BBa_K2066501
1
BBa_K2066501
ICA:BsmBI Cut Site + G + Sticky End 1
2016-08-24T11:00:00Z
2016-08-25T07:32:44Z
This part was synthesized as part of a gBlock / using IDT DNA synthesis. Part sequence based off of supplemental material from Briggs et al., 2012.
This is an intermediate part used in the construction of WM16_002. This part contains the BsmBI cut site followed by a single nucleotide spacer (G) followed by sticky end 1. Sticky end 1 is one of three sticky ends used by WM iGEM 2016 for Iterative Capped Assembly. ICA design method based off of Briggs, A. W., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., & Church, G. M. (2012). Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic acids research, gks624.
false
false
_2534_
27446
27446
9
false
G was selected as the spacer nucleotide as per Briggs et al., 2012. Sticky End 1 was chosen as per Briggs et al., 2012.
false
Joseph L Maniaci
BBa_K2066505
1
BBa_K2066505
BsmBI Cut Site + G + Sticky End 3
2016-08-24T11:00:00Z
2016-08-25T12:10:40Z
Briggs, A. W., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., & Church, G. M. (2012). Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic acids research, gks624.
This is an intermediate part used in the construction of WM16_002. This part contains the BsmBI cut site followed by a single nucleotide spacer (G) followed by sticky end 2. Sticky end 2 is one of three sticky ends used by WM iGEM 2016 for Iterative Capped Assembly. ICA design method based off of Briggs, A. W., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., & Church, G. M. (2012). Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic acids research, gks624.
false
false
_2534_
31526
31526
9
false
G was selected as the spacer nucleotide as per Briggs et al., 2012. Sticky End 2 was chosen as per supplemental material from Briggs et al., 2012.
false
Kalen Clifton, Christine Gao, Andrew Halleran, Ethan Jones, Likhitha Kolla, Joseph Maniaci, John Marken, John Mitchell, Callan Monette, Adam Reiss
BBa_K2066018
1
BBa_K2066018
UNS 2 Sequence, from Torella et al., 2013
2016-07-11T11:00:00Z
2016-10-19T05:41:43Z
Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
This is Unique Nucleotide Sequence 2, (UNS 2), from Torella et al., 2013. The William and Mary iGEM team has adopted this as our standard prefix; as such, all of our parts will have this sequence immediately following the BioBrick prefix. We took this measure in order to allow easier Gibson Assembly cloning of our parts. Primer sequences which can be used to clone with the UNS 2/3 standard can be found on our wiki.
false
false
_2534_
31544
27446
9
false
UNS 2 was chosen because it works well with UNS 3 and it is in accordance with the BioBrick standard.
false
Kalen Clifton, Christine Gao, Andrew Halleran, Ethan Jones, Likhitha Kolla, Joseph Maniaci, John Marken, John Mitchell, Callan Monette, Adam Reiss
BBa_K2066502
1
BBa_K2066502
1xTetO Binding Site
2016-08-24T11:00:00Z
2016-08-25T07:55:30Z
This part was synthesized as part of a gBlock / using IDT DNA synthesis. Tet Operator Sequence based off of Addgene Plasmid #17655.
This is an intermediate part used in the construction of WM16 TetO ICA parts (WM16_K2066002-WM16_K2066010). This part contains the TetO repeat sequence used by WM for ICA creation of TetO binding arrays. Tet Operator Sequence based off of Addgene Plasmid #17655. ICA design method based off of Briggs, A. W., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., & Church, G. M. (2012). Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic acids research, gks624.
false
false
_2534_
27446
27446
9
false
n/a
false
Joseph L Maniaci
BBa_K2066522
1
BBa_K2066522
64BP Spacer, UNS X + first 24 UNS X
2016-10-08T11:00:00Z
2016-10-09T08:55:48Z
This part was synthesized as part of a gBlock/ using IDT DNA synthesis. Part sequence is first 16 bp of UNS X sequence from Torella et al., 2013.
This is an intermediate part used in the construction of WK2066008 - K2066010. This part is a spacer region.
