SynBioFromLeukipposInstitute

systems. However, based on a survey of 100 publications, we find that a majority of the publications does not report critical experimental settings of plate-reader assays, suggesting wide spread issues in their reproducibility. Specifically, critical plate-reader settings, including shaking time and covering method, either vary between labs or are not reported by the publications. Here, we demonstrate that the settings of plate-reader assays have significant impact on bacterial growth, recombinant gene expression, and biofilm formation. Furthermore, we show that the plate-reader settings affect the apparent activity, sensitivity, and chemical kinetics of synthetic constructs, as well as alter the apparent effectiveness of antibiotics. Our results suggest the critical need for consistent reporting of plate-reader protocols, in order to ensure the reproducibility of the protocols. In addition, our work provides data for the setup of plate-reader protocols in synthetic biology experiments.

RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

Extreme makeover: protein edition

The details of CRISPR, the new genome-editing tool, baffled Science magazine reporter Jon Cohen so he decided to run his own experiment with the help of scientist Roland Wagner at the Sanford Burnham Prebys Medical Discovery Institute in San Diego, California. Cohen had heard that “any idiot” could do CRISPR, so his experiment tests this hypothesis. As he hoped, conducting a CRISPR experiment with his own hands clarified how it actually works and what the challenges are to properly carrying out the cutting of DNA. But to find out whether any idiot can do it, read the story.

In its “grand challenge” format in chemistry, “synthesis” as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work.

The field of drug delivery has grown tremendously in the past few decades by developing a wide range of advanced drug delivery systems. An interesting category is cell-based drug delivery, which includes encapsulation of drugs inside cells or attached to the surface and subsequent transportation through the body. Another approach involves genetic engineering of cells to secrete therapeutic molecules in a controlled way. The next-generation systems integrate expertise from synthetic biology to generate therapeutic gene networks for highly advanced sensory and output devices. These developments are very exciting for the drug delivery field and could radically change the way we administer biological medicines to chronically ill patients. This review is covering the use of living cells, either as transport system or production-unit, to deliver therapeutic molecules and bioactive proteins inside the body. It describes a wide range of approaches in cell-based drug delivery and highlights exceptional examples.