Freiburg University 2006

From 2006.igem.org

Welcome! We are Alife Mutants.

This term was invented by Martin Schneider on the Rule 110 Winter Workshop in 2004 [http://www.rule110.org/amhso/index.html]. We play without rules. We discover the rules that govern life, the universe and everything to exploit these rules and to create Artificial Life. Our short-time aim is the trip to Boston in November 2006 to take a prize in the iGEM.

The Freiburg Team (well, at least half of it...) from left to right: Irina Petrova, Andrei Kouznetsov, Daniel Hautzinger.

Contents 1 The Team 1.1 Students 1.2 iGEM instructor 1.3 Faculty/staff 2 The project: DNA Folding 2.1 Basic Idea 2.1.1 Abstract 2.1.2 Scetches - Pipes 2.2 Application: Barbie Nanoatelier 2.2.1 Scetches - T-Shirt 2.2.2 Scetches - Bluse 3 GEM Freiburg 3.1 Club 3.2 SB Preliminary 4 Old project ideas 5 Hey Mutant, have a look! 5.1 The easy and serious way 5.2 These people do great things 5.3 Local

The Team

Students

• Daniel Hautzinger
• Olga Soboleva
• Irina Petrova
• Tim Barrel
• Mona Klein

iGEM instructor

• Andrei Kouznetsov

Faculty/staff

• Svetlana Santer

The project: DNA Folding

Basic Idea

Abstract

The idea is to design a strand of DNA such that it wraps into some meaningful shape. There are three different stages for this project: First, the DNA should fold into a two-dimensional rectangular sheet. Secondly, this sheet should wrap itself up into the shape of a short pipe. And last, these little pipes should hook themselves up to each other such that they form one single long pipe.

Scetches - Pipes

The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/pipe/Tube-M13mp18-NEB-d.txt here].

Application: Barbie Nanoatelier

Once the process of DNA folding into 3D-structures is understood, shapes can be chosen arbitrarily. The idea of the Barbie Nanoatelier is that the DNA should wrap into a 3D-TShirt, 3D-Pants, etc.

Scetches - T-Shirt

The DNA sequence for the T-Shirt design can be found [http://omnibus.uni-freiburg.de/~kouznet/t-shirt/T-shirt_M13mp18_NEB_d.txt here], the picture is [http://omnibus.uni-freiburg.de/~kouznet/t-shirt/T-shirt.jpg here], and the staples are [http://omnibus.uni-freiburg.de/~kouznet/t-shirt/T-shirt_staples.txt here] where.

Hey, venture capitalists, where are you? The price of all of 50 billions T-Shirts would be only 7200bases x €0.17/base = €1224. Don’t miss the chance!

Scetches - Bluse

GEM Freiburg

Club

• [http://omnibus.uni-freiburg.de/~kouznet/iGEM.htm Manifesto, Self-education program]
• [http://omnibus.uni-freiburg.de/~kouznet/Fellow06.htm GEM Freiburg Fellow 2006]
• [http://omnibus.uni-freiburg.de/~kouznet/GEMnews.htm News]

SB Preliminary

• DNA plug-and-play platform [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6.pdf 24.05.06] [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6-1.pdf 27.06.06]
• [http://omnibus.uni-freiburg.de/~kouznet/BioVLSI.pdf Very Large-Scale Integration design in Biology]
• [http://omnibus.uni-freiburg.de/~kouznet/GS-design.pdf Genetic systems design from the DNA modules]

Old project ideas

• Life with a price of 6000 €

Hey Mutant, have a look!

The easy and serious way

• [http://www.edge.org/documents/archive/edge187.html#church George Church CONSTRUCTIVE BIOLOGY] - a nice paper about the challenges of modern biology
• [http://webcast.berkeley.edu/events/details.php?webcastid=15766 The webcast from SB2.0]

These people do great things

Albert Libchaber [http://www.rockefeller.edu/research/abstract.php?id=93] Carlos Bustamante's lab [http://alice.berkeley.edu/] David Deamer [http://www.chemistry.ucsc.edu/deamer_d.html] Eric Kool’s group [http://www.stanford.edu/group/kool/] Erik Winfree [http://www.dna.caltech.edu/~winfree/] Fred Menger’s group [http://www.chemistry.emory.edu/faculty/menger/index.html] Jack Szostak’s lab [http://genetics.mgh.harvard.edu/szostakweb/] Norman Packard’s Protolife [http://www.protolife.net/] Pier Luigi Luisi’s group [http://www.plluisi.org/index.html] Radhika Nagpal [http://www.eecs.harvard.edu/~rad/] Steven Benner’s group [http://www.chem.ufl.edu/groups/benner/]

Local

An Analysis of Synthetic Biology Research in Europe and North America [http://www2.spi.pt/synbiology/]

DNA synthesis: ATG-Biosynthetics [http://www.atg-biosynthetics.com/]