The sequence is the UNS X sequence followed by the first 24 base pairs from the USN X sequence. UNS X sequence is from the supplemental material of Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
false
false
_2534_
27446
27446
9
false
N/A
false
Kalen Clifton, Christine Gao, Andrew Halleran, Ethan Jones, Likhitha Kolla, Joseph Maniaci, John Marken, John Mitchell, Callan Monette, Adam Reiss
BBa_K2066019
1
BBa_K2066019
UNS 3 Sequence, from Torella et al., 2013
2016-07-11T11:00:00Z
2016-10-19T05:43:00Z
Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
This is Unique Nucleotide Sequence 3, (UNS 3), from Torella et al., 2013. The William and Mary iGEM team has adopted this as our standard prefix; as such, all of our parts will have this sequence immediately following the BioBrick prefix. We took this measure in order to allow easier Gibson Assembly cloning of our parts. Primer sequences which can be used to clone with the UNS 2/3 standard can be found on our wiki.
The sequence for this part came from the following paper: Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860. A huge thanks to all the researchers involved in its original creation!
false
false
_2534_
31544
27446
9
false
This UNS sequence was chosen to serve as the 3' primer in our standard because it works well with UNS 2 and it adheres to the BioBrick standards.
false
Kalen Clifton, Christine Gao, Andrew Halleran, Ethan Jones, Likhitha Kolla, Joseph Maniaci, John Marken, John Mitchell, Callan Monette, Adam Reiss
BBa_K2066021
1
BBa_K2066021
UNS 5 Sequence, from Torella et al., 2013
2016-08-24T11:00:00Z
2016-10-19T05:45:29Z
This part was synthesized as part of a gBlock / using IDT DNA synthesis. Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
This is Unique Nucleotide Sequence 5, (UNS 5), from Torella et al., 2013. The William and Mary iGEM team has adopted this as our standard prefix; as such, all of our parts will have this sequence immediately following the BioBrick prefix. We took this measure in order to allow easier Gibson Assembly cloning of our parts. Primer sequences which can be used to clone with the UNS 2/3 standard can be found on our wiki. The sequence for this part came from the following paper: Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860. A huge thanks to all the researchers involved in its original creation!
false
false
_2534_
31544
27446
9
false
UNS 5 was chosen along with UNS 4 to serve as primer binding sites which will create an amplicon that contains the base sequence for our ICA monomer but does not contain USN 2 or 3.
false
Joseph L Maniaci
BBa_K2066010
1
BBa_K2066010
Tet Monomer C w/ 64 bp spacer for ICA
2016-10-11T11:00:00Z
2016-10-12T12:02:45Z
ICA method and sequence design based on Briggs et al., 2012 and its supplement. Briggs, A. W., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., & Church, G. M. (2012). Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic acids research, gks624. The UNS2, UNS3, UNS 4, and UNS 5 sequences are taken from Torella et al. 2013 and are ideal for cloning long sequences of monomers. Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
The part is flanked by UNS 2 and UNS 3 as per the WM UNS gibson cloning standard. This part is the TetO, 64BP spacer 'C' monomer for use in ICA to create repeated TetO Arrays of variable length. The monomer can be PCR amplified using UNS 4 and UNS 5 PCR landing pads. Next, the part should cut with BsmBI restriction enzyme to expose sticky ends and used to extend monomer in ICA. Monomer C (this part) can bind to a Monomer B or the terminator sequence (see our wiki). This part contains the following: UNS 2 (WM standard gibson/amplification primer site) ??? UNS 4 (used to provide orthogonal amplification of monomers alone) ??? BsmBI site ??? sticky end 3 - Tet Repeat ??? 64 bp spacer (taken as first 64 bp from UNS X) ??? BsmBI site ??? Sticky end 1 - UNS 5 (orthogonal amplification in conjunction with UNS 4) ??? UNS 3 (WM standard gibson/amplification primer site).
ICA method and sequence design based on Briggs et al., 2012 and its supplement.
