Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results: Difference between revisions
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[[Image:Insertion.jpg|thumb|center| | [[Image:Insertion.jpg|thumb|center|700px|Figure 0. Verification of random walking on origami using fluorophore and quencer. When a walker reaches to the walker goal, fluorophore is quenched and bulk fluorescent level decreases]] | ||
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|[[Image:sslide9.jpg |thumb|center|alt=test|400px|Longest track ]] | |[[Image:sslide9.jpg |thumb|center|alt=test|400px|Longest track ]] | ||
[[Image:sslide10.jpg |thumb|center|400px|alt=test| | [[Image:sslide10.jpg |thumb|center|400px|alt=test|Medium Length track]] | ||
|[[Image:sslide11.jpg |thumb|center|400px|alt=test|Shortest track ]] | |[[Image:sslide11.jpg |thumb|center|400px|alt=test|Shortest track ]] | ||
[[Image: sw.jpg |thumb|center|400px|alt=test|Space Walk]] | [[Image: sw.jpg |thumb|center|400px|alt=test|Space Walk]] | ||
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[[Image:SPEX_Sum. | [[Image:SPEX_Sum.PNG |thumb|center|600px|Figure 4. A plot of half completion time versus distance from goal.]] | ||
== Random Walking with full length of tracks: Comparison == | |||
Same starting positions that we used in the previous section were tested with full tracks, this time. Full track is longer than the longest track we tried previously. This new set of experiment also included space walk control. Results are plotted with the previous data to compare. Space walk control of two different set of experiment was very consistent, and the completion time of full tracks was slower than that of partial tracks. Full track samples showed similar completion time regardless of different starting position, even though starting position 22, which is a middle length track, showed a little digression; it needs a further discussion. Overall, SPEX data consistently shows that completion time is dependent on track length, suggesting a high probability of random walk on origami. | |||
[[Image: full_tracks.jpg |thumb|center|650px|Figure 5.Comparison between samples with various lengths of tracks. PT = partial tracks. FT = full tracks. SP = starting positions. SW = space walk]] | |||
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We used a [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Simulation|stochastic MATLAB simulation]] to estimate half-completion times for walkers starting on truncated tracks of varying lengths: | We used a [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Simulation|stochastic MATLAB simulation]] to estimate half-completion times for walkers starting on truncated tracks of varying lengths: | ||
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! Start Site, Truncated Track | ! Start Site, Truncated Track | ||
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[[Image:SPEX_Theo_2.PNG |thumb|center|alt=test|500px|Figure 7(1). SPEX data fitting for random walking on the longest track (SP10). ]] | |||
[[Image:SPEX_Theo_3.PNG |thumb|center|500px|alt=test|Figure 7(2). SPEX data fitting for random walking on the medium length track (SP22). ]] | |||
[[Image:SPEX_Theo_4.PNG |thumb|center|500px|alt=test|Figure 7(3). SPEX data fitting for random walking on the shortest track (SP34). ]] | |||
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We made a comparison between the models from Matlab simulation and random walk formulae. Results are summarized in the table below. | We made a comparison between the models from Matlab simulation and random walk formulae. Results are summarized in the table below. | ||
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Latest revision as of 19:50, 3 November 2011
Friday, April 19, 2024
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SPEX ResultsAs discussed in SPEX Experimental Design, two sets of experiments were conducted to verify the random walking mechanism. The first set was performed to detect potential leak reactions in the system, while the second set of experiments were used to verify the random walking mechanism. In short, walker goal with fluorophore is planted the end of the track, and walker with quencher is planted at the various positions on the track. When we input walker trigger, walker starts walking on the track. When it gets to the walker goal, it stops there and quenches the fluorophore. Therefore, by analyzing fluorescent level using SPEX, we can perform a bulk analysis of a percentage of walkers that reach the walker goals.
Detection of Potential Leak ReactionsTo verify that the walker walks on the origami using the intended mechanisms, we set up control groups where either tracks (TR), except for the one that the walker is bound to, or walker triggers (WT), or both, were missing in the reactions. Walkers are not expected to perform random walking under such conditions. As shown in Figure 1, no decrease in fluorescent signals were observed unless both tracks and walker triggers were added into the system. Hence potential leak reactions are negligible.
Random Walking with Different lengths of tracks using different starting sitesTo test space walk hypothesis, we annealed a control origami with unmodified staples at the track position. When we add tracks to this control origami, since unmodified staples does not contain the probe region, no track is formed on origami while added tracks are free floating in solution. This is called a space walk control, abbreviated as SW. In addition to the space walk control, we varied the lengths of tracks on origami, and observed the completion level with timely manner.
Random Walking with full length of tracks: ComparisonSame starting positions that we used in the previous section were tested with full tracks, this time. Full track is longer than the longest track we tried previously. This new set of experiment also included space walk control. Results are plotted with the previous data to compare. Space walk control of two different set of experiment was very consistent, and the completion time of full tracks was slower than that of partial tracks. Full track samples showed similar completion time regardless of different starting position, even though starting position 22, which is a middle length track, showed a little digression; it needs a further discussion. Overall, SPEX data consistently shows that completion time is dependent on track length, suggesting a high probability of random walk on origami.
Data AnalysisMatlab SimulationWe used a stochastic MATLAB simulation to estimate half-completion times for walkers starting on truncated tracks of varying lengths:
Mathematical Formulae
ConclusionWe made a comparison between the models from Matlab simulation and random walk formulae. Results are summarized in the table below.
References[1] Wickham, S. F. J., Endo, M., Katsuda, Y., Hidaka, K., Bath, J., Sugiyama, H., & Tuberfield, A. J. (2010). Direct observation of stepwise movement of a synthetic molecular transporter. Nature Nanotechnology, 6, 166–169.
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