Biomod/2014/Kashiwa/Protocols

From OpenWetWare
Jump to: navigation, search

<html> <head> <div id="#top"></div>

<script type="text/javascript" src="http://code.jquery.com/jquery-1.9.1.min.js"></script>

<script type="text/javascript"> new Image(120,80) = "http://openwetware.org/images/7/7a/Logo2Kashiwa.png";

new image(120,80) = "http://openwetware.org/images/1/1d/Logo2.5.png";

new image(71,143) = "http://openwetware.org/images/2/2a/Top1.gif";

new image(71,143) = "http://openwetware.org/images/f/f0/Top2.gif";

new image() = "http://openwetware.org/images/3/38/BackgroundKashiwa.png";

new image() = "http://openwetware.org/images/9/9c/BackgroundKashiwa2.png"; </script>


<script type="text/javascript">

  $(function(){
     $("#menu li").hover(function(){
        $("ul",this).show();
     },
     function(){
        $("ul",this).hide();
     });
  });

</script>


<script type="text/javascript"> <!-- if (document.images) {

// 設定開始(使用する画像を設定してください)

// 通常の画像 var img0 = new Image(120,80); img0.src = "http://openwetware.org/images/e/ec/LogoKashiwa.png";

// ポイント時の画像1 var img1 = new Image(120,80); img1.src = "http://openwetware.org/images/2/26/Logo3Kashiwa.png";


// 設定終了

} // ポイント時の処理 function On(name) { if (document.images) { document.images['def'].src = eval(name + '.src'); } } // 放した時の処理 function Off() { if (document.images) { document.images['def'].src = img0.src; } } // --> </script>

<META http-equiv="Content-Style-Type" content="text/css">

<style type="text/css">


.page-back { position: fixed; bottom: 25px; right: 25px;}

p.paragraph {

 font-size :100%;
 line-height: 135%;
 margin: 10px 25px;

}

p.reference {

 font-size :90%;
 line-height: 135%;
 margin: 10px 20px;

}

p.indent-paragraph {

 font-size :110%;
 line-height:1.5;
 margin:0 30px;
 text-indent: 1em;
 }

h1.title a{

 font-size :100%;
 display: block;
 text-decoration: none;
 color: #000000;

 font-weight:bolder;

 border-left: solid 5px #e00000;
 }

h2.reference a{

 font-size :90%;
 display: block;
 text-decoration: none;
 border-left: solid 5px;
 }

body {

 font-size: 12px;
 font-family: Frutiger, Helvetica, Arial;
 background-color: #B5D3FF;
 overflow-y:scroll;
 overflow-x:hidden;

} article {

 background-color: #ffffff

} .container {

  background-color: #ffffff;
  margin-top:0px

}

.OWWNBcpCurrentDateFilled {display: none;}

}

  1. column-content

{

  width: 0px;
  margin: 0;
  padding: 0;
  float:left;

} .firstHeading {

  display:none;
  width:0px;

}

  1. globalWrapper

{

  width:900px;
  background-color: #ffffff;
  margin-left: auto;
  margin-right: auto;

}

  1. column-one

{

  display:none;
  width:0px;
  background-color: #ffffff;

}

  1. content

{

  margin: 0px;
  align: center;
  padding: 0px 12px;
  width:876px;
  border: 0;

}

  1. bodyContent

{

  width: 800px;
  padding: 0px 38px;
  align: center;
  background-color: #ffffff;
  position:relative;
  

}

  1. column-content

{

  width: 900px;
  background-color: #ffffff;

}


  1. footer

{

  position: center;
  width: 900px;

}

div.menubar {

  position: fixed;
  background-color: none; /* バーの背景色 */
  opacity: 0.95;
  border-top: 0px double white; /* バーの上端線 */
  border-bottom: 0px double white; /* バーの下端線 */
  min-width: 900px; /* メインメニュー全部が収まる最低横幅 */
  z-index:3

}

div.menubar ul#menu {

  margin: -33px 0px 0px -50px; /* メニューバー外側の余白 */
  padding: 0px; /* メニューバー内側の余白 */
  height: 80px; /* メニューバーの高さ */
  list-style-type: none;

}

div.menubar ul#menu li {

  min-width: 110px; /* メニュー項目の横幅 */
  height: 80px; /* メニュー項目の高さ(「メニューバーの高さ」と一致させる) */ 
  float: left;
  list-style-type: none;
  list-style-image: none;
  position: relative;

}

div.menubar ul#menu a {

  text-decoration: none; /* メニュー項目の装飾(下線を消す) */
  display: block; 
  background-color: #1F003E;/* メニュー項目の背景色 */
  color: white; /* メニュー項目の文字色 */
  line-height: 80px; /* メニュー項目のリンクの高さ(「メニュー項目の高さ」と一致させる) */
  text-align: center; /* メインメニューの文字列の配置(中央寄せ) */ 
  width: 100%;
  height: 100%;

}

div.menubar ul#menu a:hover {

  background-image: url("http://openwetware.org/images/3/38/BackgroundKashiwa.png"); /* メニュー項目にマウスが載ったときの背景色 */
  color: #8B008B; /* メニュー項目にマウスが載ったときの文字色 */

