Updated on 2021-11-18: We are keeping figures and text in the Registry as it was. You might found this file, which we prepared for the Judging Session, helpful to understand our parts.
Updated on 2021-11-10: we were nominated for the Best New Basic Part award.
In our project, a total of 56 parts are designed. Among them, there are 20 basic parts and 36 composite parts. We have sequencing verified all parts and tested most the parts.
# Basic Parts, Lead by Chongwen Cao
Among the 20 basic parts designed this year by ourselves, BBa_K3790014 is our favorite one.
# Composite Parts, Lead by Guanqiao Chi
Most of our composite parts were designed to help obtain the critical product of our project - the Bst polymerase. Our favorite composite parts are BBa_K3790212 and BBa_K3790232.
The former one was the original version of our Bst expression system, and the latter one was T7 gene product 5.7 driven by pBAD promoter. Both of them were proved to be reliable and effective.
Left: Gel electrophoresis of plasmids containing K3790212 digested with NcoI and KpnI, indicating that our composite part BBa_K3790212 had been successfully constructed; Right: Compare proteins in the pellet vs. supernatant, after BPCB lysis, indicating that our composite part BBa_K3790212 had been successfully expressed.
# Parts Collection, Lead by Renbin Liu
Our parts could be divided into three major groups:
(I) parts that were designed to regulate the bacteria expression, including the first full characterized σS promoter http://parts.igem.org/Part:BBa_K3790014 for the iGEM community, as well as parts were used for validation. These parts provide a set of new tools for bacteria expression regulation.
Group I: BBa_K3790014,
BBa_K3790009 - BBa_K3790013, BBa_K3790086,
BBa_K3790050, BBa_K3790085,
BBa_K3790231, BBa_K3790235,
BBa_K3790225 - BBa_K3790230, BBa_K3790236, BBa_K3790237, BBa_K3790242
(II) a set of DNA binding domains that could be used to improve DNA polymerases, including our favorite Sso7d http://parts.igem.org/Part:BBa_K3790002 for the iGEM community. These parts provide mutiple choices for improving the binding efficiency of a specific DNA polymerase.
Group II: BBa_K3790002,
BBa_K3790001, BBa_K3790003, BBa_K3790004, BBa_K3790005, BBa_K3790006
(III) IPTG induced Bst polymerase for isothermal DNA amplification, as well as a complete set of fusions with parts in (II). We showed that even without improvement, native Bst produced in bacterial lysate is sufficient to support LAMP, documented in http://parts.igem.org/Part:BBa_K3790212. This provide a new perspective in isothermal DNA amplification that purified enzymes can also be replaced by bacterial lysate containing the enzymes.
Group III: BBa_K3790212,
BBa_K3790213 - BBa_K3790224,
BBa_K3790150 - BBa_K3790162
Below lists all the parts we built for our project. Please check each part's Main Page on the Registry http://parts.igem.org/Main_Page
| Name | Type | Description | Designer | Length | |||
|---|---|---|---|---|---|---|---|
| W | BBa_K3790212 | Composite | T7lac::RBS::Bst::K395601 | Renbin Liu | 1938 | ||
| W | BBa_K3790232 | Composite | T7 gene product 5.7 driven by pBAD/araC | Chongwen Cao | 1558 | ||
| W | BBa_K3790000 | Coding | Bst polymerase I (large fragment) for E. coli | Renbin Liu | 1767 | ||
| BBa_K3790001 | Coding | DbpA | Guanqiao Chi | 219 | |||
| W | BBa_K3790002 | Coding | Sso7d | Guanqiao Chi | 174 | ||
| BBa_K3790003 | Coding | Sso10b | Guanqiao Chi | 291 | |||
| BBa_K3790004 | Coding | albA1 | Guanqiao Chi | 288 | |||
| BBa_K3790005 | Coding | S.ssb | Guanqiao Chi | 441 | |||
| BBa_K3790006 | Coding | E.ssb | Guanqiao Chi | 531 | |||
| W | BBa_K3790007 | Protein_Domain | (G2S)3 | Guanqiao Chi | 27 | ||
| W | BBa_K3790009 | Regulatory | The simplest form of csiD promoter, a weak σS promoter | Chongwen Cao | 38 | ||
| W | BBa_K3790010 | Regulatory | The simplest form of a mutated csiD promoter, a medium σS promoter | Chongwen Cao | 38 | ||
