Biomod/2011/TUM/TNT/Results

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<h2>New practical methods and theories will be needed</h2>
<h2>New practical methods and theories will be needed</h2>
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Therefore, FRET measurements would be an appropriate method. Although we cannot present final results for FRET analyses, first single molecule analyses can be provided, and the fluorescence tracking approach already displays some tendencies. For an optimization of the FRET studies, the origami structure needs some slight improvements. For this, we have laid a thorough fundament not only of experimental results, but also lots of theoretical considerations, which can explain flexibility and correlate observable (via TEM and / or fluorescence measurements: distances, angles) with unobservable (twists) structural changes. <br>
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Therefore, FRET measurements would be an appropriate method. Although we cannot present final results for FRET analyses, first single molecule analyses can be provided. For an optimization of the FRET studies, the origami structure needs some slight improvements. For this, we have laid a thorough fundament not only of experimental results, but also lots of theoretical considerations, which can explain flexibility and correlate observable (via TEM and / or fluorescence measurements: distances, angles) with unobservable (twists) structural changes. <br>
On the experimental side, one could  try to eliminate some uncertainties regarding the applied concentrations. We did some [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Calculation_of_intercalator_concentrations calculations] to determine the fraction of occupied binding sites even at small concentrations, but as mentioned above, binding could be cooperative and for a proper testing of such a behavior, concentrations of bound DNA binders must be checked experimentally. This is very trying due to the small concentrations and the little fraction of compounds bound compared to those free in solution. We suggest to try some radiolabeled DNA binders, of which the bound fraction can be determined from radioassays. <br>
On the experimental side, one could  try to eliminate some uncertainties regarding the applied concentrations. We did some [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Calculation_of_intercalator_concentrations calculations] to determine the fraction of occupied binding sites even at small concentrations, but as mentioned above, binding could be cooperative and for a proper testing of such a behavior, concentrations of bound DNA binders must be checked experimentally. This is very trying due to the small concentrations and the little fraction of compounds bound compared to those free in solution. We suggest to try some radiolabeled DNA binders, of which the bound fraction can be determined from radioassays. <br>
Using this information, it should be possible to unravel deformation events step by step on even tinier levels. This not only allows for sophisticated understanding of the flexibility of origamis in response to varying triggers, thereby enabling the development of custom-made dynamic structures, but also helps elucidating the mechanic and maybe also mechanistic effects of DNA binders.  
Using this information, it should be possible to unravel deformation events step by step on even tinier levels. This not only allows for sophisticated understanding of the flexibility of origamis in response to varying triggers, thereby enabling the development of custom-made dynamic structures, but also helps elucidating the mechanic and maybe also mechanistic effects of DNA binders.  

Revision as of 19:32, 2 November 2011

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