B3,B4チーム/B3,B4 team: Difference between revisions

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[[pilot ver.]]
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[[pilot2]]

Revision as of 06:45, 22 August 2012

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<a href="http://openwetware.org/wiki/Biomod">BIOMOD</a> > <a href="http://openwetware.org/wiki/Biomod/2012 ">2012</a> > <a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Team Sendai</a> > <a href="http://openwetware.org/wiki/Pilot_ver. ">Team Sendai A Top</a>> <a href=" http://openwetware.org/wiki/Methods.html ">Methods</a>



<html> <font size=4> '''Our project''' </font> <br/><br/>


Our idea is a molecular Lego block. First, as a body of the block, we create a hollow cube made of DNA origami. This cube is designed so that it can be combined with other cubes. You can realize various designs by combining these cubes, where each cube has its own feature or functionality. First, we put a drug molecule in an empty cube and close the lid. Make another cube with mobility with some molecular motors. By connecting these two cubes, autonomous molecular delivery will be achieved. If this is realized, recombination of the drug is easy, and may be used in DDS. The DDS is the acronym for a “drug delivery system”, a technology to deliver drugs to target cells. Something lacking in this story is a method to connect the cubes, binding surfaces of the cubes. The problem with the binding surfaces is electric charge of DNA molecules. DNA is highly charged molecule. The strong negative charge on the backbone of DNA molecules helps it to dissolve in water, but at the same time it causes repulsion between DNA. Consequently, it is relatively easily to align them in a line where the interaction by the charge is weak. However, between the surface made of parallel DNAs, there is much stronger repulsion between them. This means that binding surface to surface is difficult. Our idea to solve this problem is to use a positively charged lipid as glue. For example, if the micelle, which is one of the typical lipid shape plays a role of the connecter between the surfaces. The micelle is a sphere like configuration of lipid molecules, exposing positive charges on the outside. So the negatively charged DNA and positively charged micelle attract each other. Therefore, it can be used as a connector or joint between the cubes in this way. However, using lipid, the problem of selectivity will come out. Namely, Lipid sticks to every cube surfaces, and the whole surface of the cube become sticky, that is not what we want. In order to adhere to the desired surfaces, we using single strand of DNA hybridization or creating special surface shapes. <br/> <br/>


<font size=4>'''Our strategy'''</font> <font size =2>

<br/><br/> <font size=3>STAGE１目的：脂質でDNAオリガミが引っ付くかの確認Check whether DNA Origamis adhere by lipid.</font><br/> ①BIOMOD2011のフィールドおよび三角柱を製作する。Make the fields and the triangular prisms of BIOMOD2011.<br/> ②DNAオリガミの精製を行う。（PEG沈、エタ沈）Purify DNA Origamis by PEG precipitation and ethanol precipitation.<br/> ③引っ付けるためにどのような脂質を用いるか決める。Decide what kinds of lipid we use to adhere Origamis.<br/> ④加える脂質のパラメータを決める。用いるDNAに対しての濃度の決定。Decide parameter of lipid.<br/> ⑤脂質を加えて引っ付くかどうかを確認する。Check whether DNA Origamis adhere to another by lipid.<br/> <br/> <font size=3>STAGE2 目的:凹凸平面が引っ付くかの確認Check whether concavity and convexity planes adhere.</font><br/> ①発注する平面をcadnanoで設計する。Design concavity and convexity planes by Cadnano.<br/> ②発注した平面がちゃんと作成できるかの確認（AFM,電気泳動）Check whether planes become shapes by AFM and electrocataphoresis.<br/> ③STAGE1で得た平面の接合条件で平面を引っ付けてみてどのような傾向があるか確かめる。平面依存性、平面and濃度依存性。<br/> 

 Check the tendency when planes adhere under the conditions of STAGE1.<br/>

④最適面形状および濃度の決定。（形状により配向性があるか確認）Decide the best shapes and density.<br/> <br/> <font size=3>STAGE2-1目的:配向性の選択（形状に配向性が無かった場合）Choose orientation.</font><br/> ① 凹凸平面にステイプルを生やす。<br/> ② 脂質+ステイプルでの結合による配向性を確認する。<br/> ③ 結合させたい平面同士を引っ付ける。<br/> <br/> <font size=3>STAGE3 目的:３次元モジュールの製作</font><br/>

① cadnanoにより３次元立方体構造を製作する。作成する立方体構造は平面および濃度により配向性があった場合はそれらを考慮し形を工夫する。<br/> 

       平面配向性が無かった場合ステイプルを生やしたものを設計する。<br/>

② 作成した３次元立方体を平面同士の結合と同じ条件で組み合わせてみる。<br/> ③ ３次元の観察方法としてAFMおよび電子顕微鏡を用いる。<br/> <br/>

</font> </html> pilot ver.

pilot2

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