Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments - Revision history

Shayan Doroudi: /* Verification of Random Walking Mechanism on Origami */

Shayan Doroudi — Thu, 03 Nov 2011 18:09:03 GMT

Verification of Random Walking Mechanism on Origami

←Older revision		Revision as of 18:09, 3 November 2011
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	White dots: regular rectangle		White dots: regular rectangle

-	Light-blue dots: marker to ~~distingusich~~ the orientation of the origami for AFM images	+	Light-blue dots: marker to distinguish the orientation of the origami for AFM images

-	Blue dots: track 1	+	Dark Blue dots: track 1

	Red dots: track 2		Red dots: track 2

	Yellow star: walker goal		Yellow star: walker goal
		+
		+	Green dot: biotinylated control staple used for AFM imaging (that staple is not biotinylated in SPEX experiments)

YAE LIM Lee at 11:47, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 11:47:51 GMT

←Older revision		Revision as of 11:47, 3 November 2011
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	[[Image: sw.jpg‎ \|thumb\|center\|400px\|alt=test\|Space Walk]]		[[Image: sw.jpg‎ \|thumb\|center\|400px\|alt=test\|Space Walk]]
	\|}		\|}
-
-
-	~~====Longest Track ====~~
-
-	~~[[Image: sslide9.jpg \| 400px]]~~
-
-	~~====Middle Track ====~~
-
-	~~[[Image: sslide10.jpg \| 400px]]~~
-
-	~~====Shortest Track ====~~
-
-	~~[[Image: sslide11.jpg \| 400px]]~~
-
-	~~====Space Walking Track ====~~
-
-	~~[[Image: sw.jpg \| 400px]]~~
-

	{{Template:DeoxyriboNucleicAwesomeFooter}}		{{Template:DeoxyriboNucleicAwesomeFooter}}

YAE LIM Lee at 11:47, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 11:47:28 GMT

←Older revision		Revision as of 11:47, 3 November 2011
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	{\| style= "background: transparent; margin: auto;"		{\| style= "background: transparent; margin: auto;"
-	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|~~500px~~\|Longest track ]]	+	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|400px\|Longest track ]]
-	[[Image:sslide10.jpg‎ \|thumb\|center\|~~500px~~\|alt=test\|Middle track]]	+	[[Image:sslide10.jpg‎ \|thumb\|center\|400px\|alt=test\|Middle track]]
-	\|[[Image:sslide11.jpg \|thumb\|center\|~~500px~~\|alt=test\|Shortest track ]]	+	\|[[Image:sslide11.jpg \|thumb\|center\|400px\|alt=test\|Shortest track ]]
-	[[Image: sw.jpg‎ \|thumb\|center\|~~500px~~\|alt=test\|Space Walk]]	+	[[Image: sw.jpg‎ \|thumb\|center\|400px\|alt=test\|Space Walk]]
	\|}		\|}

YAE LIM Lee at 11:47, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 11:47:12 GMT

←Older revision		Revision as of 11:47, 3 November 2011
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	{\| style= "background: transparent; margin: auto;"		{\| style= "background: transparent; margin: auto;"
-	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|~~300px~~\|Longest track ]]	+	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|500px\|Longest track ]]
-	[[Image:sslide10.jpg‎ \|thumb\|center\|~~300px~~\|alt=test\|Middle track]]	+	[[Image:sslide10.jpg‎ \|thumb\|center\|500px\|alt=test\|Middle track]]
-	\|[[Image:sslide11.jpg \|thumb\|center\|~~300px~~\|alt=test\|Shortest track ]]	+	\|[[Image:sslide11.jpg \|thumb\|center\|500px\|alt=test\|Shortest track ]]
-	[[Image:sw.jpg‎ \|thumb\|center\|~~300px~~\|alt=test\|Space Walk]	+	[[Image: sw.jpg‎ \|thumb\|center\|500px\|alt=test\|Space Walk]]
	\|}		\|}

YAE LIM Lee at 11:46, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 11:46:24 GMT

←Older revision		Revision as of 11:46, 3 November 2011
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	Yellow star: walker goal		Yellow star: walker goal
		+
		+
		+	{\| style= "background: transparent; margin: auto;"
		+	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|300px\|Longest track ]]
		+	[[Image:sslide10.jpg‎ \|thumb\|center\|300px\|alt=test\|Middle track]]
		+	\|[[Image:sslide11.jpg \|thumb\|center\|300px\|alt=test\|Shortest track ]]
		+	[[Image:sw.jpg‎ \|thumb\|center\|300px\|alt=test\|Space Walk]
		+	\|}
		+

	====Longest Track ====		====Longest Track ====

Zibo Chen: /* Verification of Random Walking Mechanism on Origami */

Zibo Chen — Thu, 03 Nov 2011 09:02:24 GMT

Verification of Random Walking Mechanism on Origami

←Older revision		Revision as of 09:02, 3 November 2011
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	[[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: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. ]]

-	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 were chosen, shown in the figures below. 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. 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.

Zibo Chen: /* Verification of Overall Mechanisms in Solution */

Zibo Chen — Thu, 03 Nov 2011 06:55:22 GMT

Verification of Overall Mechanisms in Solution

←Older revision		Revision as of 06:55, 3 November 2011
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	Walkers were tagged with quenchers while goals for walkers were tagged with fluorophores. The expected reaction is shown below.		Walkers were tagged with quenchers while goals for walkers were tagged with fluorophores. The expected reaction is shown below.

