Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Verification - Revision history

Shayan Doroudi: /* Random walking mechanism and initiation of walking by triggering the walker */

Shayan Doroudi — Thu, 03 Nov 2011 16:26:09 GMT

Random walking mechanism and initiation of walking by triggering the walker

←Older revision		Revision as of 16:26, 3 November 2011
Line 118:		Line 118:


-	[[Image:Dnawesome_gel2.png\|~~700px~~\|thumb\|center]]<br />	+	[[Image:Dnawesome_gel2.png\|600px\|thumb\|center]]<br />

YAE LIM Lee: /* Dropping off mechanism */

YAE LIM Lee — Thu, 03 Nov 2011 16:26:06 GMT

Dropping off mechanism

←Older revision		Revision as of 16:26, 3 November 2011
Line 384:		Line 384:
	\| Control<br />		\| Control<br />
	\|-		\|-
-	\| Lane 2: CG1 : Control<br />	+	\| Lane 2
		+	\| CG1
		+	\| Control<br />
		+	\|-
	\| Lane 3		\| Lane 3
	\| PCG1		\| PCG1
Line 433:		Line 436:
	\| Dropping off mechanism with track 2 <br />		\| Dropping off mechanism with track 2 <br />
	\|}		\|}
-

	==Gel 7==		==Gel 7==

Shayan Doroudi: /* Random walking mechanism and initiation of walking by triggering the walker */

Shayan Doroudi — Thu, 03 Nov 2011 16:25:26 GMT

Random walking mechanism and initiation of walking by triggering the walker

←Older revision		Revision as of 16:25, 3 November 2011
Line 118:		Line 118:


-	[[Image:Dnawesome_gel2.png\|~~600px~~\|thumb\|center]]<br />	+	[[Image:Dnawesome_gel2.png\|700px\|thumb\|center]]<br />


Line 194:		Line 194:

	[[Image:equilibrium.jpg\|600px\|center\|thumb\|NUPACK simulation; equilibrium between (walker – track 1) and (walker – track2) after random walking in solution ]]<br />		[[Image:equilibrium.jpg\|600px\|center\|thumb\|NUPACK simulation; equilibrium between (walker – track 1) and (walker – track2) after random walking in solution ]]<br />
-

	==Gel 3==		==Gel 3==

YAE LIM Lee at 16:25, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 16:25:04 GMT

←Older revision		Revision as of 16:25, 3 November 2011
Line 250:		Line 250:
	\| Lane 1		\| Lane 1
	\| C1, TR1		\| C1, TR1
-	\| Control<br />	+	\| Control<br />
	\|-		\|-
	\| Lane 2		\| Lane 2
Line 331:		Line 331:
	\|-		\|-
	\| Lane 4		\| Lane 4
-	\| (W-TR1-C1) : Control <br />	+	\| (W-TR1-C1)
		+	\| Control <br />
	\|-		\|-
	\| Lane 5		\| Lane 5

YAE LIM Lee at 16:23, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 16:23:28 GMT

←Older revision		Revision as of 16:23, 3 November 2011
Line 121:		Line 121:


-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #
Line 203:		Line 203:
	[[Image:Dnawesome_gel3.png\|600px\|thumb\|center]]<br />		[[Image:Dnawesome_gel3.png\|600px\|thumb\|center]]<br />

-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #
Line 242:		Line 242:
	[[Image:Dnawesome_gel4.png\|600px\|thumb\|center]]<br />		[[Image:Dnawesome_gel4.png\|600px\|thumb\|center]]<br />

-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #
Line 312:		Line 312:
	[[Image:Dnawesome_gel5.png\|600px\|thumb\|center]]<br />		[[Image:Dnawesome_gel5.png\|600px\|thumb\|center]]<br />

-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #
Line 374:		Line 374:
	[[Image:Dnawesome_gel6.png\|600px\|thumb\|center]]<br />		[[Image:Dnawesome_gel6.png\|600px\|thumb\|center]]<br />

-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #
Line 442:		Line 442:
	[[Image:dnawesome_gel7.png\|600px\|thumb\|center]]<br />		[[Image:dnawesome_gel7.png\|600px\|thumb\|center]]<br />

