Revision as of 17:34, 20 October 2009

5. 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 alltogether 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.

Development of BioBricks

Linker-extension standard

A new developed linker-extension standard is also described in detail under BBF RFC37(link to http://dspace.mit.edu/bitstream/handle/1721.1/46705/BBFRFC37.pdf?sequence=1) To improve the efficacy of cloning, we designed a NEW BioBrick standard that enables simplified and efficient linker extension between protein domains (link to Figure 0) and at the same time preserve the characteristics of the most extensively used BioBrick standards. Two variations of linker-extension standard were designed. Both variations contain 5' and 3' cloning restriction sites EcoRI, PstI, NotI, XbaI and SpeI characteristic for BBa standard (Figure 1 - link). Additionally, core restriction sites NgoMIV, AgeI, XmaI, BspEI are added. These restriction sites are used for linker extension and their positions differ among two variations of linker-extension standard. The position and the usage of these core restriction sites determine amino acid residues incorporated in the linker between protein domains (Figure 2 - link).

News

Our standard has been approved!

Description of the improved BioBrick Standard has been added. For more info see: BioBricks & Standard

Wisdom of the day

A daily piece of semi-random wisdom (respectfully taken from http://www.phdcomics.com/):

Preliminary project description

Self-assembly is one of the important properties of biological systems. Application of this principle along with the ability to genetically encode the modular building blocks could revolutionize manufacturing, particularly since the self-assembled structures in nature span from the nano- to the macroscopic scale.

We plan to investigate the feasibility and potentials of BioBricks principle to prepare structural elements that will self-assemble into the defined structures that could be used for different applications, from materials sciences to health.

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 __NOTOC__
-=Abstract=
+=5. BioBRICKS=
-=== ''nanoBRICKs'' – synthetic smart nanomaterials from nano to macro ===
+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 alltogether 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.
-Nanotechnology designs materials with advanced properties based on the control of structure at the nanoscale. Biological systems provide an attractive opportunity to design and easily manufacture material with programmable properties. DNA origami demonstrated the power of this technology by creating a variety of assemblies that can be easily encoded in the nucleotide sequence. However, for biological nanodevices nature favors polypeptides over nucleic acids due to stability and versatility of amino-acid side chains. With few exceptions protein and peptide assemblies have been considered too difficult for the bottom-up design due to complex interactions and manufacturing problems specific for each case. We present technology for manufacturing nanomaterials based on combinations of modular peptide elements and protein domains, which allow self-assembly into complex tertiary structures with designed macroscopic properties. We will demonstrate the feasibility and potentials of protein nanotechnology by design, streamlining the production and technological application of nanomaterials based on ''nanoBRICKs''.
+== Development of BioBricks ==
+=== Linker-extension standard ===
+A new developed linker-extension standard is also described in detail under BBF RFC37(link to http://dspace.mit.edu/bitstream/handle/1721.1/46705/BBFRFC37.pdf?sequence=1)
+To improve the efficacy of cloning, we designed a NEW BioBrick standard that enables simplified and efficient linker extension between protein domains (link to Figure 0) and at the same time preserve the characteristics of the most extensively used BioBrick standards.
+Two variations of linker-extension standard were designed. Both variations contain 5' and 3' cloning restriction sites EcoRI, PstI, NotI, XbaI and SpeI characteristic for BBa standard (Figure 1 - link). Additionally, core restriction sites NgoMIV, AgeI, XmaI, BspEI are added. These restriction sites are used for linker extension and their positions differ among two variations of linker-extension standard. The position and the usage of these core restriction sites determine amino acid residues incorporated in the linker between protein domains (Figure 2 - link).

Development of BioBricks.html

From 2009.igem.org