Biomod/2011/TUM/TNT/LabbookA/Structure page

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<head> <title> 

       TUM NanU - Labbook

</title> </head> <body> <body background-color="#F0F0F0"> <div id="contentSub"> <span class="subpages"> < <a href="/wiki/Tnt_-_Labbook" title="Tnt - Labbook">TUM-NanU - Labbook</a> 

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<a href="/wiki/Tnt_-_Labbook/2011" title="Tnt - Labbook/2011">2011</a> 

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The TUM Biomod Team 2011 folded several structures, that are described on this page.

BM1
this the_U structure contains polyT staples to prevent aggregation via stacking interactions.

BM2
The same like BM1, but without polyT staples. Observation at the transmission electron microscope displays no negative effects of the missing polyT staples.

BM3_4/29
This structure is fluorophore labeled for FRET measurements. Atto 550 ddCTP is attached to staple the_U 175 in helix 4 and Atto 647N ddUTP to the_U 225 in helix 29. No polyT staples are included.

BM4_8/23
This structure is fluorophore labeled for FRET measurements. Atto 550 ddCTP is attached to staple the_U 197 in helix 8 and Atto 647N ddUTP to the_U 218 in helix 23. No polyT staples are included.

BM5_5/20
This structure is fluorophore labeled for FRET measurements. Atto 550 ddCTP is attached to staple the_U 183 in helix 5 and Atto 647N ddUTP to the_U 204 in helix 20. No polyT staples are included.

BM6_4
This is the donor only control to BM3_4/29, including only Atto 550 ddCTP at the_U 175 in helix 4.

BM7_29
This is the acceptor only control to BM3_4/29, including only Atto 647N ddUTP at the_U 225 in helix 29.

BM8_8
This is the donor only control to BM4_8/23, including only Atto 550 ddCTP at the_U 197 in helix 8.

BM9_23
This is the acceptor only control to BM4_8/23, including only Atto 647N ddUTP at the_U 218 in helix 23.

BM10_5
This is the donor only control to BM5_5/20, including only Atto 550 ddCTP at the_U 183 in helix 5.

BM11_20
This is the acceptor only control to BM5_5/20, including only Atto 647N ddUTP at the_U 204 in helix 20.

The following structures all include seven special staples, which are used as adapters. With one side, they bind at he bottom of the_U, with the other side they bind to biotinylated staples, so they can be immobilised for single molecule fluorescence microscopy.

BM12_4/29
This structure is fluorophore labeled for FRET measurements. Atto 550 ddCTP is attached to staple the_U 175 in helix 4 and Atto 647N ddUTP to the_U 225 in helix 29. No polyT staples are included, but the seven adapter staples for immbolisiation.

BM13_8/23
This structure is fluorophore labeled for FRET measurements. Atto 550 ddCTP is attached to staple the_U 197 in helix 8 and Atto 647N ddUTP to the_U 218 in helix 23. No polyT staples are included, but the seven adapter staples for immbolisiation.

BM14_5/20
This structure is fluorophore labeled for FRET measurements. Atto 550 ddCTP is attached to staple the_U 183 in helix 5 and Atto 647N ddUTP to the_U 204 in helix 20. No polyT staples are included, but the seven adapter staples for immbolisiation.

BM15_4
This is the donor only control to BM12_4/29, including only Atto 550 ddCTP at the_U 175 in helix 4.

BM16_29
This is the acceptor only control to BM12_4/29, including only Atto 647N ddUTP at the_U 225 in helix 29.

BM17_8
This is the donor only control to BM13_8/23, including only Atto 550 ddCTP at the_U 197 in helix 8.

BM18_23
This is the acceptor only control to BM17_8/23, including only Atto 647N ddUTP at the_U 218 in helix 23.

BM19_5
This is the donor only control to BM14_5/20, including only Atto 550 ddCTP at the_U 183 in helix 5.

BM20_20
This is the acceptor only control to BM14_5/20, including only Atto 647N ddUTP at the_U 204 in helix 20.

The following structures also include the adapters for immobilisation and additionally labeled oligonucleotides to measure changes in length.

BM21_172/173 Atto 550 ddCTP is attached to staple the_U 172 and Atto 647N ddUTP to the_U 173, both in helix 4. No polyT staples are included, but the seven adapter staples for immbolisiation.

BM22_172 This is the donor only control to BM21_172/173, including only Atto 550 ddCTP at the_U 172 in helix 4.

BM23_173 This is the acceptor only control to BM21_172/173, including only Atto 647N ddUTP at the_U 173 in helix 4.



BM24 This structure is intrinsically twisted. It does not contain fluorophores.

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