Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design - Revision history

Shayan Doroudi: /* Toehold Domains */

Shayan Doroudi — Thu, 03 Nov 2011 17:53:01 GMT

Toehold Domains

←Older revision		Revision as of 17:53, 3 November 2011
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	\|-		\|-
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u</sub>1</sub>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>GACTCT</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>GACTCT</code>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTC</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTC</code>

	\|-		\|-
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u</sub>2</sub>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>2</sub>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTTTC</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTTTC</code>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGG</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGG</code>

Shayan Doroudi: /* Toehold Domains */

Shayan Doroudi — Thu, 03 Nov 2011 17:52:36 GMT

Toehold Domains

←Older revision		Revision as of 17:52, 3 November 2011
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	\|-		\|-
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u</sub>1</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>~~ACACAC~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>GACTCT</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>~~GTGTGT~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTC</code>
		+
		+	\|-
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u</sub>2</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTTTC</code>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGG</code>

	\|-		\|-

Shayan Doroudi: /* List of Strands */

Shayan Doroudi — Thu, 03 Nov 2011 17:50:01 GMT

List of Strands

←Older revision		Revision as of 17:50, 3 November 2011
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| lp* up<sub>cg</sub>* cgd*		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| lp* up<sub>cg</sub>* cgd*
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 87		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 87
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>Staple - ~~TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGTGTGGGTAGGAGTTAGTTCATCT~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>Staple - TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGTGTGGGTAGGAGTTAGT</code>

	\|-		\|-
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>* x* l*		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>* x* l*
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 27		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 27
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>~~GTGTGTAATAGAAAGGAGATAGAATGG~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTCAATAGAAAGGAGATAGAATGG</code>

	\|-		\|-
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l x u<sub>1</sub> up<sub>cg</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l x u<sub>1</sub> up<sub>cg</sub>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 47		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 47
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>~~CCATTCTATCTCCTTTCTATTACACACACTAACTCCTACCCACACCT~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>CCATTCTATCTCCTTTCTATTGACTCTACTAACTCCTACCCACACCT</code>

		+	\|-
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Cargo 2
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| C<sub>1</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>* x* l*
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 27
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGGAATAGAAAGGAGATAGAATGG</code>
		+
		+	\|-
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Cargo Goal 2
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| CG<sub>1</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l x u<sub>1</sub> up<sub>cg</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 47
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>CCATTCTATCTCCTTTCTATTCCTTTCCAACTCTCCACTCCAATCAA</code>
	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Sub Cargo Goal		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Sub Cargo Goal

Shayan Doroudi: /* Design Process */

Shayan Doroudi — Thu, 03 Nov 2011 17:45:03 GMT

Design Process

←Older revision		Revision as of 17:45, 3 November 2011
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	After having designed our mechanism at the domain level, we needed to fill in our domains with actual sequences. To start, we picked specific lengths for each of our domains. We decided to stick with the general precedent that toeholds be 6 nucleotides in length, then decided that any domain that was part of a probe be 20 nucleotides in length, as this length is both not wastefully long and long enough to ensure that no spontaneous dissociation would occur. We then decided that any domain longer than a toehold, but not part of the probe system should be 15 base pairs in length, as this would not spontaneously dissociate, but could be easily strand displaced.		After having designed our mechanism at the domain level, we needed to fill in our domains with actual sequences. To start, we picked specific lengths for each of our domains. We decided to stick with the general precedent that toeholds be 6 nucleotides in length, then decided that any domain that was part of a probe be 20 nucleotides in length, as this length is both not wastefully long and long enough to ensure that no spontaneous dissociation would occur. We then decided that any domain longer than a toehold, but not part of the probe system should be 15 base pairs in length, as this would not spontaneously dissociate, but could be easily strand displaced.

-	After these numbers were decided, we consulted a list of 20 nucleotide sequences that are known to be relatively inert and chose sequences from this list to fill in our 20 and 15 nucleotide domains. We used NUPACK and a little trial and error to find our 7 necessary relatively inert toeholds. We then ran a number of simulations in NUPACK to check for unwanted secondary structures and interactions in our designed sequences.	+	After these numbers were decided, we consulted a list of 20 nucleotide sequences that are known to be relatively inert and chose sequences from this list to fill in our 20 and 15 nucleotide domains. We used NUPACK and a little trial and error to find our 7 necessary relatively inert toeholds. We then ran a number of simulations in NUPACK to check for unwanted secondary structures and interactions in our designed sequences.
		+
		+	Detachers were strands that were meant to detach the corresponding strand from the origami, so we could test our results on origami using gel electrophoresis, but we decided to not run such experiments due to the potential difficulty of seeing bands corresponding to small strands of DNA when running origami in a gel. Additionally, we felt our other methods (fluorescence spectroscopy and atomic force microscopy) were sufficient for showing our mechanisms work on origami. Therefore, we have never used the detacher strands.

