Team:TU Munich

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Welcome to the iGEM Team of the Technische Universität München.


Contents

Preliminary Project Description

Molecular Networks and State of the Art

A fundamental task in the creation of a new biological systems is the development of sophisticated and flexible logic networks. A logic network responds to incoming signals and creates output signals in a precisely determined manner. This is accomplished by interconnecting and rearranging basic logical units. Until now, several types of networks have been developed using logical units such as riboswitches or genetic switches. However, these biological logic units relied mainly on protein-based or metabolite-based interactions, which remain poorly understood. The undissolved de novo creation of specific protein or metabolite interactions limits the ability to design large networks of sufficient complexity.

Project Goals

To overcome the limitations mentioned above, our goal is to design a new type of logical unit. This novel "switch" has to be capable of building up logic gates which in turn can form a complex network. To fulfill this requirement, we used the main principle of electric circuits as template. An electric circuit consists of several transistors and interconnecting wires. Whereas all transistors are built equally, wires generate a specific addressing resulting in the desired logic operation. For our switch, each logic units contains a recognition element for addressing and a switching core resembling the transitor. To implement this basic concept, the recognition site uses specific RNA-RNA-hybridization, the switching core is designed in the style of transcriptional termination/antitermination processes occuring in nature.

Current work

Currently we are developing an assay to screen several termination processes in vivo and in vitro to obtain an optimized switching core, capable of antitermination and compatible to our recognition site. Future work will focus on fine-tuning one or more switching candidates. The goal is to establish a robust switching core as module, which can simply and specifically be addressed by varing the sequence of the recognition site.


Abstract Among the goals of iGEM is the creation of synthetic biological parts and their utilization to achieve novel features and behavior in biological systems. The emphasis of our project is put on this latter, "systems" aspect of iGEM. More precisely, we aim at the development and experimental demonstration of a scalable approach for the realization of logical functions in vivo. By developing a computational biological network based on RNA logical devices we will offer everyone the opportunity to 'program' their own cells with individual AND/OR/NOT connections between BioBricks of their choice. Thereby, BioBricks can finally fulfill their original assignment as biological parts that can be connected in many different ways. We will achieve this by engineering simple and easy-to-handle switches based on predictable RNA/RNA-interactions regulating transcriptional termination. These switches represent a complete set of logical functions and are capable of forming arbitrarily complex networks.

Zusammenfassung Das Entwerfen von neuen Bausteinen für die synthetische Biologie und ihr Zusammenfügen, um neue Funktionen und Charakteristika in biologische System zu bringen, sind mit die Hauptziele des iGEM-Wettbewerbes. Dabei wollen wir uns besonders auf letzteres konzentrieren und suchen eine systemische Anwendung von iGEM-Bausteinen zu etablieren. Unser Ziel ist es, einen skalierbaren Ansatz zu entwerfen, mit dem biologische Teile in vivo zu einem skalierbaren Netzwerk zusammengefügt werden können, das fähig ist zur logischen Informationsprozessierung. Durch die Entwicklung eines biologischen Netzwerkes, das analog zu einem Computer aufgebaut ist, bieten wir allen die Mögichkeit, Zellen zu programmieren und logische Netzwerke basierend auf AND/OR/NOT-Verbindungen zwischen Biobrick-Parts zu entwickeln. Dadurch können Biobricks auch endlich ihre Funktion als biologische Bausteine, die beliebig miteinander verknüpft werden können, erfüllen. Um das zu erreichen, haben wir einfache und benutzerfreundliche Schalter basierend auf berechenbaren RNA-RNA-Interaktion konstruiert, die durch Antitermination schalten können. Mit Hilfe dieser Schalter kann man komplette logische Funktionen aufbauen und beliebig komplexe Netzwerke entwerfen.


(Abstrait) L'un des plusieurs buts d'iGEM est la création des parties biologiques synthétiques qui peuvent être utiliser pour découvrir des nouvelles caractéristiques et comportements des systèmes biologiques. L'accent de notre projet est mis sur ce dernier aspect de "systèmes". Plus précis, notre objectif et de réaliser des fonctions logiques in vivo sur la base d'une approche expérimentale. En développant un réseau biologique et quantificatif à l'aide des structures logiques de l'ARN, nous offrirons à chacun la possibilité de programmer ses propres cellules avec les connexions AND/OR/NOT individuelles entre les biobriques de son choix. Ainsi, les biobriques peuvent finalement réaliser leur fonction initiale: alors comme parties biologiques qui peuvent être connecter de plusieurs façons différentes. Nous atteignons cela avec des interrupteurs facile à commander. Ils sont installés d'après le modèle des interactions ARN/ARN et régulent aussi l'achèvement transcriptional. Ces interrupteurs représentent un ensemble complet des fonctions logiques et ils sont arbitrairement capables de former des réseaux complexes. 


    Abstract
   Unul dintre scopuri dela iGEM este a crea părţi artificiale bioligice care se pot utiliza pentru descoperirea unor caracteristici noi într-un sistem biologic. Accentul proiectului nostru este pus pe punctul de "sistem" al-ui iGEM. Mai exact, scopul nostru este să demonstrâm funcţi logice "in vivo" prin ataşare şi dezvoltare continuă. 

   Proiectul iGem dezvolta prin calcul o reţea biologica, cu componente basate pe logica acidului ribonucleic. Aşa oferim tuturor posibilitatea să controleze celulele lor cu o legatură (AND/OR/NOT) între BioBricks care sunt alese individual. Ca părţi biologice care pot fi conectate în mai multe moduri diferite, BioBricks poate îndeplini sarcina iniţială. Vom realiza acest lucru prin întrerupătoare simple şi uşoare de manevrat care sunt bazate pe interacţiuni ARN/ARN  previsibile şi care controlează încetarea transcripţională. Aceste întrerupătoare reprezintă un set complet de funcţii logice şi sunt capabile să formeze arbitrar reţele complexe.

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