Difference between revisions of "Part:BBa K3505007"
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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. | ||
| − | GB proposes an alternative view of modular cloning, and essentially the change is that you can infinitely build 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 pUPD2 is derived from iGEM-borne pSB1C3) for any GBpart one needs. | + | <p>GB proposes an alternative view of modular cloning, and essentially the change is that you can infinitely build 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 pUPD2 is derived from iGEM-borne pSB1C3) for any GBpart 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. | 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 ‘Level alpha’ (Level a) | |
But this is not the end, GoldenBraid outperforms GoldenGate (which everyone knows) because of the ability to continuously clone TUs in an “exponential” manner, compared to the linear progression GoldenGate. Bianry 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 GoldenGate (which everyone knows) because of the ability to continuously clone TUs in an “exponential” manner, compared to the linear progression GoldenGate. Bianry 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. | ||
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===Functional Parameters=== | ===Functional Parameters=== | ||
<partinfo>BBa_K3505007 parameters</partinfo> | <partinfo>BBa_K3505007 parameters</partinfo> | ||
| + | |||
| + | ===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 | ||
Revision as of 19:17, 13 October 2020
pUPD2 for Golden Braid
Level 0 vector for Golden Braid assembly. The Level 0 modules are Interchangable parts in order everyone can use it as it is without any modification based on Golden Braid grammar.LacZa module as cargo between 2 BsmBI sites and 2 BtgzI sites. Resistance in Chloramphenicol and ori pMB1.
Figure 1. The GB2.0 grammar
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.
<p>GB proposes an alternative view of modular cloning, and essentially the change is that you can infinitely build 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 pUPD2 is derived from iGEM-borne pSB1C3) for any GBpart 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 ‘Level alpha’ (Level a)
But this is not the end, GoldenBraid outperforms GoldenGate (which everyone knows) because of the ability to continuously clone TUs in an “exponential” manner, compared to the linear progression GoldenGate. Bianry 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.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal EcoRI site found at 260
Illegal EcoRI site found at 2674
Illegal XbaI site found at 233
Illegal SpeI site found at 627
Illegal PstI site found at 221
Illegal PstI site found at 641 - 12INCOMPATIBLE WITH RFC[12]Illegal EcoRI site found at 260
Illegal EcoRI site found at 2674
Illegal SpeI site found at 627
Illegal PstI site found at 221
Illegal PstI site found at 641
Illegal NotI site found at 634
Illegal NotI site found at 2680 - 21INCOMPATIBLE WITH RFC[21]Illegal EcoRI site found at 260
Illegal EcoRI site found at 2674
Illegal BamHI site found at 239
Illegal XhoI site found at 1658
Illegal XhoI site found at 2550 - 23INCOMPATIBLE WITH RFC[23]Illegal suffix found in sequence at 627
Illegal EcoRI site found at 260
Illegal EcoRI site found at 2674
Illegal XbaI site found at 233
Illegal PstI site found at 221 - 25INCOMPATIBLE WITH RFC[25]Illegal EcoRI site found at 260
Illegal EcoRI site found at 2674
Illegal XbaI site found at 233
Illegal SpeI site found at 627
Illegal PstI site found at 221
Illegal PstI site found at 641 - 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 14
Illegal BsaI.rc site found at 611