Designing and using RNA scaffolds to assemble proteins in vivo

RNA scaffolds are synthetic noncoding RNA molecules with engineered 3D folding harnessed to spatially organize proteins in vivo. Here we provide a protocol to design, express and characterize RNA scaffolds and their cognate proteins within 1 month. The RNA scaffold designs described here are based on either monomeric or multimeric units harboring RNA aptamers as … Read moreDesigning and using RNA scaffolds to assemble proteins in vivo

JBEI-ICE, part registry platform and tools

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsisseeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code (http://code.google.com/p/gd-ice/) , a hosting site for community-driven open source projects.

 

Maximum expected accuracy structural neighbors of an RNA secondary structure

Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure.

 

Source code for RNAborMEA can be downloaded from http://sourceforge.net/projects/rnabormea/ or http://bioinformatics.bc.edu/clotelab/RNAborMEA/

Apps Collections for Synthetic Biology

 

Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization [1]. Here are bio-apps collections for you. Personally Tinkercell and UNAFold are mostly used.

Circuit design and simulation
 Biojade http://web.mit.edu/jagoler/www/biojade/
 Tinkercell http://www.tinkercell.com/Home
 Asmparts http://soft.synth-bio.org/asmparts.html
 ProMoT http://www.mpimagdeburg.mpg.de/projects/promot
 GenoCAD http://www.genocad.org/genocad/
 GEC http://research.microsoft.com/gec
 TABASCO http://openwetware.org/wiki/TABASCO#TabascoSimulator
 Hy3S http://hysss.sourceforge.net/index.shtml
Circuit optimization
 Genetdes http://soft.synth-bio.org/genetdes.html
 RoVerGeNe http://iasi.bu.edu/∼batt/rovergene/rovergene.htm
DNA and RNA design
 Gene Designer https://www.dna20.com/index.php?pageID=220
 GeneDesign http://www.genedesign.org
 UNAFold http://www.bioinfo.rpi.edu/applications/hybrid/download.php
 mfold http://mfold.bioinfo.rpi.edu/download/
 DINAMelt http://dinamelt.bioinfo.rpi.edu/
 Vienna RNA package http://www.tbi.univie.ac.at/∼ivo/RNA/
 Vienna RNA web servers http://rna.tbi.univie.ac.at/
 Zinc Finger Tools http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
Protein design
 Rosetta http://www.rosettacommons.org/main.html
 RAPTOR http://www.bioinformaticssolutions.com/products/raptor/index.php
 HHpred http://toolkit.lmb.uni-muenchen.de/hhpred
 Modeler http://salilab.org/modeller/
 PFP http://dragon.bio.purdue.edu/pfp/
 Autodock 4.2 http://autodock.scripps.edu/
 HEX 5.1 http://webloria.loria.fr/∼ritchied/hex/
Integrated workflows
 SynBioSS http://synbioss.sourceforge.net/
 Clotho http://biocad-server.eecs.berkeley.edu/wiki/index.php/Tools
 Biskit http://biskit.sf.net

 

Suggested pages listing useful bio-apps maybe you will like in synthetic biology research:

  1. WikiGenes Toolbox ( http://www.wikigenes.org/e/art/e/187.html). As a free on-line tutorial edited by people all around the world, WikiGenes has spirits of Linux: open-source, sharing, interest, so is WikiGenes-Synthetic-Biology page. It enables you fast-learn what is synthetic life.
  2. OpenWetWare (http://openwetware.org/wiki/Computational_Tools).
  3. JCVI (http://www.jcvi.org/cms/research/software/#c614). This page is from J. Craig Venter Institute.

 

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[1] Marchisio, M. A., & Stelling, J. (2009). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 20(4), 479-485. Retrieved from http://www.sciencedirect.com/science/article/pii/S0958166909001001

DNA Nanotechnology Kills Cancer

Here I recommend you a wonderful bio-app, named: caDNAno. The open-source software, caDNAno,  will enables you  design  three-dimensional DNA origami nanostructures. You can fold your DNA in any shapes. One of the features is no programming required, thus even our kids can give it a try, and perhaps can get a Science paper published [1]. What will … Read moreDNA Nanotechnology Kills Cancer