Difference between revisions of "Team:Lambert GA/Composite Part"
NithikB123 (Talk | contribs) |
NithikB123 (Talk | contribs) |
||
| Line 290: | Line 290: | ||
T7 promoter with a trigger sequence to match the toehold sequence of part BBa_K2550000</b></div><div id="content1"><br> | T7 promoter with a trigger sequence to match the toehold sequence of part BBa_K2550000</b></div><div id="content1"><br> | ||
T7 Toehold LacZ Trigger is an RNA sequence to be used in conjunction with part BBa_K22550000 to induce LacZ expression for a biosensor system. Toehold Switches are biosensors that can activate gene expression in response to a chosen RNA sequence. It is comprised of a switch and a trigger. The switch is comprised of a hairpin loop that is designed to be complementary to the trigger sequence along with a reporter protein downstream. The RBS and starting sequence is concealed in the toehold switch, preventing the reporter from being expressed. When the trigger RNA sequence is present, it will bind to the complementary sequence in the toehold switch and unbind the hairpin loop allowing the reporter protein to be expressed.</div><br><br><br><br><br><br> | T7 Toehold LacZ Trigger is an RNA sequence to be used in conjunction with part BBa_K22550000 to induce LacZ expression for a biosensor system. Toehold Switches are biosensors that can activate gene expression in response to a chosen RNA sequence. It is comprised of a switch and a trigger. The switch is comprised of a hairpin loop that is designed to be complementary to the trigger sequence along with a reporter protein downstream. The RBS and starting sequence is concealed in the toehold switch, preventing the reporter from being expressed. When the trigger RNA sequence is present, it will bind to the complementary sequence in the toehold switch and unbind the hairpin loop allowing the reporter protein to be expressed.</div><br><br><br><br><br><br> | ||
| − | <div id="target1"><div id="subheading1" style="line-height:1.3em;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550000"><b>BBa_K2550000:</a> T7 Promoter Toehold Ribosome Switch with LacZ expression</b></div><div id="content1"><br> | + | <div id="target1"></div><div id="subheading1" style="line-height:1.3em;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550000"><b>BBa_K2550000:</a> T7 Promoter Toehold Ribosome Switch with LacZ expression</b></div><div id="content1"><br> |
| − | T7 Toehold LacZ is a construct that was developed to be applied as a biosensor. The part BBa_I732005 was submitted by 2007 UTSC iGEM that singularly included the LacZ gene encoding the Beta-galactosidase protein. In effort to build on this biobrick and implement LacZ blue color expression as a biosensor, Lambert iGEM obtained a LacZ toehold switch construct assembled with a T7 promoter from the Styczynski Lab at Georgia Institute of Technology. When assembled with a distinct RNA sequence complementary to the trigger sequence, the produced blue pigment expression can be characterized based on a Red, Green, Blue (RGB) scale. | + | T7 Toehold LacZ is a construct that was developed to be applied as a biosensor. The part BBa_I732005 was submitted by 2007 UTSC iGEM that singularly included the LacZ gene encoding the Beta-galactosidase protein. In effort to build on this biobrick and implement LacZ blue color expression as a biosensor, Lambert iGEM obtained a LacZ toehold switch construct assembled with a T7 promoter from the Styczynski Lab at Georgia Institute of Technology. When assembled with a distinct RNA sequence complementary to the trigger sequence, the produced blue pigment expression can be characterized based on a Red, Green, Blue (RGB) scale.</div><br><br> |
| − | <div id="target2"><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550003"><b>BBa_K2550003:</a> T7 Cholera ctxB1 Toehold LacZ 1</b></div><div id="content1"><br> | + | <div id="target2"></div><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550003"><b>BBa_K2550003:</a> T7 Cholera ctxB1 Toehold LacZ 1</b></div><div id="content1"><br> |
| − | This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 1 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. | + | This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 1 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested.</div> |
<br><br> | <br><br> | ||
| − | <div id="target3"><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550004"><b>BBa_K2550004:</a> T7 Cholera ctxB1 Toehold LacZ 2</b></div><div id="content1"><br> | + | <div id="target3"></div><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550004"><b>BBa_K2550004:</a> T7 Cholera ctxB1 Toehold LacZ 2</b></div><div id="content1"><br> |
| − | This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 2 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. | + | This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 2 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested.</div> |
<br><br> | <br><br> | ||
| − | <div id="target4"><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550005"><b>BBa_K2550005:</a> T7 Cholera ctxB1 Toehold LacZ 3</b></div><div id="content1"><br> | + | <div id="target4"></div><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550005"><b>BBa_K2550005:</a> T7 Cholera ctxB1 Toehold LacZ 3</b></div><div id="content1"><br> |
| − | This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 3 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. | + | This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 3 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested.</div> |
<br><br> | <br><br> | ||
| − | <div id="target5"><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550006"><b>BBa_K2550006:</a> T7 Cholera ctxB1 trigger 1</b></div><div id="content1"><br> | + | <div id="target5"></div><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550006"><b>BBa_K2550006:</a> T7 Cholera ctxB1 trigger 1</b></div><div id="content1"><br> |
