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http://openwetware.org/index.php?title=Biomod/2011/TUM/TNT/Project/Structure&action=edit

The structure

Weg zum U

Kriterien für die Struktur

caDNAno

Deformation theory

arm-twist Theorie

[math]\displaystyle{ \vec{r} = \binom{0}{\frac{D}{2}} + R \binom{-sin \alpha}{-cos \alpha} }[/math]

[math]\displaystyle{ \vec{d} = 2 \vec{r} }[/math]

[math]\displaystyle{ d =2 \cdot \sqrt{R^2 + \left( \frac{D}{2} \right)^2 + -RD cos \alpha} }[/math]

base-twist Theorie

Design von Referenzstruktur mit Twist

cando

comparison of model structures

TEM images are useful to examine the twist of the arms and in the base.

twist of the arms

In TEM images a dark line can be observed between the two six helix buldles of each arm. If the arms are twisted, this line is no longer exactly in the middle of one arm but "moves around" it. There should also be a variation in the visualized width of the arms due to the asymetric cross-sectional area.

twist of the base

The twist of the base can be observed at structures that are shown from the side. The twist of the base (in this case the middle part of the base) can be related to a speading of the arms. The following picture shows a structure in a control measurement of BM2 without DNA binders on the left and a twisted structure of the reference BM24 that is designed as a twisted structure on the right.

Experimental considerations

short FRET-theory -> distance

FRET labels

As FRET labels we use the fluorophores Atto 550 and Atto 647N. The Förster distance for this pair is 6.5nm according to AttoTec. Both dyes are commercially available linked to ddNTPs, so they can be attached to oligonucleotides using terminal transferase. The fluorophores not only exhibit a high stability against photobleaching, but also have excitation and fluorescence spectra that fit to the set-up of the self-made fluorescence microscope in our lab. Thus we have not only the possibility to measure FRET at the photospectrometer and the more sensitive RT-PCR, but can also perform single molecule experiments at our TIRF.

@@ Line 47: / Line 47: @@
 <h2>Experimental considerations</h2>
 <h3>short FRET-theory -> distance</h3>
+<h3>FRET labels</h2>
+As FRET labels we use the fluorophores [https://www.atto-tec.com/attotecshop/product_info.php?info=p103_ATTO-550.html&XTCsid=ucvoaehx Atto 550] and [https://www.atto-tec.com/attotecshop/product_info.php?info=p114_ATTO-647N.html&XTCsid=ucvoaehx Atto 647N]. The Förster distance for this pair is 6.5nm according to AttoTec. Both dyes are commercially available linked to ddNTPs, so they can be attached to oligonucleotides using terminal transferase. The fluorophores not only exhibit a high stability against photobleaching, but also have excitation and fluorescence spectra that fit to the set-up of the self-made fluorescence microscope in our lab. Thus we have not only the possibility to measure FRET at the photospectrometer and the more sensitive RT-PCR, but can also perform single molecule experiments at our TIRF. <br>
 <h3>FRET-pair positions</h3>

Biomod/2011/TUM/TNT/Project/Structure: Difference between revisions

Revision as of 00:41, 25 October 2011

Contents

The structure

Weg zum U

Kriterien für die Struktur

caDNAno

Deformation theory

arm-twist Theorie

base-twist Theorie

Design von Referenzstruktur mit Twist

cando

comparison of model structures

twist of the arms

twist of the base

Experimental considerations

short FRET-theory -> distance

FRET labels

FRET-pair positions

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