire</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/HP/questionnaire" >Questionnaire</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/HP/Gold#consulting" >Consulting</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/HP/consulting" >Consulting</a></li> |
| − | <li><a href="https://2016.igem.org/Team:Peking/HP/Gold#questionnaire" >Other work</a></li> | + | <li><a href="https://2016.igem.org/Team:Peking/HP/otherHP" >Education & Other</a></li> |
| | </ul> | | </ul> |
| | </li> | | </li> |
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| | </div> | | </div> |
| | <!--/Navigation --> | | <!--/Navigation --> |
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| | <div class="row"> | | <div class="row"> |
| | <div class="twelve columns centered text-center"> | | <div class="twelve columns centered text-center"> |
| − | <h1>Uranyl Adsorption<span>.</span></h1> | + | <h1>Uranyl Adsorption</h1> |
| | <p class="title1" style="text-align:center"></p> | | <p class="title1" style="text-align:center"></p> |
| | </div> | | </div> |
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| − | @media (min-width:1024px){
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| − | #sidebar{position:relative;top:120px;max-width:200px;}}
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| − | var scrollTop = document.documentElement.scrollTop || document.body.scrollTop -230;
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| − | }
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| − | </script>
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| | <div class="three columns"> | | <div class="three columns"> |
| − | | + | |
| − | <div id="sidebar" style="color:#000000"> | + | <div id="sidebar" style="color:#000000"> |
| − | <h4>Background</h4>
| + | <h4><a href="javascript:void(0);" onclick="naver('Background')">Background</a></h4> |
| − | <h4>Design</h4>
| + | <h4><a href="javascript:void(0);" onclick="naver('Methods')">Methods</a></h4> |
| − | <h4>Methods</h4>
| + | <h4><a href="javascript:void(0);" onclick="naver('Results')">Results<a></h4> |
| − | <h4>Results</h4>
| + | |
| − | | + | <li><a href=" javascript:void(0);" onclick="naver('basic')">Basic Adsorption</a></li> |
| − | <li><a href=" #background">Basic <sub>_</sub>Adsorption</a></li> | + | <li><a href=" javascript:void(0);" onclick="naver('ratio')">Ratio Optimization</a></li> |
| − | <li><a href=" #Ratio">Ratio <sub>_</sub>Optimization</a></li> | + | <li><a href=" javascript:void(0);" onclick="naver('conditions')">Different Conditions</a></li> |
| − | <li><a href=" #Conditions">Different <sub>_</sub>Conditions</a></li> | + | <li><a href=" javascript:void(0);" onclick="naver('low')">Low Uranyl Concentration< /a></ li> |
| − | <li><a href=" #Low">Low< sub> _</ sub> Uranyl< sub> _< /sub> Concentration< /a></ li> | + | </ul> |
| − | </ul>
| + | < h4><a href="javascript:void(0);" onclick="naver('discussion')"> Discussion</ a></ h4> |
| − | <h4>Discussion</h4>
| + | <h4><a href="javascript:void(0);" onclick="naver('references')">References</a></h4> |
| | + | </div> |
| | </div> | | </div> |
| − | </div>
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| | + | <a id="Background"></a> |
| | + | <div class="texttitle">Background</div> |
| | + | <p>Uranium is a key element used in nuclear energy production and is crucial in many other applications. The most stable and relevant uranium ion in aerobic environments is the uranyl cation. Super Uranyl-binding Protein (SUP) has been rationally designed via structural calculations and functional modification to specifically bind uranyl cations. According to the researchers’ results, SUP is thermodynamically stable and offers very high affinity and selectivity for uranyl with a K<SUB>d</SUB> of 7.4 fM and >10,000-fold selectivity over other metal ions<sup>1</sup>. The binding features of SUP are described later in more detail (Fig. 1.).</p> |
| | + | <figure> |
| | + | <p style="text-align:center;"><img style="width: 100% ;" src="https://static.igem.org/mediawiki/2016/7/76/T--Peking--images_uo2_fig1.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig. 1. Uranyl-binding affinity and selectivity of SUP. (A) Competition assay of SUP versus total carbonate for uranyl revealing a K<SUB>d</SUB> of 7.4 fM at pH 8.9. (B) Binding selectivity of SUP for uranyl over various other metal ions. |
| | + | </figcaption> |
| | + | </figure> |
| | + | <p>It was found that UO<sub>2</sub><sup>2+</sup> is coordinated by five carboxylate oxygen atoms from four amino acid residues in SUP. The hydrogen bonds between the amino acid residues coordinating UO<sub>2</sub><sup>2+</sup> and residues in its second coordination sphere also affects the protein’s uranyl binding ability (Fig. 2.) <sup>2</sup>.</p> |
| | + | <figure> |