| W | BBa_K3790011 | Regulatory | The simplest form of fic promoter, a weak σS promoter | Chongwen Cao | 37 | ||
| W | BBa_K3790012 | Regulatory | The simplest form of a mutated fic promoter, a medium σS promoter | Chongwen Cao | 37 | ||
| W | BBa_K3790013 | Regulatory | The simplest form of osmY promoter, a strong σS promoter | Chongwen Cao | 39 | ||
| W | BBa_K3790014 | Regulatory | The simplest form of dps promoter, a strong σS promoter | Chongwen Cao | 39 | ||
| U | W | BBa_K3790050 | Coding | T7 phage gene product 5.7, an E.coli transcription inhibitor (RFC compatible) | Chongwen Cao | 210 | |
| BBa_K3790084 | RBS | RBS for Gram-positive species (Schofield, 2003) | Chongwen Cao | 17 | |||
| BBa_K3790085 | Coding | T7 phage gene product 2, an E.coli transcription inhibitor | Chongwen Cao | 195 | |||
| BBa_K3790086 | Regulatory | pBAD+dps promoter fusion | Chongwen Cao | 1210 | |||
| BBa_K3790150 | Composite | Bst-(G2S)3-DbpA | Guanqiao Chi | 2013 | |||
| BBa_K3790151 | Composite | Bst-(G2S)3-S.ssb | Guanqiao Chi | 2235 | |||
| BBa_K3790152 | Composite | Bst-(G2S)3-E.ssb | Guanqiao Chi | 2325 | |||
| BBa_K3790153 | Composite | Bst-(G2S)3-albA1 | Guanqiao Chi | 2082 | |||
| BBa_K3790154 | Composite | Bst-(G2S)3-Sso7d | Guanqiao Chi | 1968 | |||
| BBa_K3790155 | Composite | Bst-(G2S)3-Sso10b | Guanqiao Chi | 2085 | |||
| BBa_K3790156 | Composite | DbpA-(G2S)3-Bst | Guanqiao Chi | 2013 | |||
| BBa_K3790157 | Composite | S.ssb-(G2S)3-Bst | Guanqiao Chi | 2235 | |||
| BBa_K3790159 | Composite | albA1-(G2S)3-Bst | Guanqiao Chi | 2082 | |||
| BBa_K3790160 | Composite | Sso10b-(G2S)3-Bst | Guanqiao Chi | 2085 | |||
| BBa_K3790161 | Composite | Sso7d-(G2S)3-Bst | Guanqiao Chi | 1982 | |||
| BBa_K3790162 | Composite | E.ssb-(G2S)3-Bst | Guanqiao Chi | 2325 | |||
| BBa_K3790213 | Composite | T7lac::RBS::Bst-(G2S)3-DbpA::K395601 | Renbin Liu | 2277 | |||
| BBa_K3790214 | Composite | T7lac::RBS::Bst-(G2S)3-S.ssb::K395601 | Renbin Liu | 2499 | |||
| BBa_K3790215 | Composite | T7lac::RBS::Bst-(G2S)3-E.ssb::K395601 | Renbin Liu | 2589 | |||
| BBa_K3790216 | Composite | T7lac::RBS::Bst-(G2S)3-albA1::K395601 | Renbin Liu | 2346 | |||
| W | BBa_K3790217 | Composite | T7lac::RBS::Bst-(G2S)3-Sso7d::K395601 | Renbin Liu | 2232 | ||
| BBa_K3790218 | Composite | T7lac::RBS::Bst-(G2S)3-Sso10b::K395601 | Renbin Liu | 2349 | |||
| BBa_K3790219 | Composite | T7lac::RBS::DbpA-(G2S)3-Bst::K395601 | Renbin Liu | 2277 | |||
| BBa_K3790220 | Composite | T7lac::RBS::S.ssb-(G2S)3-Bst::K395601 | Renbin Liu | 2499 | |||
| BBa_K3790221 | Composite | T7lac::RBS::E.ssb-(G2S)3-Bst::K395601 | Renbin Liu | 2589 | |||
| BBa_K3790222 | Composite | T7lac::RBS::albA1-(G2S)3-Bst::K395601 | Renbin Liu | 2346 | |||
| BBa_K3790223 | Composite | T7lac::RBS::Sso10b-(G2S)3-Bst::K395601 | Renbin Liu | 2349 | |||
| W | BBa_K3790224 | Composite | T7lac::RBS::Sso7d-(G2S)3-Bst::K395601 | Renbin Liu | 2246 | ||
| BBa_K3790225 | Composite | GFP controlled by σS promoter csiD | Chongwen Cao | 923 | |||
| BBa_K3790226 | Composite | GFP controlled by σS promoter csiD_improved | Chongwen Cao | 923 | |||
| BBa_K3790227 | Composite | GFP controlled by σS promoter fic | Chongwen Cao | 922 | |||
| BBa_K3790228 | Composite | GFP controlled by σS promoter fic_improved | Chongwen Cao | 922 | |||
| BBa_K3790229 | Composite | GFP controlled by σS promoter osmY | Chongwen Cao | 924 | |||
| BBa_K3790230 | Composite | GFP controlled by σS promoter dps | Chongwen Cao | 924 | |||
| W | BBa_K3790231 | Composite | T7 gene product 2 controlled by pBAD/araC | Chongwen Cao | 1543 | ||
| BBa_K3790235 | Composite | T7 gene product 5.7 controlled by pBAD+dps promoter fusion | Chongwen Cao | 1554 | |||
| BBa_K3790236 | Composite | GFP controlled by pBAD+dps promoter fusion | Chongwen Cao | 2064 | |||
| BBa_K3790237 | Composite | GFP controlled by pBAD/araC | Chongwen Cao | 2064 | |||
| BBa_K3790242 | Composite | T7lac::RBS::mScarlet::K395601 | Renbin Liu | 897 |