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<img src="http://openwetware.org/images/9/9f/Stack.png" alt="stack">   
<ul id="stack">   
<ul id="stack">   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Reference_papers"><span>Reference Papers</span><img src="http://openwetware.org/images/1/13/Papers.png" alt="Papers"></a></li>
 
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Protocols"><span>Protocols</span><img src="http://openwetware.org/images/7/7b/Protocols_pr1.gif" alt="Overveiw"></a></li>  
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Brain_storming"><span>Brain Stroming</span><img src="http://openwetware.org/images/3/3f/Brain.png" alt="Brain Storming"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Brain_storming"><span>Brain Stroming</span><img src="http://openwetware.org/images/3/3f/Brain.png" alt="Brain Storming"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Work_diary"><span>Work Diary</span><img src="http://openwetware.org/images/2/2a/Diary.png" alt="Work diary"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Work_diary"><span>Work Diary</span><img src="http://openwetware.org/images/2/2a/Diary.png" alt="Work diary"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Team"><span>Team</span><img src="http://openwetware.org/images/6/62/Team_iitm.jpg" alt="Team"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Overveiw"><span>Overview</span><img src="http://openwetware.org/images/1/13/Papers.png" alt="Overveiw"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Project"><span>Project</span><img src="http://openwetware.org/images/f/f0/Home-sm.png" alt="Project"></a></li>   
<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists"><span>Home</span><img src="http://openwetware.org/images/f/f0/Home-sm.png" alt="Project"></a></li>   
</ul>   
</ul>   
</div>   
</div>   
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<div id="contents_stuff">
<div id="contents_stuff">
<h1>Reversible collection of nano-bots </h1><br/><br/>
<h1>Project -- Reversible collection of nano-bots </h1><br/><br/>
<h2>Abstract: </h2>
<h2>Abstract: </h2>
<p>The project aims at designing a molecular construct consisting of appendages in the form of single stranded DNA molecules which bind with target molecules to form an aggregate that can be filtered from the containing solution. The appendage strands have DNA sequences complementary to those present on the molecules of interest thus enabling binding between them. The construct is designed using caDNAno and single strands are added to it by extending staple strands at specific locations. The aggregate dimensions are sufficient to be filtered by a porosity of 0.2 μm. The binding between molecules is reversible in nature so as to facilitate reuse of molecules, thereby enhancing cost effectiveness of the technique. The technique can be incorporated into DNA robotics wherein “nano-bots” can be withdrawn from their environment. The long-term objective of the proposed work is to develop similar DNA-origami constructs capable of high-affinity and high-selectivity bio-molecule targeting in vivo.</p><br/>
<p>The project aims at designing a molecular construct consisting of appendages in the form of single stranded DNA molecules which bind with target molecules to form an aggregate that can be filtered from the containing solution. The appendage strands have DNA sequences complementary to those present on the molecules of interest thus enabling binding between them. The construct is designed using caDNAno and single strands are added to it by extending staple strands at specific locations. The aggregate dimensions are sufficient to be filtered by a porosity of 0.2 μm. The binding between molecules is reversible in nature so as to facilitate reuse of molecules, thereby enhancing cost effectiveness of the technique. The technique can be incorporated into DNA robotics wherein “nano-bots” can be withdrawn from their environment. The long-term objective of the proposed work is to develop similar DNA-origami constructs capable of high-affinity and high-selectivity bio-molecule targeting in vivo.</p><br/>
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<p>A major problem in India is the sanitary condition of water. While large substances can be filtered out using crude techniques; it is particles of smaller dimensions that are a cause of concern. We thought hard along the lines of purification of water. Our idea began with an aim to develop a DNA based nano-molecular structure that can bind to other structures of similar or smaller dimensions and can be filtered out in due time. On further exploration into the field we realized that we are restricting ourselves to only a part of a much wider spectrum and subsequently took our idea a step further. </p>
<p>A major problem in India is the sanitary condition of water. While large substances can be filtered out using crude techniques; it is particles of smaller dimensions that are a cause of concern. We thought hard along the lines of purification of water. Our idea began with an aim to develop a DNA based nano-molecular structure that can bind to other structures of similar or smaller dimensions and can be filtered out in due time. On further exploration into the field we realized that we are restricting ourselves to only a part of a much wider spectrum and subsequently took our idea a step further. </p>
<h2>Our Idea:</h2>
<h2>Our Idea:</h2>
