Nucleic Acid Engineering
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Contents
Nucleic acid engineering
Mindblowingly cool design of riboswitches, nucleic acid logic circuits, etc.
This page mostly focuses on deliberate attempts to imitate electronic circuit design, and is obviously waaaay incomplete; I haven't even scratched the surface, really. It's strongest for logic gates and suchlike, and very weak on applications and on the chemical diversity of RNA. I haven't even gone near DNA nanotech. (go start a page!)
Literature
...currently a very incomplete list... please add/update!
Logic gates
- Automatic Design of Digital Synthetic Gene Circuits (Marchisio & Stelling)
- Enzyme-Free Nucleic Acid Logic Circuits (Seelig, Winfree et al)
- DNA logic gates with no catalysis required -- everything is done by binding and conformational changes.
- Winfree: a bistable circuit using T7 polymerase and E.coli ribonuclease
- Penchovsky & Breaker: Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat. Biotechnol. 2005;23:1424-33.
- One-shot YES,NOT,AND,OR gates using hammerhead ribozyme
- in silico design pipeline using VIENNA
- RNAfold, RNAinverse, RNAheat, kinRNA
- Rinaudo et al.: A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 2007;25:795-801.
- RNAi logic
- Automated design and programming of a microfluidic DNA computer. M.S. Livstone, R. Weiss & L.F. Landweber. Natural Computing (2006), 5:1-13.
- uses attached heating elements to control DNA annealing
- Rodrigo et al.: De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc. Natl. Acad. Sci. U.S.A. 2012;109:15271-6.
- an evolutionary algorithm
- Ausländer et al.: Programmable single-cell mammalian biocomputers. Nature 2012;487:123-7.
- not just nucleic acids (transcription factors involved too)
Energy
- Seelig et al.: Catalyzed relaxation of a metastable DNA fuel. J. Am. Chem. Soc. 2006;128:12211-20.
- Powering nucleic acid devices with DNA
I/O
- Stojanovic & Kolpashchikov: Modular aptameric sensors. J. Am. Chem. Soc. 2004;126:9266-70.
- noncovalent attachment to fluorophore
- Bayer & Smolke: Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 2005;23:337-43.
- ligand-gated riboswitches, GFP reporter
- Cheah et al.: Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 2007;447:497-500.
- riboswitches in eukaryotes
Need more on aptamers here..
Ethics
- Cello et al.: Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 2002;297:1016-8.
- total synthesis of poliovirus
- ethical implications of this? my grandparents were killed by polio. discuss: what is the justification for building this thing?
- some discussion at FAS
- more in this article in the Indian Journal of Medical Ethics
- apparently it was funded by the military
- Craig Venter: "I think it's inflammatory without scientific justification. To purposely make a synthetic human pathogen is irresponsible."
Design principles, reviews
- Dirks et al.: Paradigms for computational nucleic acid design. Nucleic Acids Res. 2004;32:1392-403.
- rational design principles
- Isaacs et al.: RNA synthetic biology. Nat. Biotechnol. 2006;24:545-54.
- review
Applications
Cancer therapy
- Adele Fielding: measles virus
- Fielding &: Measles as a potential oncolytic virus. Rev. Med. Virol. 2005;15:135-42.
- Bucheit et al.: An oncolytic measles virus engineered to enter cells through the CD20 antigen. Mol. Ther. 2003;7:62-72.
- Journals
Gene therapy
- "Human Gene Therapy: Present and Future"
- review from 1999
- Kimelman et al.: Review: gene- and stem cell-based therapeutics for bone regeneration and repair. Tissue Eng. 2007;13:1135-50.
- bone engineering
- Asif-Ullah et al.: Development of ribozyme-based gene-inactivations; the example of the hepatitis delta virus ribozyme. Curr Gene Ther 2007;7:205-16.
- designed ribozymes and gene therapy
- Jang et al.: Library selection and directed evolution approaches to engineering targeted viral vectors. Biotechnol. Bioeng. 2007;98:515-24.
- directed evolution of viruses for gene therapy
- Journals
- Gene Therapy (Nature group)
- Current Gene Therapy (Bentham)
- Human Gene Therapy (Liebert)
- Molecular Therapy (Elsevier)
need more up-to-date stuff here... this is a huge field
Design tools
Nupack
- Dirks & Pierce: An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem 2004;25:1295-304.
- Dirks et al.: Paradigms for computational nucleic acid design. Nucleic Acids Res. 2004;32:1392-403.
Vienna
http://www.tbi.univie.ac.at/~ivo/RNA/
- Hofacker &: Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31:3429-31.
Sribo
http://sfold.wadsworth.org/sribo.pl
- Ding et al.: Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004;32:W135-41.
RNA-SSD
- Andronescu et al.: A new algorithm for RNA secondary structure design. J. Mol. Biol. 2004;336:607-24.