}

div.menubar ul#menu a:active {

  background-image: url("http://openwetware.org/images/3/33/Background2.png"); /* メニュー項目にマウスが載ったときの背景色 */
  color: #8B008B; /* メニュー項目をクリックした時の文字色 */

}

/* メニューバー直後のClearfix */ div.menubar ul#menu {

  zoom:1; 

} div.menubar ul#menu:after {

  height: 0; visibility: hidden; content: "."; display: block; clear: both;

}

div.menubar ul#menu ul.sub {

  background-color: #1F003E; /* サブメニュー全体の背景色 */
  border-width: 0px 0px 0px 0px; /* サブメニュー全体の枠線の太さ */
  border-style: solid; /* サブメニュー全体の枠線の線種 */
  border-color: #191970; /* サブメニュー全体の枠線の色 */
  margin: 0px;
  padding: 0px;
  display: none;
  position: absolute;

}

div.menubar ul#menu ul.sub li {

  width: 110px;
  height: 50px; /* サブメニュー1項目の高さ */
  border-width: 0px 0px 0px 0px; /* サブメニュー1項目の枠線の太さ */
  border-style: solid; /* サブメニュー1項目の枠線の線種 */
  border-color: #191970; /* サブメニュー1項目の枠線の色 */
  z-index: 3

}

div.menubar ul#menu ul.sub li a {

  line-height: 50px; /* サブメニュー1項目の行の高さ(「サブメニュー1項目の高さ」と合わせる) */
  text-align: center;  /* サブメニュー1項目の項目名の配置(中央寄せ) */
  text-indent: 0px;  /* サブメニュー1項目の項目名前方の余白 */

}

div.menubar ul#menu ul.sub li a:hover {

  background-image: ('back');
  background-size: 100% auto;
  background-color: #FF00FF; /* サブメニュー項目にマウスが載ったときの背景色 */
  color:  #8B008B; /* サブメニュー項目にマウスが載ったときの文字色 */

}

div.menubar ul#menu ul.sub li a:active {

  background-image: ('backclick') /* メニュー項目にマウスが載ったときの背景色 */
  backround-size: 100% auto;
  color: #8B008B; /* メニュー項目をクリックした時の文字色 */

}

</style>

<div class="menubar">

 <ul id="menu">
 <font face="Frutiger,Helvetica,Arial">
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa"><img src="http://openwetware.org/images/e/ec/LogoKashiwa.png" onmouseover="this.src='http://openwetware.org/images/7/7a/Logo2Kashiwa.png'" onclick="this.src='http://openwetware.org/images/1/1d/Logo2.5.png'" onmouseout="this.src='http://openwetware.org/images/e/ec/LogoKashiwa.png'" height="80px" width="120px" name="def"></a>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Project" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">PROJECT</span></a>
     <ul class="sub">
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Project#1" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Background</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Project#2" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Motivation</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Project#3" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Project Goals</span></a></li>
     </ul>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Trial" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">&nbsp;EARLY TRIAL&nbsp;</span></a>
     <ul class="sub">
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Trial#1" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Design</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Trial#2" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Approaches</span></a></li>
     </ul>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Design" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">DESIGN</span></a>
     <ul class="sub">
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Design#2" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">The Receptor</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Design#1" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">The Motor</span></a></li>
     </ul>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Highlights" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">&nbsp;EXPERIMENT&nbsp;&nbsp;</span></a>
     <ul class="sub">
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Highlights" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Highlights</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Receptor" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">The Receptor</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Motor" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">The Motor</span></a></li>
     </ul>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Discussion" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">&nbsp;&nbsp;DISCUSSION&nbsp;</span></a>
     <ul class="sub">
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Discussion#1" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Achievements</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Discussion#2" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Future</span></a></li>
     </ul>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Protocols" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">PROTOCOL</span></a>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Team" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">TEAM</span></a>
     <ul class="sub">
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Team#1" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Members</span></a></li>
       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Team#2" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Sponsors</span></a></li>
     </ul>
   </li>
 </font>
 </ul>

</div> <br> <br> <br> <div class="page-back"><a href="#top"> <img src="http://openwetware.org/images/2/2a/Top1.gif" onmouseover="this.src='http://openwetware.org/images/f/f0/Top2.gif'" onmouseout="this.src='http://openwetware.org/images/2/2a/Top1.gif'" height="150px"/></a></div> </head>


</html>

<html>

<head>

<style> h1.big{

 font-size :16px;
 text-decoration: none;
 color: #000000;
 margin: 10px 15px;
 font-weight: bolder;
 }

h1.sub {

 font-size:20px;
 font-weight: bolder;
 margin: 10px 5px;

}

p.menu {

 font-size :100%;
 line-height: 135%;
 margin: 0px 40px;

}

p.small {

 font-size :85%;
 line-height: 130%;
 margin: 0px 40px;

}

.sample_01 { width: 300px; font-size: 80%; border-collapse: collapse; margin: 10px 40px; }

.sample_01 caption { font-weight: bold; width: auto; text-align: left; maegin: 0; border-radius: 3px; padding: 5px; background-color: #ADD8E6; border: 1px solid #b9b9b9; }