<p>Our idea primarily deals with the collection and retrieval of nano-robots from their working environment. However, the dimensions of these bots are too miniscule to be filtered out by any commercially existing filter. In order to separate them from their surroundings we need to affix them onto a larger molecule; whose dimensions are sufficient enough to enable filtration. The nanobots in question have single stranded DNA attached to them. These single strands are essential in facilitating the binding to the larger molecule. We have modelled this larger molecule with the assistance of CaDNAno; a software that is used to design nano-structures using DNA strands. This larger molecule is our primary construct. This construct contains DNA single strands as appendages. These strands are of sequences complementary to those on the strands attachedOur idea primarily deals with the collection and retrieval of nano-robots from their working environment. However, the dimensions of these bots are too miniscule to be filtered out by any commercially existing filter. In order to separate them from their surroundings we need to affix them onto a larger molecule; whose dimensions are sufficient enough to enable filtration. The nanobots in question have single stranded DNA attached to them. These single strands are essential in facilitating the binding to the larger molecule. We have modelled this larger molecule with the assistance of CaDNAno; a software that is used to design nano-structures using DNA strands. This larger molecule is our primary construct. This construct contains DNA single strands as appendages. These strands are of sequences complementary to those on the strands attached to the nanobots existing in the environment. On addition of the aggregator molecule the complementary strands begin binding to each other thereby increasing the dimensions of the aggregate. The aggregate must reach dimensions of atleast 0.2 microns in order to be filtered since that is the minimum pore size of commercially available filters. Further down the line we aspire to make the aforementioned binding reversible. This will facilitate the reuse of the nanobots as well as the aggregator in future. The reuse of both components will enhance the cost effectiveness of the technique being employed. </p>
<p><i>We recommend you to watch our <a href="#">video</a> in order to gain an insight into our idea</i></p>
<p>Our idea primarily deals with the collection and retrieval of nano-robots from their working environment. However, the dimensions of these bots are too miniscule to be filtered out by any commercially existing filter. In order to separate them from their surroundings we need to affix them onto a larger molecule; whose dimensions are sufficient enough to enable filtration. The nanobots in question have single stranded DNA attached to them. These single strands are essential in facilitating the binding to the larger molecule. We have modeled this larger molecule with the assistance of CaDNAno; a software that is used to design nano-structures using DNA strands. This larger molecule is our primary construct. This construct contains DNA single strands as appendages. These strands are of sequences complementary to those on the strands attached Our idea primarily deals with the collection and retrieval of nano-robots from their working environment. However, the dimensions of these bots are too miniscule to be filtered out by any commercially existing filter. In order to separate them from their surroundings we need to affix them onto a larger molecule; whose dimensions are sufficient enough to enable filtration. The nanobots in question have single stranded DNA attached to them. These single strands are essential in facilitating the binding to the larger molecule. We have modeled this larger molecule with the assistance of CaDNAno; a software that is used to design nano-structures using DNA strands. This larger molecule is our primary construct. This construct contains DNA single strands as appendages. These strands are of sequences complementary to those on the strands attached to the nanobots existing in the environment. On addition of the agregator molecule the complementary strands begin binding to each other thereby increasing the dimensions of the aggregate. The aggregate must reach dimensions of atleast 0.2 microns in order to be filtered since that is the minimum pore size of commercially available filters. Further down the line we aspire to make the aforementioned binding reversible. This will facilitate the reuse of the nanobots as well as the agregator in future. The reuse of both components will enhance the cost effectiveness of the technique being employed. </p>
<H2>Future Applications</H2>
<H2>Future Applications</H2>
<p>We foresee a myriad of applications for the techniques we are using. Some of the applications we intend to pursue in future are 'Protein Purification' and 'Extraction of Heavy Metal Ions'. </p><br/>
<p>We foresee a myriad of applications for the techniques we are using. Some of the applications we intend to pursue in future are 'Protein Purification' and 'Extraction of Heavy Metal Ions'. </p><br/>
<ol>
<ol>
<li>Protein Purification<br/><li>On thorough reading of literature we identified protein purification as a potential application of our idea. The proteins we have in mind are those that have the amino acid, cysteine at an end terminal post translation. There are a certain species of enzymes that recognize and bind to a particular alkyl chain. The alkyl chain in question has an azide molecule (N3) at one end and "something???" at the other. On addition of the aforementioned enzyme and alkyl chain to a solution containing the target proteins a series of reactions take place following which we observe the attachment of the alkyl chain to a protein end terminus. Essentially we obtain a molecule which has a protein, an alkyl chain and an azide group bound to each other in that particular order. Subsequently we add single stranded DNA to the solution containing these aggregates. Due to their chemical properties these DNA single strands bind to the azide groups which provides us with DNA strands tagged with proteins. </li></li>
<li><b>Protein Purification</b><br/>On thorough reading of literature we identified protein purification as a potential application of our idea. The proteins we have in mind are those that have the amino acid, cysteine at an end terminal post translation. There are a certain species of enzymes that recognize and bind to a particular alkyl chain. The alkyl chain in question has an azide molecule (N3) at one end and "something???" at the other. On addition of the aforementioned enzyme and alkyl chain to a solution containing the target proteins a series of reactions take place following which we observe the attachment of the alkyl chain to a protein end terminus. Essentially we obtain a molecule which has a protein, an alkyl chain and an azide group bound to each other in that particular order. Subsequently we add single stranded DNA to the solution containing these aggregates. Due to their chemical properties these DNA single strands bind to the azide groups which provides us with DNA strands tagged with proteins. </li>