	==List of Domains==		==List of Domains==

YAE LIM Lee at 11:07, 3 November 2011

YAE LIM Lee — Thu, 03 Nov 2011 11:07:26 GMT

←Older revision		Revision as of 11:07, 3 November 2011
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| <code>AGATGAACTAACTCCTACCCACACCT</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| <code>AGATGAACTAACTCCTACCCACACCT</code>
	\|}		\|}
		+
		+	Staple sequences for the rectangular origami were from Rothemund, P. W. K. (2006).

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

Zibo Chen: /* List of Strands */

Zibo Chen — Thu, 03 Nov 2011 06:08:57 GMT

List of Strands

←Older revision		Revision as of 06:08, 3 November 2011
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	==List of Strands==		==List of Strands==
		+	*The M13 scaffold was used to construct an origami.
	A star(*) denotes the complement of a domain.		A star(*) denotes the complement of a domain.

Sarah Wittman: /* Probe Domains */

Sarah Wittman — Mon, 11 Jul 2011 23:04:28 GMT

Probe Domains

Sarah Wittman: /* Toehold Domains */

Sarah Wittman — Mon, 11 Jul 2011 23:02:59 GMT

Toehold Domains

Sarah Wittman: /* Other Domains */

Sarah Wittman — Mon, 11 Jul 2011 23:01:58 GMT

Other Domains

←Older revision		Revision as of 23:01, 11 July 2011
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	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| b		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| b
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| CCTCAAAACTTATCC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTCAAAACTTATCC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GGATAAGTTTTGAGG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GGATAAGTTTTGAGG</code>

	\|- <!--Last Row: It's different from the others-->		\|- <!--Last Row: It's different from the others-->
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| x		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| x
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| TATCTCCTTTCTATT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| <code>TATCTCCTTTCTATT</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| AATAGAAAGGAGATA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| <code>AATAGAAAGGAGATA</code>
	\|}<br><br>		\|}<br><br>

Sarah Wittman: /* List of Strands */

Sarah Wittman — Mon, 11 Jul 2011 23:01:33 GMT

List of Strands

Show changes

←Older revision		Revision as of 17:53, 3 November 2011
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	\|-		\|-
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u</sub>1</sub>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>GACTCT</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>GACTCT</code>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTC</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTC</code>

	\|-		\|-
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u</sub>2</sub>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>2</sub>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTTTC</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTTTC</code>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGG</code>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGG</code>

←Older revision		Revision as of 17:50, 3 November 2011
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| lp* up<sub>cg</sub>* cgd*		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| lp* up<sub>cg</sub>* cgd*
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 87		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 87
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>Staple - ~~TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGTGTGGGTAGGAGTTAGTTCATCT~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>Staple - TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGTGTGGGTAGGAGTTAGT</code>

	\|-		\|-
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>* x* l*		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>* x* l*
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 27		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 27
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>~~GTGTGTAATAGAAAGGAGATAGAATGG~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGAGTCAATAGAAAGGAGATAGAATGG</code>

	\|-		\|-
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	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l x u<sub>1</sub> up<sub>cg</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l x u<sub>1</sub> up<sub>cg</sub>
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 47		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 47
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>~~CCATTCTATCTCCTTTCTATTACACACACTAACTCCTACCCACACCT~~</code>	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>CCATTCTATCTCCTTTCTATTGACTCTACTAACTCCTACCCACACCT</code>

		+	\|-
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Cargo 2
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| C<sub>1</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u<sub>1</sub>* x* l*
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 27
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAAAGGAATAGAAAGGAGATAGAATGG</code>
		+
		+	\|-
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Cargo Goal 2
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| CG<sub>1</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l x u<sub>1</sub> up<sub>cg</sub>
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| 47
		+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>CCATTCTATCTCCTTTCTATTCCTTTCCAACTCTCCACTCCAATCAA</code>
	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Sub Cargo Goal		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| Sub Cargo Goal

←Older revision		Revision as of 23:01, 11 July 2011
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	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| b		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| b
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| CCTCAAAACTTATCC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCTCAAAACTTATCC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GGATAAGTTTTGAGG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GGATAAGTTTTGAGG</code>