-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #

YAE LIM Lee at 16:22, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 16:22:35 GMT

←Older revision		Revision as of 16:22, 3 November 2011
Line 61:		Line 61:


-	{\| class="wikitable" border="1~~" style="text-align: center~~"	+	{\| class="wikitable" border="1"
	\|-		\|-
	\| Lane #		\| Lane #

YAE LIM Lee at 15:24, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 15:24:32 GMT

Show changes

YAE LIM Lee at 15:13, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 15:13:54 GMT

←Older revision		Revision as of 15:13, 3 November 2011
Line 67:		Line 67:
	\| Information from the gel		\| Information from the gel
	\|-		\|-
-	\| Lane 1 \| W \| Control	+	\| Lane 1
		+	\| W
		+	\| Control
	\|-		\|-
	\| Lane 2		\| Lane 2
Line 119:		Line 121:


-	~~Lane~~ 1: W : Control~~<br />~~	+	{\| class="wikitable" border="1" style="text-align: center"
-	Lane 2: TR1: Control ~~<br />~~	+	\|-
-	Lane 3: TR2: Control ~~<br />~~	+	\| Lane #
-	Lane 4: PTR2 : Control ~~<br />~~	+	\| Input and Expected Reaction
-	Lane 5: TR2 + PTR2 → (TR2-PTR2): Track 2 binds with its probe. This will allow us to distinguish between Track 2 and Track 1 in future experiments. <br />	+	\| Information from the gel
-	Lane 6: W + (TR2-PTR2) → W-TR2-PTR2: Track 2's probe does not interfere with the binding of the Walker to track 2~~. <br />~~	+	\|-
-	Lane 7: (W-TR1): Control ~~<br />~~	+	\| Lane 1
-	Lane 8: (W-TR1) + (TR2-PTR2) ↔ (W-TR2-PTR2) + TR1 : Walker can move between tracks, specifically from Track 1 to Track 2. The system should equalize with walkers on both tracks. ~~<br />~~	+	\| W
-	Lane 9: (W-TR2-PTR2) + TR1 ↔ (W-TR1) + (TR2-PTR2) : Walker can move between tracks, specifically from Track 2 to Track 1. The system should equalize with walkers on both tracks~~.<br />~~	+	\| Control
-	Lane 10: (WI-WT): Control ~~<br />~~	+	\|-
-	Lane 11: (W-WI): Control ~~<br />~~	+	\| Lane 2
-	Lane 12: (W-TR1-WI): Control ~~<br />~~	+	\| TR1
-	Lane 13: (W-TR1-WI) + (TR2-PTR2) : NULL experiment - Walker Inhibitor does in fact inhibit walking~~.<br />~~	+	\| Control
-	Lane 14: (W-TR1-WI) + (TR2-PTR2) + WT → (WI-WT) + TR1 + (W-TR2-PTR2) + (W-TR1-WI) +(TR2-PTR2): Walker Trigger initiates walking ~~<br />~~	+	\|-
		+	\| Lane 3
		+	\| TR2
		+	\| Control
		+	\|-
		+	\| Lane 4
		+	\| PTR2
		+	\| Control
		+	\|-
		+	\| Lane 5
		+	\| TR2 + PTR2 → (TR2-PTR2)
		+	\| Track 2 binds with its probe. This will allow us to distinguish between Track 2 and Track 1 in future experiments. <br />
		+	\|-
		+	\| Lane 6
		+	\| W + (TR2-PTR2) → W-TR2-PTR2
		+	\| Track 2's probe does not interfere with the binding of the Walker to track 2
		+	\|-
		+	\| Lane 7
		+	\| (W-TR1)
		+	\| Control
		+	\|-
		+	\| Lane 8
		+	\| (W-TR1) + (TR2-PTR2) ↔ (W-TR2-PTR2) + TR1
		+	\| Walker can move between tracks, specifically from Track 1 to Track 2. The system should equalize with walkers on both tracks.
		+	\|-
		+	\| Lane 9
		+	\| (W-TR2-PTR2) + TR1 ↔ (W-TR1) + (TR2-PTR2)
		+	\| Walker can move between tracks, specifically from Track 2 to Track 1. The system should equalize with walkers on both tracks
		+	\|-
		+	\| Lane 10
		+	\| (WI-WT)
		+	\| Control
		+	\|-
		+	\| Lane 11
		+	\| (W-WI)
		+	\| Control
		+	\|-
		+	\| Lane 12
		+	\| (W-TR1-WI)
		+	\| Control
		+	\|-
		+	\| Lane 13
		+	\| (W-TR1-WI) + (TR2-PTR2)
		+	\| NULL experiment - Walker Inhibitor does in fact inhibit walking
		+	\|-
		+	\| Lane 14
		+	\| (W-TR1-WI) + (TR2-PTR2) + WT → (WI-WT) + TR1 + (W-TR2-PTR2) + (W-TR1-WI) +(TR2-PTR2)
		+	\| Walker Trigger initiates walking
		+	\|}
		+
	*In lanes 12, 13, and 14 there is 2x of WI, and in lane 14 there is 4x of WT.		*In lanes 12, 13, and 14 there is 2x of WI, and in lane 14 there is 4x of WT.

