Difference between revisions of "Part:BBa K2560010"
Line 5: Line 5:
 
<html>
 
<html>
 
<p align="justify">This is the Phytobrick version of the ribosome binding site <a href="https://parts.igem.org/Part:BBa_B0032">BBa_B0032</a> and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page. </p>
 
<p align="justify">This is the Phytobrick version of the ribosome binding site <a href="https://parts.igem.org/Part:BBa_B0032">BBa_B0032</a> and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page. </p>
 +
</html>
 +
 +
===Overview===
 +
 +
<html>
 +
<p align="justify">
 +
 +
The ribosome binding site (RBS) is a short sequence upstream the transcription start. It can be identified easily by the typical Shine-Dalgarno sequence that pairs with the anti Shine-Dalgarno sequence at the 3’ end of the 16S rRNA
 +
<a href=" https://www.ncbi.nlm.nih.gov/pubmed/7934914"><abbr title =" de Smit MH, van Duin J., Translational initiation at the coat-protein gene of phage MS2: native upstream RNA relieves inhibition by local secondary structure. (1993) 1079-88" >( Smit MH and Duin J van., 1993)</abbr></a>.
 +
The effectiveness of this sequence is determined by its base-pairing potential to the ribosome and its spacing from the start codon
 +
<a href=" http://www.sciencedirect.com/science/article/pii/S0022283605800245"><abbr title =" Maarten H. de Smit, Jan van Duin, Translational initiation on structured messengers: Another role for the shine-dalgarno interaction (1994) 173-184" >( Smit MH and Duin J van., 1994)</abbr></a>. The presence of the RBS is crucial for protein translation.
 +
 +
</p>
 
</html>
 
</html>
  

Revision as of 10:52, 17 October 2018


Phytobrick version of BBa_B0032

This is the Phytobrick version of the ribosome binding site BBa_B0032 and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page.

Overview

The ribosome binding site (RBS) is a short sequence upstream the transcription start. It can be identified easily by the typical Shine-Dalgarno sequence that pairs with the anti Shine-Dalgarno sequence at the 3’ end of the 16S rRNA ( Smit MH and Duin J van., 1993). The effectiveness of this sequence is determined by its base-pairing potential to the ribosome and its spacing from the start codon ( Smit MH and Duin J van., 1994). The presence of the RBS is crucial for protein translation.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Marburg Toolbox

We proudly present the Marburg Collection, a novel golden-gate-based toolbox containing various parts that are compatible with the PhytoBrick system and MoClo. Compared to other bacterial toolboxes, the Marburg Collection shines with superior flexibility. We overcame the rigid paradigm of plasmid construction - thinking in fixed backbone and insert categories - by achieving complete de novo assembly of plasmids.

36 connectors facilitate flexible cloning of multigene constructs and even allow for the inversion of individual transcription units. Additionally, our connectors function as insulators to avoid undesired crosstalk.

The Marburg Collection contains 123 parts in total, including:
inducible promoters, reporters, fluorescence and epitope tags, oris, resistance cassettes and genome engineering tools. To increase the value of the Marburg Collection, we additionally provide detailed experimental characterization for V. natriegens and a supportive software. We aspire availability of our toolbox for future iGEM teams to empower accelerated progression in their ambitious projects.


Figure 3: Hierarchical cloning is facilitated by subsequent Golden Gate reactions.
Basic building blocks like promoters or terminators are stored in level 0 plasmids. Parts from each category of our collection can be chosen to built level 1 plasmids harboring a single transcription unit. Up to five transcription units can be assembled into a level 2 plasmid.
Figure 4: Additional bases and fusion sites ensure correct spacing and allow tags.
Between some parts, additional base pairs were integrated to ensure correct spacing and to maintain the triplet code. We expanded our toolbox by providing N- and C- terminal tags by creating novel fusions and splitting the CDS and terminator part, respectively.


Parts of the Marburg Toolbox




Tags and Entry Vectors




  • K2560001 (Entry Vector with RFP dropout)
  • K2560002 (Entry Vector with GFP dropout)
  • K2560005 (Resistance Entry Vector with RFP Dropout)
  • K2560006 (Resistance Entry Vector with GFP Dropout)
  • K2560305 (gRNA Entry Vector with GFP Dropout)