Briggs, A. W., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., & Church, G. M. (2012). Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic acids research, gks624. The UNS2, UNS3, UNS 4, and UNS 5 sequences are taken from Torella et al. 2013 and are ideal for cloning long sequences of monomers. Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
false
false
_2534_
27446
27446
9
false
Design of monomer part was based off of TALEN monomer design in Briggs et al., 2012.
false
Kalen Clifton, Christine Gao, Andrew Halleran, Ethan Jones, Likhitha Kolla, Joseph Maniaci, John Marken, John Mitchell, Callan Monette, Adam Reiss
component2494504
1
BBa_K2066018
component2494509
1
BBa_K2066501
component2494511
1
BBa_K2066019
component2494506
1
BBa_K2066505
component2494505
1
BBa_K2066020
component2494508
1
BBa_K2066522
component2494507
1
BBa_K2066502
component2494510
1
BBa_K2066021
annotation2494510
1
BBa_K2066021
range2494510
1
186
225
annotation2494508
1
BBa_K2066522
range2494508
1
111
174
annotation2494507
1
BBa_K2066502
range2494507
1
92
110
annotation2494511
1
BBa_K2066019
range2494511
1
226
265
annotation2494506
1
BBa_K2066505
range2494506
1
81
91
annotation2494504
1
BBa_K2066018
range2494504
1
1
40
annotation2494505
1
BBa_K2066020
range2494505
1
41
80
annotation2494509
1
BBa_K2066501
range2494509
1
175
185
BBa_K2066020
1
BBa_K2066020
UNS 4 Sequence, from Torella et al., 2013
2016-08-24T11:00:00Z
2016-10-19T05:44:31Z
This part was synthesized as part of a gBlock / using IDT DNA synthesis. Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860.
This is Unique Nucleotide Sequence 4, (UNS 4), from Torella et al., 2013. The William and Mary iGEM team has adopted this as our standard prefix; as such, all of our parts will have this sequence immediately following the BioBrick prefix. We took this measure in order to allow easier Gibson Assembly cloning of our parts. Primer sequences which can be used to clone with the UNS 2/3 standard can be found on our wiki.
The sequence for this part came from the following paper: Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860. A huge thanks to all the researchers involved in its original creation!
false
false
_2534_
31544
27446
9
false
UNS 4 was chosen along with UNS 5 to serve as primer binding sites which will create an amplicon that contains the base sequence for our ICA monomer but does not contain USN 2 or 3.
false
Kalen Clifton, Christine Gao, Andrew Halleran, Ethan Jones, Likhitha Kolla, Joseph Maniaci, John Marken, John Mitchell, Callan Monette, Adam Reiss
BBa_K2066501_sequence
1
cgtctcgcctg
BBa_K2066019_sequence
1
gcactgaaggtcctcaatcgcactggaaacatcaaggtcg
BBa_K2066505_sequence
1
cgtctcgactt
BBa_K2066010_sequence
1
gctgggagttcgtagacggaaacaaacgcagaatccaagcctgacctcctgccagcaatagtaagacaacacgcaaagtccgtctcgactttccctatcagtgatagagaccaggatacatagattaccacaactccgagcccttccaccccaggatacatagattaccacaaccgtctcgcctggagccaactccctttacaacctcactcaagtccgttagaggcactgaaggtcctcaatcgcactggaaacatcaaggtcg
BBa_K2066018_sequence
1
gctgggagttcgtagacggaaacaaacgcagaatccaagc
BBa_K2066502_sequence
1
tccctatcagtgatagaga
BBa_K2066020_sequence
1
ctgacctcctgccagcaatagtaagacaacacgcaaagtc
BBa_K2066021_sequence
1
gagccaactccctttacaacctcactcaagtccgttagag
BBa_K2066522_sequence
1
ccaggatacatagattaccacaactccgagcccttccaccccaggatacatagattaccacaac
igem2sbol
1
iGEM to SBOL conversion
Conversion of the iGEM parts registry to SBOL2.1
James Alastair McLaughlin
Chris J. Myers
2017-03-06T15:00:00.000Z