Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design: Difference between revisions
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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== | ||
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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=== | ||
The length of these sequences is 7 nucleotides. | The length of these sequences is 7 nucleotides. | ||
{|style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #aaaaaa;" cellpadding="5" | |||
|- | |||
<!--Headings--> | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Domain Name | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 0 1px 0"| Sequence (5' → 3') | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 0 1px 1px"| Complement Sequence (5' → 3') | |||
|- | |||
|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"| <code>CTCCTC</code> | |||
|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 0 1px"| <code>ATCCAC</code> | |||
|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 0 1px"| <code>ATCC</code> | |||
|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 0 1px"| <code>AAAAAA</code> | |||
|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 0 1px"| <code>CCATTC</code> | |||
|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<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 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> | |||
|- | |||
|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"| <code>GGTAAG</code> | |||
|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 0 1px"| <code>ATGTTG</code> | |||
|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 0 1px"| <code>AGATGA</code> | |||
|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--> | |||
|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"| <code>AGATGA</code> | |||
|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> | |||
‡ 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=== | ||
The length of these sequences is 15 nucleotides. | The length of these sequences is 15 nucleotides. | ||
{|style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #aaaaaa;" cellpadding="5" | |||
|- | |||
<!--Headings--> | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Domain Name | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 0 1px 0"| Sequence (5' → 3') | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 0 1px 1px"| Complement Sequence (5' → 3') | |||
|- | |||
|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"| <code>CCTCAAAACTTATCC</code> | |||
|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--> | |||
|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"| <code>TATCTCCTTTCTATT</code> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 0 1px"| <code>AATAGAAAGGAGATA</code> | |||
|}<br><br> | |||
==List of Strands== | ==List of Strands== | ||
*The M13 scaffold was used to construct an origami. | |||
A star(*) denotes the complement of a domain. | |||
{|style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #aaaaaa;" cellpadding="5" | |||
|- | |||
<!--Headings--> | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Strand Name | |||
!scope="col" width="100" style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Shorthand Abbreviation | |||
!scope="col" width="100" style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Domain Composition (5' → 3') | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 0 1px 0"| Length | |||
!style="border-style: solid; background-color:#f2f2f2; border-color: #aaaaaa; border-width: 0 0 1px 1px"| Sequence (5' → 3') | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Probe for Track 1 | |||
|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"| 54 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>CCAACTCAACCCATTTCATCTT - Staple</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Probe for Track 2 | |||
|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"| 54 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>TACATACACCAACCTCCACCTT - Staple</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Probe for Cargo Attacher | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| P<sub>ca</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| lp* up<sub>ca</sub>* | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 81 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>Staple - TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTAGGGAGAGGTAAGGT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Probe for Cargo Goal<sub>1</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| P<sub>cg1</sub> | |||
|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 1px"| <code>Staple - TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGTGTGGGTAGGAGTTAGT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Probe for Walker Goal | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| P<sub>wg</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| wgd p<sub>wg</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 60 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>AGATGACCTCTTTCTTATCACTTCAATT - Staple</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Track 1 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| TR<sub>1</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| p<sub>tr1</sub>* a<sub>1</sub>* b* z* | |||
|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>GATGAAATGGGTTGAGTTGGGAGGAGGGATAAGTTTTGAGGTTTTTT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Track 2 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| TR<sub>2</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| p<sub>tr2</sub>* z* b* a<sub>2</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>GGTGGAGGTTGGTGTATGTATTTTTTGGATAAGTTTTGAGGGTGGAT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| W | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| l x a<sub>2</sub> b a<sub>1</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 48 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>CCATTCTATCTCCTTTCTATTATCCACCCTCAAAACTTATCCCTCCTC</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker Inhibitor | |||
|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"| a<sub>2</sub>* x* wi* | |||
|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>GTGGATAATAGAAAGGAGATACTTACC</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker Trigger | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| WT | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| wi x a<sub>2</sub>' | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 25 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>GGTAAGTATCTCCTTTCTATTATCC | |||
</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker Detacher<sub>1</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| WD<sub>1</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| z b a<sub>1</sub> | |||
|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>AAAAAACCTCAAAACTTATCCCTCCTC</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker Detacher<sub>2</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| WD<sub>2</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| a<sub>2</sub> b z | |||
|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>ATCCACCCTCAAAACTTATCCAAAAAA</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker Goal | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| WG | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| p<sub>wg</sub>* a<sub>1</sub>* b* a<sub>2</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>TTGAAGTGATAAGAAAGAGGGAGGAGGGATAAGTTTTGAGGGTGGAT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Walker Goal Detacher | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| WGD | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| p<sub>wg</sub>* wgd* | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 26 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>TTGAAGTGATAAGAAAGAGGTCATCT | |||
</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Cargo Attacher | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| CA | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| x up<sub>ca</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 35 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>TATCTCCTTTCTATTACCTTACCTCTCCCTAACTT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Sub Cargo Attacher | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| S<sub>ca</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| lp | |||
|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>TTTTTTTTTTTTTTTTTTTTTTTTTTT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Cargo 1 | |||
|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>AGAGTCAATAGAAAGGAGATAGAATGG</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Cargo Goal 1 | |||
|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>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"| S<sub>cg</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| lp | |||
|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>TTTTTTTTTTTTTTTTTTTTTTTTTTT</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Cargo Goal Inhibitor | |||
|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"| x* cgi* | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 21 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>AATAGAAAGGAGATACAACAT | |||
</code> | |||
|- | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| Cargo Goal Trigger | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| CGT | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 1px 0"| cgi x | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px"| 21 | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 0 1px 1px"| <code>ATGTTGTATCTCCTTTCTATT | |||
</code> | |||
|- <!--Last Row: It's different from the others--> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"| Cargo Goal Detacher | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"| CGD | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0 1px 0 0"| cgd up<sub>cg</sub> | |||
|style="border-style: solid; background-color:#f9f9f9; border-color: #aaaaaa; border-width: 0"| 26 | |||
|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}} |
Latest revision as of 10:53, 3 November 2011
Thursday, March 28, 2024
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Sequence DesignDesign ProcessAfter 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. 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 DomainsProbe DomainsThe length of these sequences is 20 nucleotides.
† The lp domain is 27 nucleotides long. Toehold DomainsThe length of these sequences is 7 nucleotides.
† The a2' domain is a subset of the a2 domain and is 4 nucleotides long. Other DomainsThe length of these sequences is 15 nucleotides.
List of Strands
A star(*) denotes the complement of a domain.
Staple sequences for the rectangular origami were from Rothemund, P. W. K. (2006).
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