| | + | <p style="text-align:center;"><img style="width:45% ;" src="https://static.igem.org/mediawiki/2016/7/72/T--Peking--images_uranyl_adsorption_fig2.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig. 2. Coordination Environment of UO<sub>2</sub><sup>2+</sup> in SUP. UO<sub>2</sub><sup>2+</sup> is coordinated by five carboxylate oxygen atoms from four amino acid residues of SUP. |
| | + | </figcaption> |
| | + | </figure> |
| | + | <p>As mentioned above, we fused SUP to three SpyTags in order to construct the 3A-SUP monomer, so the function of SUP might be affected by these additional modules. To make sure that 3A-SUP could still function when bound in the polymer network, we tested its ability to adsorb UO<sub>2</sub><sup>2+</sup> in various environments.</p> |
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| | + | <a id="Methods"></a> |
| | + | <div class="texttitle">Methods</div> |
| | + | <p>Appropriate volume of 3/4/6A-SUP and 3B were mixed and incubated for 1 hour. Subsequently, a uranyl solution in TBS buffer was prepared and its pH value adjusted appropriately. After complete cross-linking, the uranyl solution was contacted with the pre-incubated proteins and mixed thoroughly by vortexing (Fig. 3.).</p> |
| | + | <figure> |
| | + | <img class="featurette-image" src="https://static.igem.org/mediawiki/2016/d/dc/T--Peking--images_uranyl_adsorption_fig3.png" style="width:100%;" alt=""/> |
| | + | <figcaption style="text-align:center;">Fig. 3. Schematic diagram of uranyl adsorption. |
| | + | </figcaption> |
| | + | </figure> |
| | + | <p>The adsorption reaction was allowed to continue for 1 min, after which the mixture was immediately transferred into 10kDa cutoff centrifuge filters and centrifuged for 10 min at 14000g to exclude non-specific protein interference by removing proteins (Fig. 4.). Finally, 100μL aliquots of the filtrate were collected for further analysis.</p> |
| | + | <figure> |
| | + | <p style="text-align:center;"><img style="width: 70% ;" src=" https://static.igem.org/mediawiki/2016/f/f9/T--Peking--images_uranyl_adsorption_fig4.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig. 4. 10kDa cutoff centrifugal filters. The reaction mixtures were immediately transferred into 10kDa cutoff centrifugal filters and centrifuged for 10 min at 14000g to exclude protein interference. |
| | + | </figcaption> |
| | + | </figure> |
| | + | <p>What makes these results more reliable is that we set up control groups which contained the same concentration of uranyl as the test groups. We used the uranyl concentration of the filtrates from the control groups as the actual uranyl concentration to account for the adsorption of uranyl on centrifuge filters. Two different methods were applied to determine the uranyl concentrations in the filtrate. For higher concentrations (>1μM), we used a modification of the Arsenazo III method<sup>1</sup>. For lower concentrations (<1μM), ICP-MS was employed. </p> |
| | + | <figure> |
| | + | <img class="featurette-image" src="https://static.igem.org/mediawiki/2016/8/80/T--Peking--images_uranyl_adsorption_fig5.png" style="width:100%;" alt=""/> |
| | + | <figcaption>Fig. 5. Uranyl detection assay with Arsenazo III. (A) Mechanism of chromogenic reaction. (B) Standard curve of uranyl concentration. |
| | + | </figcaption> |
| | + | </figure> |
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| | + | <div class="panel panel-default"> |
| | + | <div class="panel-heading panel-title"> |
| | + | <a href="https://2016.igem.org/Team:Peking/Notebook/Protocol:testing_adsorption_capacity_of_protein" aria-expanded="false">Protocol: Testing Adsorption Capacity of Protein</a> |
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| | + | <a id="Results"></a> |
| | + | <div class="texttitle">Results</div> |
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| | <div class="panel-heading panel-title" role="tab" id="heading1"> | | <div class="panel-heading panel-title" role="tab" id="heading1"> |
| − | <a role="button" data-toggle="collapse" href="#collapse1" aria-expanded="false" aria-controls="collapse1">Uranyl Adsorption onto Fusion Proteins and the Protein Hydrogel</a> | + | <a role="button" data-toggle="collapse" href="#collapse1" aria-expanded="false" aria-controls="collapse1"> 1. Uranyl Adsorption onto Fusion Proteins and the Protein Polymer network </a> |
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| | <div id="collapse1" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading1"> | | <div id="collapse1" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading1"> |
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| + | <p>The adsorption capacities of 10μM proteins and polymer network were measured in TBS buffer against uranyl in equimolar quantities. In very short time, 3A-SUP alone showed an adsorption capacity of up to 87% and cross-linked 3A-SUP+3B could effectively sequester 96% of the total uranyl (Fig. 6.).</p> |
