Biomod/2011/TUM/TNT/Results

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<h1>Discussion</h1>
<h1>Discussion</h1>
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<h2>Origamis respond in another way than single DNA helices on local deformations</h2>
Spermine causes a positive twist (46°) of double stranded DNA, and additionally decreases the length of DNA (base step rise reduced from 0.34nm to 0.29nm; [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Tari et.al.]). According to [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Salerno et.al.], each bound molecule of ethidium bromide increases the length of a DNA double helix by 3.4nm, which is exactly the length of one base pair. Additionally, it induces a twist of -27°, in contrast to the +36° twist of one base pair. <br>
Spermine causes a positive twist (46°) of double stranded DNA, and additionally decreases the length of DNA (base step rise reduced from 0.34nm to 0.29nm; [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Tari et.al.]). According to [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Salerno et.al.], each bound molecule of ethidium bromide increases the length of a DNA double helix by 3.4nm, which is exactly the length of one base pair. Additionally, it induces a twist of -27°, in contrast to the +36° twist of one base pair. <br>
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Although both DNA binders induce length changes in opposite directions on DNA helices, both shorten the whole origami structure. The crosslinking between the helices in theU alters the type of deformation compared an isolated double helix. <br>
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Although both DNA binders induce length changes in opposite directions on DNA helices, both shorten the whole origami structure. The crosslinking between the helices in theU alters the type of deformation compared to an isolated double helix. One could assume that local changes in twist and length combine in an origami, causing a length change effect with all local deformations integrated. <br>
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Regarding the measured twist angles, for small concentrations no effects can be seen with spermine. Without spermine, as well with ca. 5% and 14% occupied binding sides, the angle remains ca. 9°. For higher occupations (50% and 67%), the angle increases to 12°. Additional data points will be needed to fit these findings, but we suggest that a cooperative behavior would be an appropriate explanation. Within DNA origamis, not only a single helices needs to be twisted, but large bundles of helices with many crosslinks. This makes the single helices more rigid, consequently hindering an induced fit of spermine molecules. Only higher concentrations could excert enough force to overcome the local restraints and induce a global twist. <br>
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To put these considerations in a nutshell, new theoretical approaches are needed to correlate effects on a single helix with effects on a huge system of interconnected helices. <br>
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Regarding the measured twist angles, for small concentrations no effects can seen with spermine. Without spermine, as well with ca. 5% and 14% occupied binding sides, the angle remains around 9°. For higher occupations (50% and 67%), the angle increases to 12°. Additional data points will be needed to fit these findings, but we suggest that a cooperative behavior would be an appropriate explanation. Within DNA origamis, not only a single helices needs to be twisted, but large bundles of helices with many crosslinks. This makes the single helices more rigid, consequently hindering an induced fit of spermine molecules. Only higher concentrations could excert enough force to overcome the local restraints and induce a global twist. <br>
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Regarding our angle distributions from the TEM data, the mean global twist for one additional base every 21bp is 21°, compared to 11° induced by one molecule ethidium bromide every 21bp. Besides some potential inaccuracies in the quite small concentrations, the strong local negative twist caused by ethidium bromide results in remarkably reduced effects on the global structure. <br>
Regarding our angle distributions from the TEM data, the mean global twist for one additional base every 21bp is 21°, compared to 11° induced by one molecule ethidium bromide every 21bp. Besides some potential inaccuracies in the quite small concentrations, the strong local negative twist caused by ethidium bromide results in remarkably reduced effects on the global structure. <br>

Revision as of 13:16, 2 November 2011

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