.sample_01 th { width: 200px; font-weight: normal; padding: 5px; text-align: left; vertical-align: top; color: #333; background-color: #fff; border: 1px solid #b9b9b9; } .sample_01 td { font-weight: normal; padding: 5px; background-color: #fff; border: 1px solid #b9b9b9; } </style>

<script type="text/javascript"><!-- function HideCBox( boxid ) {

  var target = document.getElementById(boxid);
  if( target.style.display != "none" ) {
     target.style.display = "none";
  }
  else {
     target.style.display = "";
  }

} // --></script>


<style type="text/css"><!-- div.CollapsibleBox {

  /* ■ボックス全体■ */
  border: 0px solid #4169E1; /* 枠線:濃青 */
  font-size: 100%;             /* 文字サイズ:100% */
  width: 600px;               /* 横幅:600px */

} div.CollapsibleBox div.CollapsibleBoxTitle {

  /* ■タイトル枠■ */
  background-color: #191970; /* 背景色:濃青 */
  color: white;               /* 文字色:白 */
  margin: 0px;
  padding: 0px;
  width: 600px;

} div.CollapsibleBox div.CollapsibleBoxTitle p.cBoxTitle {

  /* ■タイトル文字列■ */
  font-size: 100% ;          /* 太字 */
  border: 1px solid #4B0082; /* 枠線:濃青 */
  margin: 0px;
  padding: 1px 0px;

} div.CollapsibleBox div.CollapsibleBoxTitle p.cBoxButtons {

  /* ■ボタン群■ */
  margin: 0px;
  padding: 2px 10px;
  float: right;
  position: relative; 

} div.CollapsibleBox div.CollapsibleBoxTitle p.cBoxButtons a img {

  /* ■ボタンそのもの■ */
  border-width: 0px;    /* リンクの枠線を消す */

} div.CollapsibleBox div.CollapsibleBoxBody {

  /* ■本文枠■ */
  margin: 0px;
  padding: 2px 0px 2px 0px;
  background-color: #ADD8E6; /* 背景色:淡青 */
  color: #191970; /* 文字色:暗青 */

} div.CollapsibleBox div.CollapsibleBoxBody p {

  /* ■本文■ */
  margin: 0px;
  padding: 0.5em;   /* 内側の余白:0.5文字分 */

} --></style>

<link rel="stylesheet" href="sample.css" type="text/css"> </head>





<body> <font face="Futura,Arial,Frutiger" font size="24px">PROTOCOLS</font> <br><br>


<div class="CollapsibleBox" id="CBoxCover1">

  <div class="CollapsibleBoxTitle">
     <p class="cBoxButtons">
        <a href="#" onclick="HideCBox('CBoxBody1');  return false;" title="折りたたみ/復元"><font color="white" font size="2">[show/hide]</font></a>
     </p>
     <p class="cBoxTitle">&nbsp; Contents:</p>
  </div>
  <div class="CollapsibleBoxBody" id="CBoxBody1">
     <ul style="list-style:none;">
        <li> <a href=#1> 1. The Sensing System: The Receptor </a>
        <ul style="list-style:none;">
           <li> <a href="#1-1">1-1. Preparing the components </a></li>
           <ul style="list-style:none;">
              <li> <a href="#1-1-1">1-1(a). Folding the Wall </a></li>
              <li> <a href="#1-1-2">1-1(b). Producing MISTIC </a></li>
              <li> <a href="#1-1-3">1-1(c). Designing the Activator </a></li>
           </ul>
           </li>
           <li> <a href="#1-2">1-2. Embedding the Wall into the liposome </a></li>
           <li> <a href="#1-3">1-3. Linking the Activator to the liposome </a></li>
           <li> <a href="#1-4">1-4. Combining the Wall and the Activator </a></li>
           <li> <a href="#1-5">1-5. Separating the Wall from the Activator </a></li>
        </ul>
        </li>
        
        <li> <a href="#2">2. The Moving System: The Motor </a>
        <ul style="list-style:none">
           <li> <a href="#2-1">2-1. Producing the Motor-Monomer </a>
           <ul style="list-style:none">
             <li> <a href="#2-1-1"> 2-1(a). Folding the Motor-Monomer body </a></li>
             <li> <a href="#2-1-2"> 2-1(b). Synthesizing divalent SA </a></li>
             <li> <a href="#2-1-3"> 2-1(c). Equipping the Motor-Monomer with divalent SA </a></li>
           </ul>
           </li>
           <li> <a href="#2-2">2-2. Deactivating and reactivating the binding capacity of streptavidin </a></li>
           <li> <a href="#2-3">2-3. Putting the Motor-Monomers into the liposome </a></li>
        </ul>
        </li>
     </ul>
  </div>

</div>



<br> <a name="1-1">&nbsp;</a> <br> <a name="1-1-1">&nbsp;</a> <h1 class="title"><a href="">&nbsp;1. The Sensing System: The Receptor</a></h1> <h1 class="sub">1-1. Preparing the components</h1> <h1 class="big">1-1(a). Folding the Wall</h1>