<li>Extraction of Heavy Metal Ions <br/><li>Our idea can be easily extended into the process of metal ion extraction from solutions. Various metal ions interact with inorganic molecules. These molecules can be incorporated into a DNA based nano-structure following the binding with the metal ions. The nano-structure is analogous to the nano-robot mentioned in our central idea. It will contain DNA single strands with sequences complementary to those on the aggregator which will be added once there are sufficient nano-structures to be withdrawn from solution. </li></li>
<li><b>Extraction of Heavy Metal Ions</b> <br/>Our idea can be easily extended into the process of metal ion extraction from solutions. Various metal ions interact with inorganic molecules. These molecules can be incorporated into a DNA based nano-structure following the binding with the metal ions. The nano-structure is analogous to the nano-robot mentioned in our central idea. It will contain DNA single strands with sequences complementary to those on the aggregator which will be added once there are sufficient nano-structures to be withdrawn from solution. </li>


</ol>
</ol>

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<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Protocols"><span>Protocols</span><img src="http://openwetware.org/images/7/7b/Protocols_pr1.gif" alt="Overveiw"></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Brain_storming"><span>Brain Stroming</span><img src="http://openwetware.org/images/3/3f/Brain.png" alt="Brain Storming"></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Work_diary"><span>Work Diary</span><img src="http://openwetware.org/images/2/2a/Diary.png" alt="Work diary"></a></li> 

