Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments: Difference between revisions
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Three different starting positions (SP10, 22 and 34) were chosen (Figure 3, A-C), named after the index of each particular position on the origami. Since it is possible for the walkers to undergo space walking (SW), namely dissociating from the origami, binding to free floating tracks in the solution and rebinding to origami, we added a control group in which only one track at the starting position 10 was planted on the origami (Figure 3, D). Excess of walker triggers were added in the beginning of the experiment to activate the walkers and excess of walkers with quenchers attached were added in the end to stop the reactions.[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results|SEPX Results]] show that fluorescent signals decreased faster when the walkers were planted nearer to goals. | Three different starting positions (SP10, 22 and 34) were chosen (Figure 3, A-C), named after the index of each particular position on the origami. Since it is possible for the walkers to undergo space walking (SW), namely dissociating from the origami, binding to free floating tracks in the solution and rebinding to origami, we added a control group in which only one track at the starting position 10 was planted on the origami (Figure 3, D). Excess of walker triggers were added in the beginning of the experiment to activate the walkers and excess of walkers with quenchers attached were added in the end to stop the reactions.[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results|SEPX Results]] show that fluorescent signals decreased faster when the walkers were planted nearer to goals. | ||
[[Image:PT_Ori.PNG|thumb| | [[Image:PT_Ori.PNG|thumb|center|800px|Figure 2. The overall origami layout used in SPEX experiments. Each type of track is indexed with a unique number. ]] | ||
[[Image:SP_Origami.bmp|thumb| | [[Image:SP_Origami.bmp|thumb|center|800px|Figure 3. Figure 9. Origami layouts in SPEX experiments. Cyan, markers used to check origami orientation under AFM. Blue, Track 1. Red, Track 2. White, DNA staples only. Five-pointed star, walker goal. Rectangles indicate the starting position for random walk. ]] | ||
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Revision as of 19:24, 31 October 2011
Friday, April 19, 2024
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SPEX ExperimentsVerification of Overall Mechanisms in SolutionVerification of Random Walking Mechanism on OrigamiFluorescent spectroscopy (SPEX) was used to verify random walk on the origami. We designed a strand named walker goal (WG) which can bind to walkers irreversibly due to its perfect complementarity with walkers. A ROX fluorophore was attached to the 5' end of the probe for the walker goal (PWG) and the corresponding quencher was attached to the 3' end of the walker (Figure 1). When the walker binds to the walker goal, its quencher is directly above the fluorophore of the walker goal, hence quenching it. Thus we can setup experiments where the fluorescent level slowly decreases as more and more walkers reach the walker goal. The overall origami layout was shown in Figure 2.
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