<table class="sample_01"><caption>Reagents (f. 10&micro;L)</caption> <tbody> <tr><th>Staple mix</th><td>5 &micro;L</td></tr> <tr><th>M13mp18ss</th><td>4 &micro;L</td></tr> <tr><th>10 x monomer buffer*1</th><td>1 &micro;L</td></tr> </tbody></table> <p class="paragraph">*1 10 x monomer buffer (100 mL) <p class="small">1.0 M Tris-HCl (pH 8.0) 10mL</p> <p class="small">1.0 M MgCl<sub>2</sub> (f. 150 mM) 15mL</p> <p class="small">1.0 M NaCl (f. 25 mM) 2.5mL</p></p>


<p class="paragraph"> <p class="menu">1) Mix the reagents.</p> <p class="menu">2) Anneal as follows</p> <p class="menu">85&deg;C, 5 min till 49.3&deg;C, 2h till 4&deg;C, forever</p> <p class="menu">Analyze by 1 % agarose gel electrophoresis.</p> <p class="menu">Stain the gel by EtBr for 30 minutes.</p> <p class="menu">Take photo of the gel by LAS-4000.</p></p>


<h1 class="big">1-1(b). Producing MISTIC</h1>

<p class="paragraph">

  • Protocol 1

</p> <p class="menu"> We used MISTIC gene inserted in plDTSmart(kan) (IDT Co.). The sequences of primers are shown in note 2. Quick Change produce were transformed into XL10-Gold, andplasmid was prepared by QIAprep Spin Miniprep Kit (QIAGEN Co.). </p> <p class="menu"> Note 1: The base sequence of MISTIC (wild type)<br> ATGTTTTGTACATTTTTTGAAAAACATCACCGGAAGTGGGACATACTGTTAGAAAAAAGCACGGGTGTGATGGAAGCTATGAAAGT<br> GACGAGTGAGGAAAAGGAACAGCTGAGCACAGCAATCGACCGAATGAATGAAGGACTGGACGCGTTTATCCAGCTGTATAATGA<br> ATCGGAAATTGATGAACCGCTTATTCAGCTTGATGATGATACAGCCGAGTTAATGAAGCAGGCCCGAGATATGTACGGCCAGGAAA<br> AGCTAAATGAGAAATTAAATACAATTATTAAACAGATTTTATCCATCTCAGTATCTGAAGAAGGAGAAAAAGAATGA<br> Note 2: The sequence of primer<br> Forward: <br>GGGTGTGATGGAAGCTATGAAATGTACGAGTGAGGAAAAGGAACAG<br> Reverse: <br>CTGTTCCTTTTCCTCACTCGTACATTTCATAGCTTCCATCACACCC </p>

<p class="paragraph">

  • Protocol 2

</p> <p class="menu"> We referred to a thesis which we mentioned at reference No.2. The primer which we used is written on note 3. PCR was first conducted using primer3 (unnatural amino acids were introduced by using primer 3-1~3-7) and primer4, then primer1 and primer4 and finally in order to increase the concentration, primer2 and primer4. Electrophoresis was done by 1% agarose gel, 100V and 1 hour. </p> <p class="menu"> Note 3:<br> 1.PURE_universal:<br> GAAATTAATACGACTCACTATAGGGAGACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACCA<br> 2.PURE_amplify:<br> GAAATTAATACGACTCACTATAGGGAGACCACAACGGTTTC<br> 3-0.Mistic_for_PURE:<br> TTTGTTTAACTTTAAGAAGGAGATATACCAATGTTTGTGACATTTTTTGAAAAACATCACC<br> 4.Mistic_rev:<br> ATACATGAATGGATCCTTAATGGTGATGGTGATGGTGTTCTTTTTCTCCTTCTTCAGATACTG<br> 3-1.Mistic_amber2_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTAGGTGACATTTTTTGAAAAACATCAC<br> 3-2.Mistic_amber3_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTTTTAGACATTTTTTGAAAAACATCAC<br> 3-3.Mistic_amber4_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTTTGTGTAGTTTTTTGAAAAACATCAC<br> 3-4.Mistic_amber5_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTTTGTGACATAGTTTGAAAAACATCAC<br> 3-5.Mistic_amber6_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTTTGTGACATTTTAGGAAAAACATCACCGG<br> 3-6.Mistic_amber7_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTTTGTGACATTTTTTTAGAAACATCACCGGAAG<br> 3-7.Mistic_amber8_for_PURE:<br> CTTTAAGAAGGAGATATACCAATGTTTGTGACATTTTTTGAATAGCATCACCGGAAGTGG</p>

<p class="paragraph">

  • Protocol 3-1

</p> <p class="menu"> We used PUREfrex® and Biotin-XX-AF (CloverDirect™) for unnatural amino acids. After electrophoresis, we rinsed and dried up the gel, copied it to IP for overnight, and scanned it to read the value of PSL by BAS. </p>

<p class="paragraph">

  • Protocol 3-2

</p> <p class="menu"> We used His Spin Trap (GE Co.) for purification. 18% acrylamide gel was used for SDS-PAGE and performed at 200V for 75 minutes. We stained the gel by SYPRO ORANGE. The composition of buffers is as follows.<br> ・Binding[Wash] Buffer: 50mM Tris-pH8.0, 300mM KCl, 10mM imidazole, 51mM n-octyl-ß-D-glucopyranoside<br> ・Elusion Buffer: 50mM Tris-pH8.0, 300mM KCl, 500mM imidazole, 51mM n-octyl-ß-D-glucopyranoside<br> </p>