| − | This part encodes Trigger Number 1 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550004. | + | This part encodes Trigger Number 1 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550004.</div> |
<br><br> | <br><br> | ||
| − | <div id="target6"><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550007"><b>BBa_K2550007:</a> T7 Cholera ctxB1 trigger 2</b></div><div id="content1"><br> | + | <div id="target6"></div><div id="subheading1"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550007"><b>BBa_K2550007:</a> T7 Cholera ctxB1 trigger 2</b></div><div id="content1"><br> |
| − | This part encodes Trigger Number 2 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550004. | + | This part encodes Trigger Number 2 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550004.</div> |
<br><br> | <br><br> | ||
| − | <div id="target7"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550008"><div id="subheading1"><b>BBa_K2550008:</a> T7 Cholera ctxB1 trigger 3</b></div><div id="content1"><br> | + | <div id="target7"></div><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2550008"><div id="subheading1"><b>BBa_K2550008:</a> T7 Cholera ctxB1 trigger 3</b></div><div id="content1"><br> |
| − | This part encodes Trigger Number 3 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550005. | + | This part encodes Trigger Number 3 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550005.</div><br><br> |
<div id="target8"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K255010"><div id="subheading1"><b>BBa_K2550100:</a> Ribosome Regulator Switch</b></div><div id="content1"><br> | <div id="target8"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K255010"><div id="subheading1"><b>BBa_K2550100:</a> Ribosome Regulator Switch</b></div><div id="content1"><br> | ||
Ribosomal regulator Toehold Switch from Alexander A. Green, Pamela A. Silver, James J. Collins, Peng Yin, Toehold Switches: De-Novo-Designed Regulators of Gene Expression, Cell, Volume 159, Issue 4, 2014, Pages 925-939, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2014.10.002. It is #2 of 144 Orthogonal Switches.</div></div> | Ribosomal regulator Toehold Switch from Alexander A. Green, Pamela A. Silver, James J. Collins, Peng Yin, Toehold Switches: De-Novo-Designed Regulators of Gene Expression, Cell, Volume 159, Issue 4, 2014, Pages 925-939, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2014.10.002. It is #2 of 144 Orthogonal Switches.</div></div> | ||
Revision as of 19:06, 17 October 2018
C O M P O S I T E
P A R T S
P A R T S
BBa_K2550001:
T7 promoter with a trigger sequence to match the toehold sequence of part BBa_K2550000
T7 Toehold LacZ Trigger is an RNA sequence to be used in conjunction with part BBa_K22550000 to induce LacZ expression for a biosensor system. Toehold Switches are biosensors that can activate gene expression in response to a chosen RNA sequence. It is comprised of a switch and a trigger. The switch is comprised of a hairpin loop that is designed to be complementary to the trigger sequence along with a reporter protein downstream. The RBS and starting sequence is concealed in the toehold switch, preventing the reporter from being expressed. When the trigger RNA sequence is present, it will bind to the complementary sequence in the toehold switch and unbind the hairpin loop allowing the reporter protein to be expressed.
BBa_K2550000: T7 Promoter Toehold Ribosome Switch with LacZ expression
T7 Toehold LacZ is a construct that was developed to be applied as a biosensor. The part BBa_I732005 was submitted by 2007 UTSC iGEM that singularly included the LacZ gene encoding the Beta-galactosidase protein. In effort to build on this biobrick and implement LacZ blue color expression as a biosensor, Lambert iGEM obtained a LacZ toehold switch construct assembled with a T7 promoter from the Styczynski Lab at Georgia Institute of Technology. When assembled with a distinct RNA sequence complementary to the trigger sequence, the produced blue pigment expression can be characterized based on a Red, Green, Blue (RGB) scale.
BBa_K2550003: T7 Cholera ctxB1 Toehold LacZ 1
This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 1 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested.
BBa_K2550004: T7 Cholera ctxB1 Toehold LacZ 2
This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 2 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested.
BBa_K2550005: T7 Cholera ctxB1 Toehold LacZ 3
This cholera toehold was built using BBa_K2550202 as the stem-loop domain for the toehold, and the target sequence domain is derived from the cholera toxin ctxB1 subunit (non-toxic). This part encodes Switch Number 3 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested.
BBa_K2550006: T7 Cholera ctxB1 trigger 1
This part encodes Trigger Number 1 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550004.
BBa_K2550007: T7 Cholera ctxB1 trigger 2
This part encodes Trigger Number 2 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550004.
BBa_K2550008: T7 Cholera ctxB1 trigger 3
This part encodes Trigger Number 3 of the Cholera Toehold Series developed by Lambert iGEM. The described structure was optimized in design using the parameters described by Pardee et al. and validation using the toehold designer software developed by To et al. The design of this switch involved consideration of numerous components including free energy of RBS-Linker, MFE of various structures, illegal stop codons, etc. in order to optimize the secondary structure sequence. The corresponding sequence was then processed using the NUPACK (Nucleic Acid Package) to determine whether the appropriate secondary structure formed and whether the RBS was sufficiently enclosed in the upper loop. Following analysis of the sequence and structure, this part was experimentally tested. This part is specifically designed to be used in complement with BBa_K2550005.