	\|- <!--Last Row: It's different from the others-->		\|- <!--Last Row: It's different from the others-->
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| x		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| x
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| TATCTCCTTTCTATT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| <code>TATCTCCTTTCTATT</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| AATAGAAAGGAGATA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| <code>AATAGAAAGGAGATA</code>
	\|}<br><br>		\|}<br><br>

←Older revision		Revision as of 23:04, 11 July 2011
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	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| P<sub>tr1</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| P<sub>tr1</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| CCAACTCAACCCATTTCATC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCAACTCAACCCATTTCATC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GATGAAATGGGTTGAGTTGG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GATGAAATGGGTTGAGTTGG
-		+	</code>
	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| P<sub>tr2</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| P<sub>tr2</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| TACATACACCAACCTCCACC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>TACATACACCAACCTCCACC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GGTGGAGGTTGGTGTATGTA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GGTGGAGGTTGGTGTATGTA
-		+	</code>
	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| lp<sup>†</sup>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| lp<sup>†</sup>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| TTTTTTTTTTTTTTTTTTTTTTTTTTT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>TTTTTTTTTTTTTTTTTTTTTTTTTTT</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| AAAAAAAAAAAAAAAAAAAAAAAAAAA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AAAAAAAAAAAAAAAAAAAAAAAAAAA</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| up<sub>ca</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| up<sub>ca</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| ACCTTACCTCTCCCTAACTT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>ACCTTACCTCTCCCTAACTT</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| AAGTTAGGGAGAGGTAAGGT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AAGTTAGGGAGAGGTAAGGT</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| up<sub>cg</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| up<sub>cg</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| ACTAACTCCTACCCACACCT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>ACTAACTCCTACCCACACCT</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| AGGTGTGGGTAGGAGTTAGT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>AGGTGTGGGTAGGAGTTAGT
		+	</code>

	\|- <!--Last Row: It's different from the others-->		\|- <!--Last Row: It's different from the others-->
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| P<sub>wg</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| P<sub>wg</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| CCTCTTTCTTATCACTTCAA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| <code>CCTCTTTCTTATCACTTCAA</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| TTGAAGTGATAAGAAAGAGG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| <code>TTGAAGTGATAAGAAAGAGG</code>
	\|}		\|}
	<small>† The lp domain is 27 nucleotides long.</small>		<small>† The lp domain is 27 nucleotides long.</small>
-

	===Toehold Domains===		===Toehold Domains===

←Older revision		Revision as of 23:02, 11 July 2011
Line 62:		Line 62:
	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| a<sub>1</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| a<sub>1</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| CTCCTC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CTCCTC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GAGGAG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAGGAG</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| a<sub>2</sub>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| a<sub>2</sub>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| ATCCAC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>ATCCAC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GTGGAT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GTGGAT</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| a<sub>2</sub>' <sup>†</sup>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| a<sub>2</sub>' <sup>†</sup>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| ATCC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>ATCC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GGAT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GGAT</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| z		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| z
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| AAAAAA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>AAAAAA</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| TTTTTT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>TTTTTT</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| l
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| CCATTC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>CCATTC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GAATGG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GAATGG</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| u
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| ACACAC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>ACACAC</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| GTGTGT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>GTGTGT</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| wi		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| wi
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| GGTAAG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>GGTAAG</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| CTTACC	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>CTTACC</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| cgi		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| cgi
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| ATGTTG	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>ATGTTG</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| CAACAT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>CAACAT</code>

	\|-		\|-
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| cgd <sup>‡</sup>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"\| cgd <sup>‡</sup>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| AGATGA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"\| <code>AGATGA</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| TCATCT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"\| <code>TCATCT</code>

	\|- <!--Last Row: It's different from the others-->		\|- <!--Last Row: It's different from the others-->
	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| wgd <sup>‡</sup>		\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"\| wgd <sup>‡</sup>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| AGATGA	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"\| <code>AGATGA</code>
-	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| TCATCT	+	\|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"\| <code>TCATCT</code>
	\|}		\|}
	<small>† The a<sub>2</sub>' domain is a subset of the a<sub>2</sub> domain and is 4 nucleotides long.<br>		<small>† The a<sub>2</sub>' domain is a subset of the a<sub>2</sub> domain and is 4 nucleotides long.<br>
	‡ Toeholds cgd and wgd are the same. This does not change the function of our system because they are never used in the same solution together.</small>		‡ Toeholds cgd and wgd are the same. This does not change the function of our system because they are never used in the same solution together.</small>
-

	===Other Domains===		===Other Domains===