<p class="paragraph">

  • Protocol 4

</p> <p class="menu"> The procedure is the same as the one of the confirmation of the MISTIC expression. Electrophoresis was performed by 18% acrylamide gel, 200V and 75 minutes. </p>

<p class="paragraph">

  • Protocol 5

</p> <p class="menu"> The procedure is the same as the confirmation of the expression of MISTIC. Streptavidin beads (TAMAGAWA SEIKI Co.) were used for SA-bead and 2µL of 20mg/mL solution of them were added to the 10µL of PURE reaction solution. Electrophoresis was performed by 18% acrylamide gel, 300V and 40 minutes. </p>

<p class="paragraph">

  • Protocol 6

</p> <p class="menu"> We used ProbeQuant™ G-50 Micro Columns (GE Co.) for purification. </p>

<h1 class="big">1-1(c). Designing the Activator</h1> <p class="paragraph"><b>(i) Evaluation of Lambda Exonuclease activity</b></p> <p class="paragraph">Procedure <p class="menu">1) Two ssDNA mixtures (a and a’ mixture ,and b and b’ mixture) were annealed at 65℃ for 5 minutes.</p> <p class="menu">2) The two dsDNA reagents were mixed.</p> <p class="menu">3) The dsDNA mixture and Lambda Exonuclease were mixed and incubated at 37&deg;C.</p> <p class="menu">4) The mixture was analyzed by 20% Native-PAGE.</p> <p class="menu">5) The gel was stained by SYBR Gold for 15 minutes.</p> <p class="menu">6) The gel was taken a photo by LAS-4000. </p>

<table class="sample_01"> <caption>Reaction Reagent</caption> <tbody> <tr><th>dsDNA mixture</th> <td>4&micro;L</td></tr> <tr><th>Lambda Exonuclease</th><td>5&micro;L</td></tr> <tr><th>10×reaction buffer</th><td>1&micro;L</td></tr> </tbody></table>

<p class="paragraph"> 10×reaction buffers in each experiment are as below. <p class="small">1) 670mM Glycine-KOH(pH7.5 8.0, 8.5, 9.0, 9.4), 2.5mM MgCl<sub>2</sub>, 50&mibro;g/ml BSA <p class="small">2) 670mM Glycine-KOH(pH8.0), 2.5, 5.0, 7.5, 10.0, 12.5mM MgCl<sub>2</sub>, 50&micro;g/ml BSA </p></p>

<p class="paragraph"><b>(ii) Oligo-modification of Lambda-Exonuclease</b></p> <table class="sample_01"> <caption>Reagent</caption> <tbody> <tr><th>0.2M KPO<sub>4</sub>(pH7.8)</th><td>5&micro;L</td></tr> <tr><th>200&micro;M Cy3-modified oligo</th><td>10&micro;L</td></tr> <tr><th>30mM BS(PEG)<sub>9</sub></th> <td>2&micro;L</td></tr></tbody></table>

<p class="paragraph"> Procedure <p class="menu">1) The solution was mixed.</p> <p class="menu">2) The mixture was incubated at room temperature for 5 minutes.</p> <p class="menu">3) The solution was refines by NAP-5 column.</p> <p class="menu">4) Lambda Exonuclease and refined oligo that are equimolecular amount were mixed.</p> <p class="menu">5) The mixture was incubated on ice for 3 hours.</p> <p class="menu">6) The solution was analyzed by 20% Native-PAGE and 20% SDS-PAGE.</p> <p class="menu">7) The Native-PAGE gel was taken a photo by LAS-4000.</p> <p class="menu">8) The SDS-PAGE gel was stained by SYPRO Orange for 60 minutes and taken a photo by LAS-400. </p></p>

<p class="paragraph"><b>(iii)Oligo-modification of Hind&#8546;</b></p> <p class="paragraph">Exchange-buffer</p> <table class="sample_01"><caption>Reagents (f: 50ml)</caption> <tbody> <tr><th>0.2M HEPES (pH8.5)</th><td> 5ml</td></tr> <tr><th>5M NaCl </th><td>500ul</td></tr> <tr><th>1M DTT </th><td>50ul</td></tr> <tr><th>0.5M EDTA </th><td>10ul</td></tr> <tr><th>MQ up to 50ml</th></tbody></table>

<p class="paragraph"> Reagents for Oligo-BS(PEG)<sub>9</sub> <p class="small">0.2M KPO<sub>4</sub> 5ul</p> <p class="small">200uM cy3-Oligonucleotide 10ul</p> <p class="small">20mM BS(PEG)<sub>9</sub></p> </p>

<p class="paragraph"> Reagents for Oligo- BS(PEG)<sub>9</sub>-Hind&#8546; <p class="small">Fraction 20ul</p> <p class="small">Hind&#8546; 20ul</p></p>