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<div id="contents_stuff"> <h1>Project -- Reversible collection of nano-bots </h1><br/><br/> <h2>Abstract: </h2> <p>The project aims at designing a molecular construct consisting of appendages in the form of single stranded DNA molecules which bind with target molecules to form an aggregate that can be filtered from the containing solution. The appendage strands have DNA sequences complementary to those present on the molecules of interest thus enabling binding between them. The construct is designed using caDNAno and single strands are added to it by extending staple strands at specific locations. The aggregate dimensions are sufficient to be filtered by a porosity of 0.2 μm. The binding between molecules is reversible in nature so as to facilitate reuse of molecules, thereby enhancing cost effectiveness of the technique. The technique can be incorporated into DNA robotics wherein “nano-bots” can be withdrawn from their environment. The long-term objective of the proposed work is to develop similar DNA-origami constructs capable of high-affinity and high-selectivity bio-molecule targeting in vivo.</p><br/> <h2>Inspiration:</h2> <p>A major problem in India is the sanitary condition of water. While large substances can be filtered out using crude techniques; it is particles of smaller dimensions that are a cause of concern. We thought hard along the lines of purification of water. Our idea began with an aim to develop a DNA based nano-molecular structure that can bind to other structures of similar or smaller dimensions and can be filtered out in due time. On further exploration into the field we realized that we are restricting ourselves to only a part of a much wider spectrum and subsequently took our idea a step further. </p> <h2>Our Idea:</h2> <p><i>We recommend you to watch our <a href="#">video</a> in order to gain an insight into our idea</i></p> <p>Our idea primarily deals with the collection and retrieval of nano-robots from their working environment. However, the dimensions of these bots are too miniscule to be filtered out by any commercially existing filter. In order to separate them from their surroundings we need to affix them onto a larger molecule; whose dimensions are sufficient enough to enable filtration. The nanobots in question have single stranded DNA attached to them. These single strands are essential in facilitating the binding to the larger molecule. We have modeled this larger molecule with the assistance of CaDNAno; a software that is used to design nano-structures using DNA strands. This larger molecule is our primary construct. This construct contains DNA single strands as appendages. These strands are of sequences complementary to those on the strands attached Our idea primarily deals with the collection and retrieval of nano-robots from their working environment. However, the dimensions of these bots are too miniscule to be filtered out by any commercially existing filter. In order to separate them from their surroundings we need to affix them onto a larger molecule; whose dimensions are sufficient enough to enable filtration. The nanobots in question have single stranded DNA attached to them. These single strands are essential in facilitating the binding to the larger molecule. We have modeled this larger molecule with the assistance of CaDNAno; a software that is used to design nano-structures using DNA strands. This larger molecule is our primary construct. This construct contains DNA single strands as appendages. These strands are of sequences complementary to those on the strands attached to the nanobots existing in the environment. On addition of the agregator molecule the complementary strands begin binding to each other thereby increasing the dimensions of the aggregate. The aggregate must reach dimensions of atleast 0.2 microns in order to be filtered since that is the minimum pore size of commercially available filters. Further down the line we aspire to make the aforementioned binding reversible. This will facilitate the reuse of the nanobots as well as the agregator in future. The reuse of both components will enhance the cost effectiveness of the technique being employed. </p> <H2>Future Applications</H2> <p>We foresee a myriad of applications for the techniques we are using. Some of the applications we intend to pursue in future are 'Protein Purification' and 'Extraction of Heavy Metal Ions'. </p><br/> <ol> <li><b>Protein Purification</b><br/>On thorough reading of literature we identified protein purification as a potential application of our idea. The proteins we have in mind are those that have the amino acid, cysteine at an end terminal post translation. There are a certain species of enzymes that recognize and bind to a particular alkyl chain. The alkyl chain in question has an azide molecule (N3) at one end and "something???" at the other. On addition of the aforementioned enzyme and alkyl chain to a solution containing the target proteins a series of reactions take place following which we observe the attachment of the alkyl chain to a protein end terminus. Essentially we obtain a molecule which has a protein, an alkyl chain and an azide group bound to each other in that particular order. Subsequently we add single stranded DNA to the solution containing these aggregates. Due to their chemical properties these DNA single strands bind to the azide groups which provides us with DNA strands tagged with proteins. </li>

<li><b>Extraction of Heavy Metal Ions</b> <br/>Our idea can be easily extended into the process of metal ion extraction from solutions. Various metal ions interact with inorganic molecules. These molecules can be incorporated into a DNA based nano-structure following the binding with the metal ions. The nano-structure is analogous to the nano-robot mentioned in our central idea. It will contain DNA single strands with sequences complementary to those on the aggregator which will be added once there are sufficient nano-structures to be withdrawn from solution. </li>

</ol> </div>


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