| − | <h3>Background</h3>
| + | <figure> |
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| + | < p style=" text-align: center;"><img style=" width:80% ;" src="https://static.igem.org/mediawiki/ 2016/ f/ f0/ T--Peking--images_uranyl_adsorption_fig6.png " alt=""/></p> |
| − | <p>In</p> | + | <figcaption style="text-align:left;"> |
| − | | + | Fig. 6. Adsorption capacities of 3A-SUP and the oligomer mixture 3A-SUP+3B. 3A-SUP alone showed an adsorption capacity of up to 87%. Cross-linked 3A-SUP+3B could effectively sequester 96% of the total uranyl. |
| − | <img class="" src="#" style="width:100%;" alt="">
| + | </figcaption> |
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| + | </figure> |
| − | <figure><img class=" featurette-image img-responsive center-block" src="https://static.igem.org/mediawiki/ 2015/ d/ d3/ Modelling_pic_9_.png" style=" width:100%; background- size: cover; " alt="Generic placeholder image"><figcaption> Figure 5: Fluorescence signal normalized by the number of cells for 0% ( w/v), 0.2% ( w/v) and 0. 5% ( w/v) rhamnose with the csgA and csgA-GFPmut3 construct. The error bars are included for all experiments.</ figcaption>< /figure> | + | <p>Furthermore, we measured the adsorption capacities of other kinds of fusion constructs and polymers, such as 4A-SUP (84%), 6A-SUP (87%), 4A-SUP+3B (88%), 6A-SUP+3B (63%) (Fig. 7.). All of these were less efficient but they also could sequester at least 60% of the total uranyl. The standard deviations were calculated from triplicate experiments (n=3). These results were promising since different kinds of fusion proteins and protein constructs were able to adsorb uranyl with great efficiency. Among these, 3A-SUP+3B (96%) showed the best adsorption capacity and was consequently used for all further experiments.</p> |
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| − | </div>
| + | <figure> |
| | + | <p style="text-align:center;"><img style="width: 86% ;" src="https://static.igem.org/mediawiki/2016/c/c9/T--Peking--images_uo2_fig7.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig. 7. Statistical analysis of adsorption capacities of several kinds of proteins and protein polymer network. ****p<0.0001, ***p<0.001. n=3. Error bars indicate standard deviations. |
| | + | </figcaption> |
| | + | </figure> |
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| | + | <a id="ratio"></a> |
| | + | <div class="panel panel-default"> |
| | + | <div class="panel-heading panel-title" role="tab" id="heading1"> |
| | + | <a role="button" data-toggle="collapse" href="#collapse2" aria-expanded="false" aria-controls="collapse2">2. Optimization of the Protein-Uranyl Ratio</a> |
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| | + | <div id="collapse2" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading1"> |
| | + | <div class="panel-body"> |
| | + | <p>We next wondered whether the adsorption capacity of 3A-SUP+3B would increase with an increased protein-uranyl ratio. We thus tested the adsorption capacity of 3A-SUP+3B at different protein-uranyl ratios in TBS buffer. In these experiments, the concentration of uranyl ions was kept at 10μM.</p> |
| | + | <p>The 3A-SUP+3B polymer network could sequester 89% and 93% of the total uranyl when the protein to uranyl ratio was one and ten, respectively (Fig. 8.). The standard deviations were calculated from triplicate experiments</p> |
| | + | <figure> |
| | + | <p style="text-align:center;"><img style="width:48% ;" src="https://static.igem.org/mediawiki/2016/9/9a/T--Peking--images_uo2_fig8.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig. 8. Adsorption capacity of 3A-SUP+3B at protein-uranyl ratios of 1 and 10. ****p<0.0001, ns means no significant difference. n=3. Error bars indicate standard deviations. |
| | + | </figcaption> |
| | + | </figure> |
| | + | <p>The results thus showed that when the protein-uranyl ratio was increased tenfold, the adsorption rate increased as well. However, the rate of increase was less than 5% and was furthermore not statistically significant.</p> |
| | + | <p>According to these results, the adsorption rate did not increase significantly when the protein to uranyl ratio was increased to ten. The reason might be that 3A-SUP+3B could sequester almost all of the available uranyl already when the ratio is 1:1, making the increase inconsequential. In conclusion, a protein-uranyl ratio of 1:1 was enough to sequester most uranyl at a concentration of 10μM.</p> |
| | + | </div> |
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| | + | <a id="conditions"></a> |
| | + | <div class="panel panel-default"> |