<h1 class="sub">1-2. Embedding the Wall into the liposome</h1> <p class="paragraph"><b>(i) Hybridization of cholesterol oligonucleotide with Wall</b></p> <p class="paragraph"> In this experiment, we optimized the concentration of the cholesterol oligonucleotide and the number of handles, which is necessary for wall penetration into liposome. The result was assayed by 1% agarose gel electrophoresis.</p> <table class="sample_01"> <caption>Reagents</caption> <tbody> <tr><th>Purified Wall (0.03&micro;M)</th><td>6&micro;L</td></tr> <tr><th>Cholesterol oligomer </th><td>1.5&micro;L</td></tr> </tbody> </table>

<p class="paragraph">Sample2 and 3 do not have handles for the cholesterol oligonucleotide to hybridize. Sample 5 and 6 have 4, sample 8 and 9 have 10, sample 11 and 12 have handles for the cholesterol oligonucleotide to hybridize.</p> <table class="sample_01"> <caption> Concentration of cholesterol oligonucleotide</caption> <tbody> <tr><th> Sample2_1, 3_1, 5_1, 6_1</th><td>0.24&micro;M</td></tr> <tr><th>Sample2_2, 3_2, 5_2, 6_2</th><td>0.48&micro;M</td></tr> <tr><th>Sample2_3, 3_3, 5_3, 6_3</th><td>2.4&micro;M</td></tr> <tr><th>Sample2_4, 3_4, 5_4, 6_4</th><td>4.8&micro;M</td></tr> <tr><th>Sample8_1, 9_1</th><td>0.60&micro;M</td></tr> <tr><th>Sample8_2, 9_2</th><td>1.2&micro;M</td></tr> <tr><th>Sample8_3, 9_3</th><td>6.0&micro;M</td></tr> <tr><th>Sample8_4, 9_4</th><td>12&micro;M</td></tr> <tr><th>Sample11_1, 12_1</th><td>1.14&micro;M</td></tr> <tr><th>Sample11_2, 12_2</th><td>2.28&micro;M</td></tr> <tr><th>Sample11_3, 12_3</th><td>11.4&micro;M</td></tr> <tr><th>Sample11_4, 12_4</th><td>22.8&micro;M</td></tr> </tbody> </table> <p class="paragraph">Procedures</p> <p class="paragraph">Reagents are mixed and incubated for 60 minutes at room temperature.</p>

<p class="paragraph"><b>(ii) Putting the Wall into the liposome</b></p> <p class="paragraph">Same as <a href="#2-3">2-3. Putting the Monomer into the liposome</a>.</p>


<h1 class="sub">1-3. Linking the Activator to the liposome</h1> <h1 class="sub">1-4. Combining the Wall and the Activator</h1> <h1 class="sub">1-5. Separating the Wall from the Activator</h1>

<h1 class="title"><a href="">&nbsp;2. The Moving System: The Motor</a></h1> <h1 class="sub">2-1. Producing the Motor-Monomer</h1> <h1 class="big">2-1(a). Folding the Motor-Monomer body</h1>

<table class="sample_01"><caption>Reagents (f. 10&micro;L)</caption> <tbody> <tr><th>Staple mix</th><td>5 &micro;L</td></tr> <tr><th>M13mp18ss</th><td>4 &micro;L</td></tr> <tr><th>10 x monomer buffer*1</th><td>1 &micro;L</td></tr> </tbody></table> <p class="paragraph">*1 10 x monomer buffer (100 mL) <p class="small">1.0 M Tris-HCl (pH 8.0) 10mL</p> <p class="small">1.0 M MgCl<sub>2</sub> (f. 150 mM) 15mL</p> <p class="small">1.0 M NaCl (f. 25 mM) 2.5mL</p> </p>

<p class="paragraph"> <p class="menu">1) Mix the reagents.</p> <p class="menu">2) Anneal as follows</p> <p class="menu">85&deg;C, 5 min till 49.3&deg;C, 2h till 4&deg;C, forever</p> <p class="menu">Analyze by 1 % agarose gel electrophoresis.</p> <p class="menu">Stain the gel by EtBr for 30 minutes.</p> <p class="menu">Take photo of the gel by LAS-4000.</p></p>

<h1 class="big">2-1(b). Synthesizing divalent SA</h1>

<h1 class="big">2-1(c). Equipping the Motor-Monomer with divalent SA</h1> <p class="paragraph"><b>(i) Modifying divalent SA with NHS</b></p>

<p class="paragraph">Procedure</p> <p class="paragraph"> <p class="menu">1) Exchange the buffer of divalent SA to the Exchange-buffer by NAP-5.</p> <p class="menu">2) Mix divalent SA with Cy5-NHS in tetraborate and incubate for 1 hour at room temperature.</p> <p class="menu">3) Add biotin-oligonucleotide to the mixture and incubate 30 minutes at room temperature.</p> <p class="menu">4) Analyze by Native-PAGE (10% Resolving Gel)</p>

<table class="sample_01"> <caption>Exchange-buffer</caption> <tbody> <tr> <th>0.2M HEPES (pH8.5)</th> <td>5ml</td></tr> <tr> <th>5M NaCl</th> <td>500&micro;l</td></tr> <tr> <th>1M DTT</th> <td>50&micro;l</td> </tr> <tr> <th>0.5M EDTA</th> <td>10&micro;l</td> </tr> <tr> <th>MQ up to 50ml</th> </tr>

