CHE.496/2008/Responses/a15

RNA synthetic biology

 * Discussion leader: Brandon Freshcorn (Discussion guide)

Kevin Hershey's Response

 *  RNA Synthetic Biology 
 * RNA Synthetic Biology by Isaacs et. al. discusses the role of RNA in synthetic biology. The idea is to use RNA to regulate gene expression. The use of RNA was very successful in Smolke’s work of getting bacteria to fluoresce different colors depending on the amount of caffeine in the coffee. This paper discusses Chin’s modified ribosomes yet again. The paper then goes on to discuss riboswitches, and their importance in post-translational control. These riboswitches were the small RNA pieces which Smolke used in her work. The paper then goes through many different examples of RNA control, and discusses their importance in rational design.
 *  RNA and RNP as New Molecular Parts in Synthetic Biology 
 * The article by Saito and Inoue discusses the importance of RNA and RNP’s as tools in synthetic biology. They begin by discussing the evolving technology of RNA, and how it can be designed to have a desirable 3D structure by using RNA modular units. RNP’s, which were discovered to counter the fact that articifical ribozymes are very unstable, can also be constructed to give a desired function. This article again discusses Smolke’s use of RNA’s as a regulatory mechanism. However, it does bring home the point that RNA’s and RNP’s can be designed to have a desired function. Thus, RNA’s are a desired material in the growing field of nanotechnology.
 * KPHershey 14:49, 6 April 2008 (EDT)

Patrick Gildea's Response

 *  RNA Synthetic Biology 
 * The purpose of this article is to review the role of RNA in synthetic biology, especially with respect to regulating gene expression and altering cellular behavior. One of the examples of utilizing RNA for gene expression is the riboregulator by Chin, for which we have already read about in other papers. Furthermore, Box 1 in the paper is a really good summary of the different tools that can modify the behavior of cellular functions listed by class, mechanism, and their activity. Another interesting tool that is listed is the ribosome-mRNA pairs that can target certain proteins and regulate their expression. There are also other tools that can affect translation listed in the paper. Furthermore, Box 2 lists the use of RNA to increase the precision of molecular switches. If we ever need to fine-tune a switch in order to make it more precise because of other factors such as stoichastic effects. Instead of depending on a DNA based switch – we could go with a RNA regulatory molecule to adjust the behavior, etc.
 *  RNA and RNP as New Molecular Parts in Synthetic Biology 
 * I could not access the pdf or the text based link on science-direct. Tried looking for other sources (only pubmed is available and still can't get it there).
 * Patrick Gildea 20:50, 8 April 2008 (EDT):

Eyad Lababidi's Response
Eyad Lababidi 18:56, 10 April 2008 (EDT)
 *  RNA and RNP as New Molecular Parts in Synthetic Biology 
 * This article by Saito starts by saying that synthetic biology is facing two problems, firs that there are not many very well understood parts and second that the networks have been simple because complex networks will face problems with crosstalk. The article goes on to say that RNA can be used for modular units and synthetic RNAs can be built. This opens up new possibilities for parts and devices that could be used in our toy cells. After explaining how an RNP enzyme can be synthetically produce the article discuses the use of RNA/RNP as switches that could be allosterically controlled. This is important because having a variety of dependable switches is the beginning to a network as is seen in any integrated circuit.