Difference between revisions of "Help:Assembly/Scars"

(Created page with "{{CSS/DNA_Table}} Scars are a byproduct of assembling samples of DNA parts together. Assembly systems that follow an assembly standard (BioBrick RFC10, iGEM Type IIS, etc.) c...")
 
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Scars are a byproduct of assembling samples of DNA parts together. Assembly systems that follow an assembly standard (BioBrick RFC10, iGEM Type IIS, etc.) create predictable scars between assembled parts. Some assembly systems can result in "scar-less" assembly (Synthesis, Gibson, "bespoke" Type IIS).
 
Scars are a byproduct of assembling samples of DNA parts together. Assembly systems that follow an assembly standard (BioBrick RFC10, iGEM Type IIS, etc.) create predictable scars between assembled parts. Some assembly systems can result in "scar-less" assembly (Synthesis, Gibson, "bespoke" Type IIS).
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It's important to know what scars, if any, will be in your designed composite parts and how to specify them on the Registry.
  
  
 
When two BioBrick part samples are assembled together to create a new BioBrick composite part, a scar forms between the subparts with the cohesive ends left by XbaI and SpeI digestion ligating together.
 
When two BioBrick part samples are assembled together to create a new BioBrick composite part, a scar forms between the subparts with the cohesive ends left by XbaI and SpeI digestion ligating together.
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Generally, scars do not provide or code for a function, like a promoter, ribosome binding site, or terminator, so they are not considered a basic part. However, they may still serve a purpose within a composite part through intentional design. Most often, this may be as a small spacer or linker region.  
 
Generally, scars do not provide or code for a function, like a promoter, ribosome binding site, or terminator, so they are not considered a basic part. However, they may still serve a purpose within a composite part through intentional design. Most often, this may be as a small spacer or linker region.  
  
As an example, the 6bp scar formed when assembling BioBrick samples of the BBa_B0034 (RBS) and BBa_E1010 (CDS) results in more optimal spacing thn
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As an example, the 6bp scar formed when assembling BioBrick samples of the BBa_B0034 (RBS) and BBa_E1010 (CDS) results in more optimal spacing for the RBS and the start codon of the CDS, where a larger or smaller scar would cause issues with translation.
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===Specifying Scars===
 
===Specifying Scars===
The composite part editor on the "Edit sequence and features" page allows users to specify scars inbetween your subparts.  
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Scars are only specified on composite parts, in between subparts. After you've added a composite part, you can specify scars between subparts on the "Edit sequence and features" page.
  
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Scars are specified through square bracket "[]" notation, either through a shorthand or entering an exact sequence. 
  
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<html>
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<center>
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<table class="dnaTable">
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<tr>
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<th>Assembly System</th>
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<th>Notation</th>
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<th>Sequence</th>
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</tr>
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<tr>
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<td>Blunt (no scar)</td>
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<td>[0]</td>
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<td class="dnaSeq"></td>
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</tr>
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<tr>
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<td>BioBrick</td>
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<td>[10]</td>
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<td class="dnaSeq">TACTAGAG</td>
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</tr>
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<tr>
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<td>BioBrick (RBS-CDS)</td>
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<td>[10]</td>
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<td class="dnaSeq">TACTAG</td>
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</tr>
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<tr>
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<tr>
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<td>User-specified</td>
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<td>[AATG]</td>
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<td class="dnaSeq">AATG</td>
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</tr>
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</tr>
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</table>
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</center>
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</html>
  
===Example===
 
 
 
 
Normally scars do not provide a function, but can serve purposes. As an example the BioBrick
 
  
  
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===Example===
  
 
Here we have four Registry parts that we will use in the design of our composite part device, an RFP generator.
 
Here we have four Registry parts that we will use in the design of our composite part device, an RFP generator.

Revision as of 21:07, 15 August 2019

Scars are a byproduct of assembling samples of DNA parts together. Assembly systems that follow an assembly standard (BioBrick RFC10, iGEM Type IIS, etc.) create predictable scars between assembled parts. Some assembly systems can result in "scar-less" assembly (Synthesis, Gibson, "bespoke" Type IIS).

It's important to know what scars, if any, will be in your designed composite parts and how to specify them on the Registry.


When two BioBrick part samples are assembled together to create a new BioBrick composite part, a scar forms between the subparts with the cohesive ends left by XbaI and SpeI digestion ligating together.


Function

Generally, scars do not provide or code for a function, like a promoter, ribosome binding site, or terminator, so they are not considered a basic part. However, they may still serve a purpose within a composite part through intentional design. Most often, this may be as a small spacer or linker region.

As an example, the 6bp scar formed when assembling BioBrick samples of the BBa_B0034 (RBS) and BBa_E1010 (CDS) results in more optimal spacing for the RBS and the start codon of the CDS, where a larger or smaller scar would cause issues with translation.


Specifying Scars

Scars are only specified on composite parts, in between subparts. After you've added a composite part, you can specify scars between subparts on the "Edit sequence and features" page.

Scars are specified through square bracket "[]" notation, either through a shorthand or entering an exact sequence.

Assembly System Notation Sequence
Blunt (no scar) [0]
BioBrick [10] TACTAGAG
BioBrick (RBS-CDS) [10] TACTAG
User-specified [AATG] AATG


Example

Here we have four Registry parts that we will use in the design of our composite part device, an RFP generator.

These parts are compatible with both BioBrick RFC10 and iGEM Type IIS RFC1000. They do not have recognition sites for restriction enzymes that are used in either assembly standard.