Line 152:		Line 203:
	[[Image:Dnawesome_gel3.png\|600px\|thumb\|center]]<br />		[[Image:Dnawesome_gel3.png\|600px\|thumb\|center]]<br />

-		+	{\| class="wikitable" border="1" style="text-align: center"
-	Lane 1: CG1 : Control~~<br />~~	+	\|-
-	Lane 2: CGI : Control~~<br />~~	+	\| Lane #
-	Lane 3: CGT : Control ~~<br />~~	+	\| Input and Expected Reaction
-	Lane 4: CG1 + CGI → (CG1-CGI) : Cargo goal inhibitor binds to the cargo goal. ~~<br />~~	+	\| Information from the gel
-	Lane 5: CGI + CGT →(CGI-CGT) : Cargo goal trigger binds with the cargo goal inhibitor~~<br />~~	+	\|-
-	Lane 6: (CG1-CGI) + CGT → (CGI-CGT)+ CG1 : Cargo goal trigger is capable of stripping the Cargo goal inhibitor off of the Cargo goal <br />	+	\| Lane 1
-		+	\| CG1
-		+	\| Control
		+	\|-
		+	\| Lane 2
		+	\| CGI
		+	\| Control
		+	\|-
		+	\| Lane 3
		+	\| CGT
		+	\| Control
		+	\|-
		+	\| Lane 4
		+	\| CG1 + CGI → (CG1-CGI)
		+	\| Cargo goal inhibitor binds to the cargo goal.
		+	\|-
		+	\| Lane 5
		+	\| CGI + CGT →(CGI-CGT)
		+	\| Cargo goal trigger binds with the cargo goal inhibitor
		+	\|-
		+	\| Lane 6
		+	\| (CG1-CGI) + CGT → (CGI-CGT)+ CG1
		+	\| Cargo goal trigger is capable of stripping the Cargo goal inhibitor off of the Cargo goal <br
		+	\|}
	==Gel 4==		==Gel 4==

YAE LIM Lee at 15:08, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 15:08:25 GMT