| | + | <div class="panel-heading panel-title" role="tab" id="heading1"> |
| | + | <a role="button" data-toggle="collapse" href="#collapse3" aria-expanded="false" aria-controls="collapse3">3. Test of Adsorption under Different Conditions</a> |
| | + | </div> |
| | + | <div id="collapse3" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading1"> |
| | + | <div class="panel-body"> |
| | + | <p>The protein constructs showed a great uranyl adsorption capacity in TBS buffer, therefore we wondered whether they could work just as well in other conditions. We prepared two experimental scenarios simulated real-life pollution, using fresh water from Weiming Lake on campus and artificial seawater, respectively.</p> |
| | + | <p>At the protein-uranyl ratio of 10:1, 3A-SUP+3B could sequester 93%, 67% and 83% of total uranyl in TBS buffer, fresh water and artificial seawater, respectively (Fig. 9.). The standard deviations were calculated from triplicate experiments.</p> |
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| | + | <figure> |
| | + | <p style="text-align:center;"><img style="width:50% ;" src="https://static.igem.org/mediawiki/2016/4/4e/T--Peking--images_uo2_fig9.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig. 9. Adsorption capacity of 3A-SUP+3B in different conditions. ****p<0.0001, n=3. Error bars indicate standard deviations. |
| | + | </figcaption> |
| | + | </figure> |
| | + | <p>When 3A-SUP+3B was used in fresh water, the adsorption capacity dropped sharply. It is possible that carbonate and other species found in the fresh water might have interfered with 3A-SUP+3B and led to the decrease. It is also possible that the proteins are unstable under low-salt conditions, as opposed to the NaCl-rich environments of TBS buffer or artificial seawater.</p> |
| | + | </div> |
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| | + | <a id="low"></a> |
| | + | <div class="panel panel-default"> |
| | + | <div class="panel-heading panel-title" role="tab" id="heading1"> |
| | + | <a role="button" data-toggle="collapse" href="#collapse4" aria-expanded="false" aria-controls="collapse4">4. Practical Usage Scenario in Low Uranyl Concentration</a> |
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| | + | <div id="collapse4" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading1"> |
| | + | <div class="panel-body"> |
| | + | <p>The adsorption capacity of 3A-SUP+3B against 13nM uranyl was tested at a protein-uranyl ratio of 6000:1, and it was able to sequester 48% and 35% of the total uranyl in TBS buffer and artificial seawater, respectively (Fig. 10.). That means that the functional polymer network could not only adsorb uranyl at high concentrations of uranium pollution, but could also bind uranyl at very low concentrations - as low as 13nM - which equals the uranyl concentration in natural seawater.</p> |
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| | + | <figure> |
| | + | <p style="text-align:center;"><img style="width:42% ;" src="https://static.igem.org/mediawiki/2016/a/a3/T--Peking--images_uo2_fig10.png" alt=""/></p> |
| | + | <figcaption style="text-align:left;"> |
| | + | Fig 10. Adsorption capacity of 3A-SUP+3B in low uranyl concentration. **p<0.01, n=3. Error bars indicate standard deviations. |
| | + | </figcaption> |
| | + | </figure> |
| | + | </div> |
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| + | <a id="discussion"></a> |
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| + | <div class="texttitle">Discussion</div> |
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| + | <p>Triple SpyTag-SUP (3A-SUP) was able to adsorb uranyl with great efficiency, and the cross-linked product of 3A-SUP+3B showed an even better adsorption capacity. What’s more, 3A-SUP+3B could also perform its function well in contaminated conditions, and could thus be used to detoxify the environment. Furthermore, we confirmed that the biological functional polymer network could indeed adsorb uranyl ions from seawater, and might even be employed to gather uranium directly from seawater in the future. Thus, our biological functional polymer network has broad potential application fields.</p> |
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| | + | <a id="references"></a> |
| | + | <div class="references"> |
| | + | <h3>References:</h3> |
| | + | <p>[1] Lu, Z. et al. A protein engineered to bind uranyl selectively and with femtomolar affinity. <i>Nature chemistry 1856</i>, <b>236-241</b> (2014).</p> |
| | + | <p>[2] Laura, G, et al. UO<sub>2</sub><sup>2+</sup> Uptake by Proteins: Understanding the Binding Features of the Super Uranyl Binding Protein and Design of a Protein with Higher Affinity. <i>J. Am. Chem. Soc 136</i>, <b>17484−17494</b> (2014).</p> |
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