Difference between revisions of "Part:BBa K3505009"

 
(5 intermediate revisions by one other user not shown)
Line 3: Line 3:
 
<partinfo>BBa_K3505009 short</partinfo>
 
<partinfo>BBa_K3505009 short</partinfo>
  
Level a vector for Golden Braid Cloning. Having cargo LacZa for blue white screening between BsaI and BsmBI sites.Resistance in Kanamycin and ori pBBR1 for multiple protein expression capacities.
+
Level a vector for GoldenBraid Cloning. Having cargo LacZa for blue white screening between BsaI and BsmBI sites.Resistance in Kanamycin and ori pBBR1 for multiple protein expression capacities.
  
 
[[File:T--Thessaly--a2.png|600px|thumb|none|<i><b>Fig.1:</b> a2 plasmid Features and Restiction Sites.</i>]]
 
[[File:T--Thessaly--a2.png|600px|thumb|none|<i><b>Fig.1:</b> a2 plasmid Features and Restiction Sites.</i>]]
  
 
===Usage and Biology===
 
===Usage and Biology===
Golden Braid (GB) is a DNA assembly strategy for Plant Synthetic Biology based on Type IIS enzymes. It is also compatible for MoClo assembly.
+
GoldenBraid (GB) is a DNA assembly strategy for Plant Synthetic Biology based on Type IIS enzymes. It is also compatible for MoClo assembly.
 
The sequences must not contain BsmBI and BsaI sites! Domestication may be done in order to vanish BsaI and BsmBI sites from the inner sequence.  
 
The sequences must not contain BsmBI and BsaI sites! Domestication may be done in order to vanish BsaI and BsmBI sites from the inner sequence.  
  
Line 16: Line 16:
 
• Using BsaI for ‘Le ting vel alpha’ (Level a)
 
• Using BsaI for ‘Le ting vel alpha’ (Level a)
  
But this is not the end, Golden Braid outperforms Golden Gate (which everyone knows) because of the ability to continuously clone TUs in an “exponential”  manner, compared to the linear progression of Golden Gate. Binary assembly of 2 Level Ω (Level 2 for MoClo) result in an alpha vector. Again Binary assembly of 2 alpha result in an omega vector. With this assembly you can insert step by step as many parts and as many TUs you want with high efficiency.
+
But this is not the end, GoldenBraid outperforms Golden Gate (which everyone knows) because of the ability to continuously clone TUs in an “exponential”  manner, compared to the linear progression of Golden Gate. Binary assembly of 2 Level Ω (Level 2 for MoClo) result in an alpha vector. Again Binary assembly of 2 alpha result in an omega vector. With this assembly you can insert step by step as many parts and as many TUs you want with high efficiency.
 
We constructed level α and level Ω plasmids with LacZa insert for blue-white screening. E.coli friendly SEVA plasmids were used as backbones and LacZa insert was taken from the original GB 2.0  pDGB1 vectors [2]. Resulting in vectors with the pDGB1 cassete and restriction enzymes (BsaI, BsmBI).  
 
We constructed level α and level Ω plasmids with LacZa insert for blue-white screening. E.coli friendly SEVA plasmids were used as backbones and LacZa insert was taken from the original GB 2.0  pDGB1 vectors [2]. Resulting in vectors with the pDGB1 cassete and restriction enzymes (BsaI, BsmBI).  
 
pDGB1 vectors have features for plants. On the other hand SEVA plasmids are applicable in all procaryotes [2].  SEVA plasmids are segmented in parts with rare restriction enzymes such us AscI, FseI, PashAI, PacI bordering the features of the plasmid. Two restriction enzymes are between the antibiotic, oriT, replication,etc. Each plasmid can be deconstructed and reconstructed with desirable parts. Also SEVA plasmids are readable in SBOL (Synthetic Biology Open Language).
 
pDGB1 vectors have features for plants. On the other hand SEVA plasmids are applicable in all procaryotes [2].  SEVA plasmids are segmented in parts with rare restriction enzymes such us AscI, FseI, PashAI, PacI bordering the features of the plasmid. Two restriction enzymes are between the antibiotic, oriT, replication,etc. Each plasmid can be deconstructed and reconstructed with desirable parts. Also SEVA plasmids are readable in SBOL (Synthetic Biology Open Language).
Line 25: Line 25:
 
===Experimental Use and Experience===
 
===Experimental Use and Experience===
 
The following parts were cloned in this vector  
 
The following parts were cloned in this vector  
 +
<bbpart>BBa_K3505026</bbpart>
 +
<bbpart>BBa_K3505032</bbpart>
 +
<bbpart>BBa_K3505034</bbpart>
 
<bbpart>BBa_K3505038</bbpart>
 
<bbpart>BBa_K3505038</bbpart>
 
<bbpart>BBa_K3505039</bbpart>
 
<bbpart>BBa_K3505039</bbpart>
  
 
=pDGB1 a2 verification with no insert=
 
=pDGB1 a2 verification with no insert=
[[File:T--Thessaly--alpha2.png|500px|thumb|none|<i><b>Fig.3:</b> pDGB1 a1R with no insert PCR with sequncing primers. Expected band 750bp (LacZa) </i>]]
+
[[File:T--Thessaly--alpha2.png|500px|thumb|none|<i><b>Fig.2:</b> pDGB1 a2 Digested with HindIII. Expected bands 2847, 416, 206 </i>]]
 +
 
 +
===Source===
 +
Christos Batianis[3]
  
 
===Sequence and Features===
 
===Sequence and Features===
Line 38: Line 44:
 
