Biomod/2011/TUM/TNT/Home: Difference between revisions

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<h1>Welcome</h1>
<h1>Welcome</h1>
Welcome to the TUM Biomod project 2011! On this page we will present a DNA origami which is used as a biosensor for DNA small molecule interactions. We would like to give you an overview about this project, how we got there, which difficulties we had to face and of course you also have the chance to get to know us a little bit.</br>  
Welcome to the TUM Biomod project 2011! On this page we will present a DNA origami which is used as a biosensor for DNA small molecule interactions. We would like to give you an overview about this project, how we got there, which difficulties we had to face and of course you also have the chance to get to know us a little bit.</br>  
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Small DNA-binding molecules including intercalators and groove binders cause changes in the geometry of double-helical DNA which may affect transcriptional regulation and nuclease activity. Elucidating the structural changes imposed on DNA including changes in pitch and length can shed light on functional mechanisms in the case of compounds that show selective toxicity such as antibiotic and antiviral activity. Here we report on our efforts in developing a self-assembled DNA-Origami device that can be used both in a fluorometric assay and for transmission electron microscopy with the aim to classify whether a DNA binding molecule is an intercalator or groove binder, and that reports quantitatively on changes in pitch and length caused by DNA-binding molecules. We have tested our device with different DNA binders, spermine, ethidium bromide and DAPI, in different concentrations. In accordance with structure simulations, the local deformations caused by addition of these small molecules led to observable global structural changes.  
Small DNA-binding molecules including intercalators and groove binders cause changes in the geometry of double-helical DNA which may affect transcriptional regulation and nuclease activity. Elucidating the structural changes imposed on DNA including changes in pitch and length can shed light on functional mechanisms in the case of compounds that show selective toxicity such as antibiotic and antiviral activity. Here we report on our efforts in developing a self-assembled DNA-Origami device that can be used both in a fluorometric assay and for transmission electron microscopy with the aim to classify whether a DNA binding molecule is an intercalator or groove binder, and that reports quantitatively on changes in pitch and length caused by DNA-binding molecules. We have tested our device with different DNA binders, spermine, ethidium bromide and DAPI, in different concentrations. In accordance with structure simulations, the local deformations caused by addition of these small molecules led to observable global structural changes.  
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<h1>Video</h1>
<h1>Video</h1>

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<html> <body> <div id="abstractandlinks"> <div id="abstract"> <h1>Welcome</h1> Welcome to the TUM Biomod project 2011! On this page we will present a DNA origami which is used as a biosensor for DNA small molecule interactions. We would like to give you an overview about this project, how we got there, which difficulties we had to face and of course you also have the chance to get to know us a little bit.</br> <br> To find out more about <i>The U</i> we highly recommend to watch the video. <br> <h1>Abstract</h1>

<b>DNA-Origami device to investigate conformational changes of DNA due to interactions with small molecules</b> <br> <br>

Small DNA-binding molecules including intercalators and groove binders cause changes in the geometry of double-helical DNA which may affect transcriptional regulation and nuclease activity. Elucidating the structural changes imposed on DNA including changes in pitch and length can shed light on functional mechanisms in the case of compounds that show selective toxicity such as antibiotic and antiviral activity. Here we report on our efforts in developing a self-assembled DNA-Origami device that can be used both in a fluorometric assay and for transmission electron microscopy with the aim to classify whether a DNA binding molecule is an intercalator or groove binder, and that reports quantitatively on changes in pitch and length caused by DNA-binding molecules. We have tested our device with different DNA binders, spermine, ethidium bromide and DAPI, in different concentrations. In accordance with structure simulations, the local deformations caused by addition of these small molecules led to observable global structural changes. </div> 

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