<table class="sample_01"> <caption>Reagents for SA and Cy5-NHS</caption> <tbody> <tr> <th>0.45&micro;M divalent SA</th> <td>10&micro;L</td> </tr> <tr> <th>Cy5-NHS</th> <td>10&micro;L</td> </tr> <tr> <th>tetraborate (pH 8.1)</th><td> 5&micro;L</td> </tr> </tbody> </table>


<p class="paragraph">Reagents for Cy5-SA-biotin-oligonucleotide: <p class="small">Fraction 5&micro;l</p> <p class="small">the threefold amounts of biotin-oligonucleotide 5&micro;l</p> </p>

<p class="paragraph"><b>(ii) Click reaction</b></p> <p class="paragraph">Procedure</p> <p class="paragraph"> <p class="menu">1) Mix click reagent and NH2-modified oligonucleotide in tetraborate (pH8.1) and incubate for 1h at room temperature.</p> <p class="menu">2) Refine with QIA quick Nucleotide Column.</p> <p class="menu">3) Add 450µL of PNI buffer to the mixture.</p> <p class="menu">4) Apply to column.</p> <p class="menu">5)Centrifuge at 6krpm for 1minutes.</p> <p class="menu">6) Add 750 µL of buffer PE.</p> <p class="menu">7) Centrifuge at 6krpm for 1minutes.</p> <p class="menu">8) Add 750 µL of buffer PE.</p> <p class="menu">9) Centrifuge at 6krpm for 1minutes.</p> <p class="menu">10) Centrifuge at 13krpm for 1minutes.</p> <p class="menu">11) Put the column on new tube and add 33µL of MQ and incubate for 3 minutes.</p> <p class="menu">12) Centrifuge at 13krpm for 1minutes.</p> <p class="menu">13) Dilute the mixture with MQ to the appropriate concentrate.</p> <p class="menu">14) Mix one of Azide group and that of Alkyne group and incubate at room temperature.</p> <p class="menu">15) Analyze by 15% Urea gel electrophoresis.</p> </p>

<table class="sample_01"> <caption>Reagent of click reagent and NH2-modified oligonucleotide</caption> <tbody> <tr> <th>10mM click reagent</th> <td>7&micro;L</td> </tr> <tr> <th>tetraborate(pH8.1)</th> <td>3&micro;L</td> </tr> <tr> <th>2&micro;g/&micro;L NH<sub>2</sub>-modified oligonucleotide</th> <td>2&micro;L</td> </tr> </tbody> </table>

<table class="sample_01"> <caption>Reagent of click reaction</caption> <tbody> <tr> <th>6&micro;M Azi-oligo</th> <td>5&micro;L</td></tr> <tr> <th>6&micro;M Alk-oligo</th> <td>5&micro;L</td> </tr> <h1 class="sub">2-2. Deactivating and reactivating the binding activity of streptavidin</h1> <p class="paragraph"><b>(i) Make Biotin-Beads</b></p> <table class="sample_01"> <caption>Reagents (f: 20uL) </caption> <tbody> <tr><th>HEPES-KOH (pH8.5, f.90 mM)</th><td> 9.0 &micro;L</td></tr> <tr><th>Biotin and amino modified Oligonucleotide (f: 65 µM)</th><td> 1 &micro;L</td></tr> <tr><th>NHS-Beads (f.10 mg/ml)</th><td> 10 &micro;L</td></tr> </tbody> </table>

<p class="paragraph"> Procedure</p> <p class="paragraph">Mix NHS-Beads with the oligonucleotide which has Biotin and amino group Remove the solvent.<p>

<p class="paragraph"><b>(ii) Deactivate and reactivate SA</b></p>

<table class="sample_01"><caption> Reagents for SA Deactivation (f: 10&micro;L)</caption> <tbody> <tr><th>Ds DNA of Leader and Blocker (f: 5&micro;M)</th> <td>2.0&micro;L</td></tr> <tr><th>Divalent SA (f: 30&micro;M)</th><td> 8.0&micro;L</td></tr> <tr><th>Biotin-Beads</th><td> 0.2mg</td> <tr><th><sub>1</sub>Ds DNA (f: 10&micro;L)</th></tr> <tr><th>Biotin modified Oligonucleotide (Leader) (f: 25&micro;M)</th><td> 5.0&micro;L</td></tr> <tr><th>Desthiobiotin modified Cy3-Oligonucleotide (Blocker) (f: 25&micro;M)</th><td> 5.0&micro;L</td></tr></tbody></table>

<table class="sample_01"><caption>Reagents for cutting dsDNA on SA (f: 15&micro;L)</caption> <tbody> <tr><th>Purified Deactivation SA-dsDNA complex</th><td> 4&micro;L</td></tr> <tr><th>Hind&#8546; (f: 6700U/ml)</th><td> 1uL</td></tr> <tr><th>10×NEB Buffer 2.1 </th><td>1.5&micro;L</td></tr> <tr><th>MQ 8.5&micro;L</th></tr></tbody></table>