*[1]Alejandro Sarrion-Perdigones, Marta Vazquez-Vilar, Jorge Palací, Bas Castelijns, Javier Forment, Peio Ziarsolo, José Blanca, Antonio Granell, Diego Orzaez (2013). “GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology.” <em>Plant Physiology</em> , 162 (3) 1618-1631; DOI: 10.1104/pp.113.217661
 
*[1]Alejandro Sarrion-Perdigones, Marta Vazquez-Vilar, Jorge Palací, Bas Castelijns, Javier Forment, Peio Ziarsolo, José Blanca, Antonio Granell, Diego Orzaez (2013). “GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology.” <em>Plant Physiology</em> , 162 (3) 1618-1631; DOI: 10.1104/pp.113.217661
 
*[2]Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo, SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts,<em> Nucleic Acids Research</em>, Volume 48, Issue D1, 08 January 2020, Pages D1164–D1170, https://doi.org/10.1093/nar/gkz1024
 
*[2]Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo, SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts,<em> Nucleic Acids Research</em>, Volume 48, Issue D1, 08 January 2020, Pages D1164–D1170, https://doi.org/10.1093/nar/gkz1024
 +
*[3]Damalas, S., Batianis, C., Martin‐Pascual, M., Lorenzo, V. and Martins dos Santos, 2020. SEVA 3.1: enabling interoperability of DNA assembly among the SEVA,
 +
BioBricks and Type IIS restriction enzyme standards. <i>Microbial
 +
Biotechnology</i>, 13(6), pp.1793-1806.

Latest revision as of 20:43, 27 October 2020


pDGB1 alpha 2 (α2) for Bacterial GoldenBraid

Level a vector for GoldenBraid Cloning. Having cargo LacZa for blue white screening between BsaI and BsmBI sites.Resistance in Kanamycin and ori pBBR1 for multiple protein expression capacities.

Fig.1: a2 plasmid Features and Restiction Sites.

Usage and Biology

GoldenBraid (GB) is a DNA assembly strategy for Plant Synthetic Biology based on Type IIS enzymes. It is also compatible for MoClo assembly. The sequences must not contain BsmBI and BsaI sites! Domestication may be done in order to vanish BsaI and BsmBI sites from the inner sequence.

GB proposes an alternative view of modular cloning, and essentially the change is that you can infinitely assemble new vectors by performing “braids”[1]. Using BsmBI another big advantage is the use of a single level 0 vector (pUPD and pUPD2, where pUPD2BBa_K3505007is derived from iGEM-borne pSB1C3) for any GB part one needs. Then combining the desirable fragments from level 0; ‘level alpha’ (level a) cloning is succeeded creating Transcription Units (TU). Desirable TUs are combined to result in (Level Ω) cloning. • Using BsmBI for Level 0 modules and ‘level omega’ (Level Ω) • Using BsaI for ‘Le ting vel alpha’ (Level a)

But this is not the end, GoldenBraid outperforms Golden Gate (which everyone knows) because of the ability to continuously clone TUs in an “exponential” manner, compared to the linear progression of Golden Gate. Binary assembly of 2 Level Ω (Level 2 for MoClo) result in an alpha vector. Again Binary assembly of 2 alpha result in an omega vector. With this assembly you can insert step by step as many parts and as many TUs you want with high efficiency. We constructed level α and level Ω plasmids with LacZa insert for blue-white screening. E.coli friendly SEVA plasmids were used as backbones and LacZa insert was taken from the original GB 2.0 pDGB1 vectors [2]. Resulting in vectors with the pDGB1 cassete and restriction enzymes (BsaI, BsmBI). pDGB1 vectors have features for plants. On the other hand SEVA plasmids are applicable in all procaryotes [2]. SEVA plasmids are segmented in parts with rare restriction enzymes such us AscI, FseI, PashAI, PacI bordering the features of the plasmid. Two restriction enzymes are between the antibiotic, oriT, replication,etc. Each plasmid can be deconstructed and reconstructed with desirable parts. Also SEVA plasmids are readable in SBOL (Synthetic Biology Open Language).

Design Notes

In order to result in an omega vector an alpha 1 and an alpha 2 must be combined. So our TUs are some in the a1R some in a2 and some in both.

Experimental Use and Experience

The following parts were cloned in this vector BBa_K3505026 BBa_K3505032 BBa_K3505034 BBa_K3505038 BBa_K3505039

pDGB1 a2 verification with no insert

Fig.2: pDGB1 a2 Digested with HindIII. Expected bands 2847, 416, 206

Source

Christos Batianis[3]

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 3224
    Illegal XbaI site found at 3251
    Illegal PstI site found at 3263
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 3224
    Illegal PstI site found at 3263
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 3224
    Illegal BamHI site found at 3245
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 3224
    Illegal XbaI site found at 3251
    Illegal PstI site found at 3263
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 3224
    Illegal XbaI site found at 3251
    Illegal PstI site found at 3263
    Illegal NgoMIV site found at 1291
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 3463
    Illegal BsaI.rc site found at 2881


References

  • [1]Alejandro Sarrion-Perdigones, Marta Vazquez-Vilar, Jorge Palací, Bas Castelijns, Javier Forment, Peio Ziarsolo, José Blanca, Antonio Granell, Diego Orzaez (2013). “GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology.” Plant Physiology , 162 (3) 1618-1631; DOI: 10.1104/pp.113.217661
  • [2]Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo, SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D1164–D1170, https://doi.org/10.1093/nar/gkz1024
  • [3]Damalas, S., Batianis, C., Martin‐Pascual, M., Lorenzo, V. and Martins dos Santos, 2020. SEVA 3.1: enabling interoperability of DNA assembly among the SEVA,

BioBricks and Type IIS restriction enzyme standards. Microbial Biotechnology, 13(6), pp.1793-1806.