Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design - Revision history

YAE LIM Lee: /* Design of the experiments */

YAE LIM Lee — Thu, 03 Nov 2011 16:27:28 GMT

Design of the experiments

←Older revision		Revision as of 16:27, 3 November 2011
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	2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.		2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.
		+
		+	:''Main article about design of the SPEX experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments Design]]''

	3. Individual system is observed directly under AFM.		3. Individual system is observed directly under AFM.
-
-	~~:''Main article about design of the gel experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments Design]]''~~
-
-	~~:''Main article about design of the SPEX experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments Design]]''~~

	:''Main article about desing of the AFM experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment Design]]''		:''Main article about desing of the AFM experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment Design]]''

YAE LIM Lee at 10:30, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 10:30:55 GMT

←Older revision		Revision as of 10:30, 3 November 2011
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	3. Individual system is observed directly under AFM.		3. Individual system is observed directly under AFM.

-	:''Main article about design of the gel experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments]]''	+	:''Main article about design of the gel experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments Design]]''

-	:''Main article about design of the SPEX experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments]]''	+	:''Main article about design of the SPEX experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments Design]]''

-	:''Main article about desing of the AFM experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment]]''	+	:''Main article about desing of the AFM experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment Design]]''


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

Zibo Chen: /* Design of the overall system */

Zibo Chen — Thu, 03 Nov 2011 07:09:23 GMT

Design of the overall system

←Older revision		Revision as of 07:09, 3 November 2011
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	:''Main article about Sequence Level Design: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design\|Sequence Design]]''		:''Main article about Sequence Level Design: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design\|Sequence Design]]''

-	:Main Article about Origami Layout Design: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts\|List of Origami Layouts]]''	+	:''Main Article about Origami Layout Design: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts\|List of Origami Layouts]]''
-		+

	== Design of the experiments ==		== Design of the experiments ==

YAE LIM Lee at 06:33, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 06:33:09 GMT

←Older revision		Revision as of 06:33, 3 November 2011
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	== Design of the experiments ==		== Design of the experiments ==

-	~~==== Verification of Mechanisms through Gel Experiments====~~	+	We used three different experimental techniques, and here is the design of each experiments.
-	~~:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments]]''~~	+
-	~~Before constructing our origami~~ and ~~observing how it behaves, we run a large number~~ of experiments ~~observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to~~.	+

		+	1. Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.

-	~~==== Verification of Mechanisms through Fluorescent Spectroscopy====~~	+	2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.
-	~~:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments]]''~~	+
-	Various DNA strands ~~were~~ tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.	+

		+	3. Individual system is observed directly under AFM.

-	~~==== Verification of Mechanisms through Atomic Force Microscopy====~~	+	:''Main article about design of the gel experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments]]''
-	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/~~AFM~~ Experiments ~~Design~~\|~~AFM Experiment~~]]''	+

-	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/~~AFM~~ Experiments\|~~AFM Imaging~~]]''	+	:''Main article about design of the SPEX experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments]]''
-	~~Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on~~ the ~~origami directly under~~ AFM.	+
		+	:''Main article about desing of the AFM experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment]]''


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

YAE LIM Lee at 06:28, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 06:28:14 GMT

←Older revision		Revision as of 06:28, 3 November 2011
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	= Progress 1: System Design =		= Progress 1: System Design =

-	==~~Domain Level~~ Design==	+	==Design of the overall system ==

	Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].		Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].
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-	== ~~Experimental~~ Design==	+	== Design of the experiments ==

	==== Verification of Mechanisms through Gel Experiments====		==== Verification of Mechanisms through Gel Experiments====

YAE LIM Lee at 06:27, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 06:27:29 GMT

←Older revision		Revision as of 06:27, 3 November 2011
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	Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].		Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].

-	~~:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Domain Level Project Design\|Domain Level Project Design]]''~~
-
-
-	~~==Sequence Level Design==~~
-	~~:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design\|Sequence Design]]''~~
	With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.		With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.

		+	Also, Random walking playground and cargo sorting playground were designed using a rectangular orgiami.

-	~~==Origami Layout==~~	+	:''Main article about Domain Level Design: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Domain Level Project Design\|Domain Level Project Design]]''

-	~~Random walking playground and cargo sorting playground were designed using a rectangular orgiami.~~	+	:''Main article about Sequence Level Design: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design\|Sequence Design]]''

-	:Main Article: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts\|List of Origami Layouts]]''	+	:Main Article about Origami Layout Design: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts\|List of Origami Layouts]]''

YAE LIM Lee at 06:26, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 06:26:10 GMT

←Older revision		Revision as of 06:26, 3 November 2011
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	== Experimental Design==		== Experimental Design==

-	=== Verification of Mechanisms through Gel Experiments===	+	==== Verification of Mechanisms through Gel Experiments====
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments\|Gel Experiments]]''
	Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.		Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.


-	=== Verification of Mechanisms through Fluorescent Spectroscopy===	+	==== Verification of Mechanisms through Fluorescent Spectroscopy====
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments\|SPEX Experiments]]''
	Various DNA strands were tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.		Various DNA strands were tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.


-	=== Verification of Mechanisms through Atomic Force Microscopy===	+	==== Verification of Mechanisms through Atomic Force Microscopy====
	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design\|AFM Experiment]]''

YAE LIM Lee at 06:25, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 06:25:40 GMT

←Older revision		Revision as of 06:25, 3 November 2011
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	{{Template:DeoxyriboNucleicAwesomeHeader}}		{{Template:DeoxyriboNucleicAwesomeHeader}}

-	= System Design =	+	= Progress 1: System Design =

	==Domain Level Design==		==Domain Level Design==

YAE LIM Lee at 06:23, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 06:23:51 GMT

←Older revision		Revision as of 06:23, 3 November 2011
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		+	{{Template:DeoxyriboNucleicAwesomeHeader}}
		+
	= System Design =		= System Design =

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	:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments\|AFM Imaging]]''		:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments\|AFM Imaging]]''
	Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM.		Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM.
		+
		+
		+	{{Template:DeoxyriboNucleicAwesomeFooter}}

YAE LIM Lee: New page: = System Design = ==Domain Level Design== Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track...

YAE LIM Lee — Thu, 03 Nov 2011 06:19:21 GMT

New page: = System Design = ==Domain Level Design== Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track...

New page

= System Design =

==Domain Level Design==

Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].

:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Domain Level Project Design|Domain Level Project Design]]''

==Sequence Level Design==
:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design|Sequence Design]]''
With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.

==Origami Layout==

Random walking playground and cargo sorting playground were designed using a rectangular orgiami.

:Main Article: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts|List of Origami Layouts]]''

== Experimental Design==

=== Verification of Mechanisms through Gel Experiments===
:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments|Gel Experiments]]''
Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.

=== Verification of Mechanisms through Fluorescent Spectroscopy===
:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments|SPEX Experiments]]''
Various DNA strands were tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.

=== Verification of Mechanisms through Atomic Force Microscopy===
:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design|AFM Experiment]]''

:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments|AFM Imaging]]''
Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM.