Team:Carnegie Mellon

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Contents 1 Introduction: Motivation and Background 2 Primary Objective: A Useful BioBrick for Synthetic Biologists 3 Secondary Objective: Humanistic Practice 4 The Team 5 Further Considerations

Introduction: Motivation and Background

• Our primary goal is to introduce novel, engineered BioBricks to the Registry of Standard Biological Parts that can be used as reporters and measurement systems.
• We seek to develop a BioBrick that will allow researchers in the field of synthetic biology to accurately measure a variety of metrics in gene expression networks including translational efficiency and transcriptional strength.

• We hypothesize that we can use Spinach (a fluorescent RNA sequence) and a FAP (fluorogen activating protein) as biosensors to reflect these metrics in vivo (in living cells), rather than in vitro (in a test tube), which has previously proven to be very costly and impractical.

• We will characterize the relationship between the rates of production of Spinach and FAP and the gene's translational efficiency and transcription rate.
  

What is fluorescence, exactly?

Fluorescence is a property of some molecules, particularly aromatic organic dyes that absorb photons at a certain wavelength and emit them at a longer, lower energy wavelength.

Fluorescence is described using quantum mechanics principles and organic chemistry. Five and six-member rings tend to fluoresce brightly because of electron delocalization and the properties that are associated with electron delocalization through the p-orbitals. Fluorescent molecules come in a variety of flavors and uses based on their properties, and shape. Fluorescent molecules are known as fluorophores and can take the form of organic dyes or proteins. So far, many different types of fluorophores have been discovered, developed and studied in great detail. Typically, fluorescent proteins have a fluorophore that consists of a few side chains that react and form a complex similar to that of an organic dye. For example, GFP (the most common fluorescent protein) has an HBI fluorophore. Our Spinach construct binds to a dye that derives from this fluorophore. Fluorescence of a molecule can depend on conformation, in the case of our fluorogen, malachite green, which is a conditional fluorophore, the molecule must be in a certain conformation to fluoresce, otherwise, it will absorb photons, but it will emit them very inefficiently (extremely low quantum yield). Fluorescence is a widely studied phenomena and a lot of research is involved with improving current fluorescence technologies and its applications.

What is Spinach?

Spinach is an RNA sequence that can be expressed in cells (in this case, E. coli ) and fluoresces green when DFHBI (an organic dye) is bound to it that can be used to quantify RNA concentration in a cell. Spinach binds to an organic dye called DFHBI which doesn't fluoresce by itself but fluoresces very brightly when it is bound to Spinach. DFHBI is chemically derived from the chromophore in GFP but is altered to increase brightness when bound to RNA. Other fluorescent RNAs have been described but many are non-specific and have many unwanted functions like cytotoxicity. Other fluorescent RNAs also are difficult to quantify because the cells' RNAses (RNA destroying enzymes) can cut out the fluorescent sequence at unpredictable times, making quantification impractical. Spinach utilizes a scaffold that derives from a tRNA sequence, which disguises the RNA so that RNAses leave it alone. Manipulations to the sequence that Spinach is attached to allows for a variety of analyses functions. RNA can be arranged to bind to just about any small molecule in the same way that Spinach was developed (using a SELEX method) to track cellular metabolites. This allows for quantification of another important system in cells. However, in our system, Spinach is incorporated in the mRNA (between the promoter and the RBS) so mRNA is quantified. Click for more information on Spinach. Spinach is the first published RNA sequence of its kind and more sequence/dye combinations are in development; as a result, in years to come, multiple genes (both RNA and protein) can be analyzed in great detail simultaneously.

What is a FAP?