<table class="sample_01"><caption>Reagents for cutting ds DNA on SA (f: 10uL)</caption> <tbody> <tr><th>Purified Deactivation SA-dsDNA complex</th><td> 2 &micro;L</td></tr> <tr><th>Biotin modified Cy5-Oligonucleotide (Chaser) (f: 5 &micro;M)</th><td> 2.0 &micro;L</td></tr> <tr><th>MQ 6 &micro;L</th></tr> </tbody></table>

<table class="sample_01"><caption>Reagents for reactivation of SA (f: 10 &micro;L)</caption> <tbody> <tr> <th>dsDNA cutted SA-dsDNA complex(solution)</th> <td>8&micro;L</td> </tr><tr> <th> Biotin modified Cy5-Oligonucleotide (Chaser) (f: 5 &micro;M)</th> <td>2.0&micro;L</td> </tr> </tbody> </table>

<p class="paragraph"> Reagents for Native-PAGE </p> <p class="paragraph">15 % Resolving Gel <p class="small">MQ 4.8 ml</p> <p class="small">30% Acrylamide mix 10 ml</p> <p class="small">1.5M Tris-HCl (pH 8.8) 5.0 ml</p> <p class="small">10 % APS 0.2 ml</p> <p class="small">TEMED 8.0 ul</p> </p>

<p class="paragraph"> 5 % Stacking Gel <p class="small">MQ 2.79 ml</p> <p class="small">30% Acrylamide mix 0.67 ml</p> <p class="small">1.0 M Tris-HCl (pH 6.8) 0.5 ml</p> <p class="small">10 % APS 40 ul</p> <p class="small">TEMED 4.0 ul</p>

<p class="paragraph">Procedure</p> <p class="menu">(i) Make Biotin-Beads</p> <p class="menu">(ii) Deactivate and reactivate SA</p> <p class="menu">1) Anneal dsDNA of Leader and Blocker (95&deg;C, 3min to 4&degC, forever)</p> <p class="menu">2) Mix the dsDNA with divalent SA at 4℃ for 30min</p> <p class="menu">3) Remove SA which is not bound to the dsDNA by Biotin-Beads </p> <p class="menu">4) Cut the dsDNA bound to SA by Hind&#8546;</p> <p class="menu">5) Add Chaser to the SA of which the dsDNA was cut</p> </p>

<p class="paragraph">Analyze <p class="menu">1) Analyze by Native PAGE (15% Resolving Gel) <p class="menu">2) Observe with LAS-4000 and take pictures</p></p>


<h1 class="sub">2-3. Putting the Motor-Monomers into the liposome</h1> <p class="paragraph"><b>(i) Binding Motor-Monomers and Qdots</b>/p> <p class="paragraph">Reagents <p class="small">Motor-Monomers (unpurified) 80&micro;L</p> <p class="small">Qdot 655 streptavidin (1&micro;M) 6.4&micro;L</p></p>

<p class="paragraph">Procedure <p class="menu">1) 80&micro;L of Motor-Monomers and 6.4&micro;L of Q-dot were mixed and incubated at room temperature for 30 minutes.</p> <p class="menu">2) The mixture was purified.</p></p>

<p class="paragraph"><b>(ii) Preparation of GUVs</b></p> <p class="paragraph">Reagents <p class="paragraph">Lipid mix (3mM) <p class="small">POPC 12mg</p> <p class="small">Paraffin 5mL</p></p>

<p class="paragraph">Outer solution <p class="small">Glucose (400mM) 250&micro;L</p> <p class="small">Tris (50mM, pH 7.5) 250&micro;L</p> </p>

<p class="paragraph">Emulsion mix <p class="small">Lipid mix (0.5mM) 500&micro;L</p> <p class="small">Inner solution(200mM) 10&micro;L</p> </p>

<p class="paragraph">Inner solution <p class="paragraph">1. GUV including DNA constructs <p class="small">Mercaptoethanol (4mM) 5.0&micro;L</p> <p class="small">DNA constructs with Qdot 2.5&micro;L</p> <p class="small">Sucrose (1M) 2.0&micro;L</p> <p class="small">Tris (500mM, pH 7.5) 0.5&micro;L</p></p> <p class="paragraph">2. GUV not including Motor-Monomers or Walls <p class="small">Sucrose (400mM) 5&micro;L</p> <p class="small">Tris (50mM, pH 7.5) 5&micro;</p></p>

<p class="paragraph">Procedure <p class="menu">1) Take Glucose (500µL) into a tube as outer solution.</p> <p class="menu">2) Add Lipid mix (0.5mM) on the glucose solution carefully.</p> <p class="menu">3) Add Emulsion mix on the top and rapidly centrifuge at 4&deg;C, 1800rpm for 10 minutes.</o> <p class="menu">4) Centrifuge again at 4&deg;C, 5000rpm for 10 minutes.</p> <p class="menu">5) The upper layer is removed and GUVs are collected using pipetman. <p class="menu">6) 5µL of GUV was mixed with 0.5µL of Nile Red (10&micro;M) and observed by confocal microscope. </p>


<br> <br> <footer style="position:relative; left:600px;"> <small> &copy; 2014 UTokyo Chem & Bio </small> </footer>

</html>