# Biomod/2011/TUM/TNT/Results

(Difference between revisions)
 Revision as of 12:36, 2 November 2011 (view source)← Previous diff Revision as of 12:47, 2 November 2011 (view source)Next diff → Line 220: Line 220: - 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.]). Length measurements based on our TEM images also indicate a decrease of the total length of the origami structure. Said changes are in good agreement. One spermine every 7bp reduces the length of a single helix to 97.9% of the original length, while the origami is shortened to ca. 98.6% by the same occupation with spermine. The changes are small, but local length changes seem to add up to comparable global changes.
+ 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.
+ Although both DNA binders induce length changes in opposite directions on DNA helices, both shorten the whole origami structure.
+ + 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.
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.
- 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. 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.
+ 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.

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