-	[[Image:SS_1.PNG‎\|thumb\|center\|~~700px~~\|Walkers are expected to walk from tracks to walker goals. ]]	+	[[Image:SS_1.PNG‎\|thumb\|center\|900px\|Walkers are expected to walk from tracks to walker goals. ]]

	Cargo strands were tagged with fluorophores and goals for cargo were tagged with quenchers. The expected reaction is shown below.		Cargo strands were tagged with fluorophores and goals for cargo were tagged with quenchers. The expected reaction is shown below.

Zibo Chen: /* Verification of Overall Mechanisms in Solution */

Zibo Chen — Thu, 03 Nov 2011 06:55:08 GMT

Verification of Overall Mechanisms in Solution

←Older revision		Revision as of 06:55, 3 November 2011
Line 9:		Line 9:
	Walkers were tagged with quenchers while goals for walkers were tagged with fluorophores. The expected reaction is shown below.		Walkers were tagged with quenchers while goals for walkers were tagged with fluorophores. The expected reaction is shown below.

-	[[Image:SS_1.PNG‎\|thumb\|center\|~~800px~~\|Walkers are expected to walk from tracks to walker goals. ]]	+	[[Image:SS_1.PNG‎\|thumb\|center\|700px\|Walkers are expected to walk from tracks to walker goals. ]]

	Cargo strands were tagged with fluorophores and goals for cargo were tagged with quenchers. The expected reaction is shown below.		Cargo strands were tagged with fluorophores and goals for cargo were tagged with quenchers. The expected reaction is shown below.

-	[[Image:SS_2.PNG‎\|thumb\|center\|~~800px~~\|Cargo strands are expected to be transferred from walkers to goals. ]]	+	[[Image:SS_2.PNG‎\|thumb\|center\|700px\|Cargo strands are expected to be transferred from walkers to goals. ]]

	==Verification of Random Walking Mechanism on Origami==		==Verification of Random Walking Mechanism on Origami==

Zibo Chen: /* Verification of Overall Mechanisms in Solution */

Zibo Chen — Thu, 03 Nov 2011 06:43:33 GMT

Verification of Overall Mechanisms in Solution

←Older revision		Revision as of 06:43, 3 November 2011
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	[[Image:SS_1.PNG‎\|thumb\|center\|800px\|Walkers are expected to walk from tracks to walker goals. ]]		[[Image:SS_1.PNG‎\|thumb\|center\|800px\|Walkers are expected to walk from tracks to walker goals. ]]
		+
		+	Cargo strands were tagged with fluorophores and goals for cargo were tagged with quenchers. The expected reaction is shown below.
		+
		+	[[Image:SS_2.PNG‎\|thumb\|center\|800px\|Cargo strands are expected to be transferred from walkers to goals. ]]

	==Verification of Random Walking Mechanism on Origami==		==Verification of Random Walking Mechanism on Origami==

Zibo Chen: /* SPEX Experiments */

Zibo Chen — Thu, 03 Nov 2011 06:39:10 GMT

SPEX Experiments

←Older revision		Revision as of 06:39, 3 November 2011
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	__TOC__		__TOC__
	==Verification of Overall Mechanisms in Solution==		==Verification of Overall Mechanisms in Solution==
		+	See also: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Results\|SPEX Results]]
		+
		+	Several strands were labeled with fluorophores and quenchers to study there interactions in solution.
		+
		+	Walkers were tagged with quenchers while goals for walkers were tagged with fluorophores. The expected reaction is shown below.
		+
		+	[[Image:SS_1.PNG‎\|thumb\|center\|800px\|Walkers are expected to walk from tracks to walker goals. ]]

	==Verification of Random Walking Mechanism on Origami==		==Verification of Random Walking Mechanism on Origami==

←Older revision		Revision as of 11:47, 3 November 2011
Line 42:		Line 42:

	{\| style= "background: transparent; margin: auto;"		{\| style= "background: transparent; margin: auto;"
-	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|~~500px~~\|Longest track ]]	+	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|400px\|Longest track ]]
-	[[Image:sslide10.jpg‎ \|thumb\|center\|~~500px~~\|alt=test\|Middle track]]	+	[[Image:sslide10.jpg‎ \|thumb\|center\|400px\|alt=test\|Middle track]]
-	\|[[Image:sslide11.jpg \|thumb\|center\|~~500px~~\|alt=test\|Shortest track ]]	+	\|[[Image:sslide11.jpg \|thumb\|center\|400px\|alt=test\|Shortest track ]]
-	[[Image: sw.jpg‎ \|thumb\|center\|~~500px~~\|alt=test\|Space Walk]]	+	[[Image: sw.jpg‎ \|thumb\|center\|400px\|alt=test\|Space Walk]]
	\|}		\|}

←Older revision		Revision as of 11:47, 3 November 2011
Line 42:		Line 42:

	{\| style= "background: transparent; margin: auto;"		{\| style= "background: transparent; margin: auto;"
-	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|~~300px~~\|Longest track ]]	+	\|[[Image:sslide9.jpg‎ \|thumb\|center\|alt=test\|500px\|Longest track ]]
-	[[Image:sslide10.jpg‎ \|thumb\|center\|~~300px~~\|alt=test\|Middle track]]	+	[[Image:sslide10.jpg‎ \|thumb\|center\|500px\|alt=test\|Middle track]]
-	\|[[Image:sslide11.jpg \|thumb\|center\|~~300px~~\|alt=test\|Shortest track ]]	+	\|[[Image:sslide11.jpg \|thumb\|center\|500px\|alt=test\|Shortest track ]]
-	[[Image:sw.jpg‎ \|thumb\|center\|~~300px~~\|alt=test\|Space Walk]	+	[[Image: sw.jpg‎ \|thumb\|center\|500px\|alt=test\|Space Walk]]
	\|}		\|}