Team:Slovenia/Biobrick

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The goal of our project was to investigate and demonstrate the feasibility of polypeptide assembly based on modular nanoBricks. Potentials of this approach are vast (see Discussion and Vision) and for the development of applications it is essential to have available a large collection of “nuts and bolts” to assemble polypeptide nanostructures. We produced all together more than 100 BioBricks, which comprise a significant number of different natural as well as designed coiled-coil forming segments as well as different polypeptide oligomerization domains. In addition we prepared several “functional polypeptides”, which provide additional useful features to the material, such as different biological activities (antimicrobial peptide, growth factors, cell attachment motifs…), optical properties, enzymatic activity...
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On the other hand we extended the BioBrick standard by introducing sites that allow extension of peptide linker sequences. Length of the linkers between polypeptide domains is crucial to determine the accessible geometry of the assembly, and our extended standard provides a tool to extend the length of a linker by any required length in increments of two residues. This task, particularly concerning small extensions would otherwise require the preparation of a new domain construct.
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=Improved BioBrick Standard=
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For further information see:
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For a multitude reasons we would like to work with the upgrade of 2007 Freiburg iGEM proposed standard (Assembly standard 25). The upgrade includes altered multiple-cloning site which enables friendly scar after part ligation and simple extension of linker between parts.
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=====Advantages:=====
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**in-frame fusion of protein parts
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**benign protein scar/scars
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<li><a href="https://2009.igem.org/Team:Slovenia/Linker-extension_standard.html" class="plavo">Linker-extension standard</a><br /></li>
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**preserving standard restriction sites of prefix and suffix
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<li><a href="https://2009.igem.org/Team:Slovenia/nanoBRICKs.html" class="plavo">nanoBRICKs PRO</a><br /></li>
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**four new restriction sites are added in multiple-cloning site
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**heat inactivation??
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<li><a href="https://2009.igem.org/Deposited_BioBricks.html" class="plavo">Deposited BioBRICKS</a><br /></li>
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**no Dam methylation problem for XbaI
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**stand-alone protein expression
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<li><a href="https://2009.igem.org/Favourite_Parts.html" class="plavo">Favourite Parts</a><br /></li>
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**full BBb compatibility and
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**blunt-cutting isochizomer of NgoMIV (NaeI) and XmaI (SmaI) possibility of directional cloning with two
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restriction enzymes enables part transfer between different formats and other potentially interesting transfer reactions
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=====Disadvantages:=====
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**unexpected site effects for users not aware of different prefix/suffix
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**N-parts could be assembled with different enzyme combination
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**not compatible to BioFusion format (frame shift; stop codon)
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**not compatible to BBb format (Berkeley format)
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**additional limitations on the nucleotide sequence to avoid additional restriction sites
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Here we describe sequence properties of modified vector BioBrick-NIC-II. All sequences defined herein are specified in the 5' to 3' direction.
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Latest revision as of 02:48, 22 October 2009


BioBRICKS


The goal of our project was to investigate and demonstrate the feasibility of polypeptide assembly based on modular nanoBricks. Potentials of this approach are vast (see Discussion and Vision) and for the development of applications it is essential to have available a large collection of “nuts and bolts” to assemble polypeptide nanostructures. We produced all together more than 100 BioBricks, which comprise a significant number of different natural as well as designed coiled-coil forming segments as well as different polypeptide oligomerization domains. In addition we prepared several “functional polypeptides”, which provide additional useful features to the material, such as different biological activities (antimicrobial peptide, growth factors, cell attachment motifs…), optical properties, enzymatic activity...

On the other hand we extended the BioBrick standard by introducing sites that allow extension of peptide linker sequences. Length of the linkers between polypeptide domains is crucial to determine the accessible geometry of the assembly, and our extended standard provides a tool to extend the length of a linker by any required length in increments of two residues. This task, particularly concerning small extensions would otherwise require the preparation of a new domain construct.





For further information see:



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