←Older revision		Revision as of 15:08, 3 November 2011
Line 67:		Line 67:
	\| Information from the gel		\| Information from the gel
	\|-		\|-
-	\| Lane 1	+	\| Lane 1 \| W \| Control
-	\| W	+
-	\| Control	+
	\|-		\|-
	\| Lane 2		\| Lane 2
Line 111:		Line 109:
	\| Walker Trigger strips the Walker inhibitor off of the Walker		\| Walker Trigger strips the Walker inhibitor off of the Walker
	\|}		\|}
-
-
-
-
-	~~Lane 1: W : Control<br />~~
-	~~Lane 2: TR1 : Control <br />~~
-	~~Lane 3: TR2 : Control <br />~~
-	~~Lane 4: WI : Control<br />~~
-	~~Lane 5: WT : Control<br />~~
-	~~Lane 6: W + TR1 → (W-TR1) : Walker binds to one of the track strands <br />~~
-	~~Lane 7: W + TR2 → (W-TR2) : Walker binds to the other track strand <br />~~
-	~~Lane 8: W + WI → (W-WI) : Walker Inhibitor Binds to the Walker <br />~~
-	~~Lane 9: WI + WT → (WI-WT) : Walker Inhibitor Binds to the Walker Trigger <br />~~
-	~~Lane 10: W + TR1 + WI → (W-TR1-WI) : Track binding to the Walker does not interfere with the binding between the Walker and Walker Inhibitor <br />~~
-	~~Lane 11: (W-WI-TR1) + WT → (W-TR1) + (WI-WT) : Walker Trigger strips the Walker inhibitor off of the Walker <br />~~
-	*In lanes 10 and 11 there is 2x of WI and in lane 11 there is 4x of WT.

YAE LIM Lee at 15:07, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 15:07:46 GMT

←Older revision		Revision as of 15:07, 3 November 2011
Line 64:		Line 64:
	\|-		\|-
	\| Lane #		\| Lane #
-	~~\| Lane 1~~
-	~~\| Lane 2~~
-	~~\| Lane 3~~
-	~~\| Lane 4~~
-	~~\| Lane 5~~
-	~~\| Lane 6~~
-	~~\| Lane 7~~
-	~~\| Lane 8~~
-	~~\| Lane 9~~
-	~~\| Lane 10~~
-	~~\| Lane 11~~
-	\|-
	\| Input and Expected Reaction		\| Input and Expected Reaction
		+	\| Information from the gel
		+	\|-
		+	\| Lane 1
	\| W		\| W
		+	\| Control
		+	\|-
		+	\| Lane 2
	\| TR1		\| TR1
		+	\| Control
		+	\|-
		+	\| Lane 3
	\| TR2		\| TR2
		+	\| Control
		+	\|-
		+	\| Lane 4
	\| WI		\| WI
-	\| WT	+	\| Control
-	~~\| W + TR1 → (W-TR1)~~	+
-	~~\| W + TR2 → (W-TR2)~~	+
-	~~\| W + WI → (W-WI)~~	+
-	~~\| WI + WT → (WI-WT)~~	+
-	~~\| W + TR1 + WI → (W-TR1-WI)~~	+
-	~~\| (W-WI-TR1) + WT → (W-TR1) + (WI-WT)~~	+
	\|-		\|-
-	\| ~~Information from the gel~~	+	\| Lane 5
-	\| ~~Control~~	+	\| WT
-	~~\| Control~~	+
-	~~\| Control~~	+
-	~~\| Control~~	+
	\| Control		\| Control
		+	\|-
		+	\| Lane 6
		+	\| W + TR1 → (W-TR1)
	\| Walker binds to one of the track strands		\| Walker binds to one of the track strands
		+	\|-
		+	\| Lane 7
		+	\| W + TR2 → (W-TR2)
	\| Walker binds to the other track strand		\| Walker binds to the other track strand
		+	\|-
		+	\| Lane 8
		+	\| W + WI → (W-WI)
	\| Walker Inhibitor Binds to the Walker		\| Walker Inhibitor Binds to the Walker
		+	\|-
		+	\| Lane 9
		+	\| WI + WT → (WI-WT)
	\| Walker Inhibitor Binds to the Walker Trigger		\| Walker Inhibitor Binds to the Walker Trigger
		+	\|-
		+	\| Lane 10
		+	\| W + TR1 + WI → (W-TR1-WI)
	\| Track binding to the Walker does not interfere with the binding between the Walker and Walker Inhibitor		\| Track binding to the Walker does not interfere with the binding between the Walker and Walker Inhibitor
		+	\|-
		+	\| Lane 11
		+	\| (W-WI-TR1) + WT → (W-TR1) + (WI-WT)
	\| Walker Trigger strips the Walker inhibitor off of the Walker		\| Walker Trigger strips the Walker inhibitor off of the Walker
	\|}		\|}