A fluorogen activating protein is a small (26-35kD) protein that derives from the variable region in an antibody. FAPs are not fluorescent unless a fluorogen (also not normally fluorescent) is added, in which case the FAP changes the conformation of the fluorogen and the complex fluoresces brightly. FAPs are currently used to tag certain proteins like actin or tubulin in mammalian cells. FAPs are not primarily expressed in E. coli although we have expressed certain FAPs in E. coli. The two main dyes that the current series of FAPs bind to are malachite green and thiazole orange; our construct uses a variant that binds to malachite green. These dyes are normally cell impermeable but can be designed to penetrate cell membranes. As a result, they were originally used to tag surface proteins. FAPs are excellent reporters because they are small proteins that are soluble and have virtually no maturation time and are highly photostable unlike traditional variants of GFP. FAP technology is widely unexplored but shows promise for new fluorescent technology. FAPs have been used to track individual molecules to 5nm definition as opposed to the typical 200nm. Engineered dyes, called dyedrons, have been developed that increase fluorescence intensity and can allow researchers to improve on live cell imaging techniques. FAPs are genetically different and respond to different excitation wavelengths so researchers can image multiple proteins at the same time in order to understand complex biological processes.

Why is this project important?

• There are many applications of this technology and it is difficult to speculate how exactly it will be used. However, a BioBrick compatible construct will allow researchers from many different fields to use this system with ease.

• The ability to monitor pathways in cells with fluorescence is a growing field that promises advances in drug development and improving quality control in drug manufacturing.

• This also allows a gateway into analyzing signaling pathways, particularly G-protein coupled receptor (GPCR) pathways. GPCR pathways are the target 30% of prescription drugs on the market and are involved in cell signaling. FAPs are currently used for this research and when this live cell imaging is supplemented with fluorescent RNA, researchers can understand how these pathways function and interact with transcription.

• Our system is designed to be user-friendly for the typical synthetic biologist so that any project in need of an RNA reporter can use it.




Primary Objective: A Useful BioBrick for Synthetic Biologists



Fluorescence Microscopy

We assert that the development of this unprecedented BioBrick will help synthetic biologists in a variety of applications, for a variety of purposes such as the following:

1. Quantifying translational efficiency in vivo
2. Troubleshooting in expression strains
3. mRNA and protein localization
4. in vivo transcription rate analysis
5. Determining promoter strength in vivo
6. Distinguish between promoter strength and RBS (Shine-Dalgarno) strength
7. Determining in vivo mRNA and protein half-lives in real time.
8. Introducing a novel and promising protein reporter that has virtually no maturation rate and is limited only by the very quick absorption rate of the fluorogen into the cell
9. Introducing a functioning mRNA reporter and measurement BioBrick
10. Providing a novel method to characterize current and future BioBricks
11. Developing methods to analyze gene expression networks in vivo without disrupting behavior by fusing our construct to other proteins

Our proposed BioBrick is novel, and potentially very useful in practice.

Secondary Objective: Humanistic Practice

FAQ/Terminology in engineering Escherichia coli to monitor these variables via fluorescence. Find out more about Carnegie Mellon: (CMU Home Page).

As part of our project, we seek to intrigue high school students about synthetic biology and engineering. In this pursuit, we developed an electrical analog of our BioBricks (with a simulated microscope using LEDs and a photoresistor) to teach high school students about:

1. Biological systems and synthetic biology
2. Teamwork in research
3. The interdisciplinary nature of synthetic biology
4. Challenges in interdisciplinary work and how teams overcome these boundaries
5. Gene expression and the central dogma of molecular biology
6. How our BioBrick can be used as a measurement system
7. How scientists tackle real-world problems using an interactive simulation that demonstrates the use of our BioBrick and synthetic biological principles

The Team

The 2012 Carnegie Mellon University iGEM team consists of students from Biology, Electrical and Computer Engineering, Biomedical Engineering and Chemical Engineering.

• Peter Wei
• Yang Choo
• Jesse Salazar
• Eric Pederson
Advisors for the team are from the Chemistry, Biomedical Engineering, Electrical and Computer Engineering, Computational Biology, and Biology departments.

Further Considerations

In the pursuit of our project, as well as the biological aspects, we:

• Considered aspects of scale-up, including the ethical, legal and social implications of our BioBrick,
• Programmed a new piece of software for modeling our BioBrick to students,
• Developed and tested techniques for measuring translational efficiency and transcriptional strength,
• Participated in human practices demonstration and modeled our biological system using a programmable and interactive, electrical analog.
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