GcatWiki - User contributions [en]

T7RNAp information page.

2011-06-21T16:46:50Z

Cbarta:

[http://www.bio.davidson.edu/courses/genomics/lab/proteomics/t7rnapframe.html] 3D computer model of T7RNAp in elongation phase. Found on Davidson's website.

[http://www.nature.com/emboj/journal/v17/n14/full/7591110a.html] Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme

[http://academic.brooklyn.cuny.edu/chem/zhuang/Nicolas/structur.htm] Structural characterization of T7 RNAp

[http://www.euchromatin.net/Durniak01.html] Structure of Transcribing T7 RNAp. If you scroll down the page you find structural diagrams of T7 RNA in the initiation, intermediate, and elongation complexes.

[http://protein.bio.msu.su/biokhimiya/contents/v67/pdf/bcm_1124.pdf] Structural–Functional Analysis
of Bacteriophage T7 RNA Polymerase

[http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1996.00234.x/pdf] Use of T7 RNA polymerase in an optimized Escherichia coZi
coupled in vitro transcription-translation system
Application in regulatory studies and expression of long transcription units

T7RNAp information page.

2011-06-21T16:27:08Z

Cbarta:

T7RNAp information page.

2011-06-21T16:26:50Z

Cbarta:

T7RNAp information page.

2011-06-21T16:08:56Z

Cbarta:

T7RNAp information page.

2011-06-21T16:08:15Z

Cbarta:

T7RNAp information page.

2011-06-21T16:03:01Z

Cbarta: Created page with '[http://www.bio.davidson.edu/courses/genomics/lab/proteomics/t7rnapframe.html] 3D computer model of T7RNAp in elongation phase. Found on Davidson's website.'

[http://www.bio.davidson.edu/courses/genomics/lab/proteomics/t7rnapframe.html] 3D computer model of T7RNAp in elongation phase. Found on Davidson's website.

Missouri Western/Davidson SynBio 2011

2011-06-21T16:00:59Z

Cbarta:

This space will be used starting May, 2011 for brainstorming and a shared whiteboard space. 

[[Davidson Protocols]] 
[[MWSU_protocols]] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
[[Laboratory_Notebooks]] 
[[Data Folder 2010]] 
[[DNA computing]] 
[[Golden Gate]] 
[[HPP Status]] 
[[HPP Oligos 6-9-11]] 
[[Set Covering Problem]] 
[[T7RNAp information page.]]

DNA computing

2011-06-02T17:59:20Z

Cbarta:

'''DNA Computing PPT Concepts''' 

Golden Gate HPP Concept: [[Media:GoldenGate_HPP.pptx]]
 

HPP DNA computer idea: [[Media:HPP_DNA_computer_MWSU_2011.pptx‎ ]]

<hr>

'''DNA Computing Papers''' 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/6/62/Adelman_1994.pdf Adleman 1994] First DNA computer, used to solve 7-node, 14-edge HPP 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/2/22/Benneson_review_2009.pdf Benneson review 2009] Review of DNA computers in terms of Tiling systems, State Machines, Logic Networks. 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/a/a2/Chen_1999.pdf Chen 1999] DNA Comuting Implementing Genetic Algorithms

[http://gcat.davidson.edu/mediawiki-1.15.0/images/6/64/ShapiroNature2004.pdf ShapiroNature2004] DNA computer to analyze mRNA levels 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/6/68/Roweis_stickers_1996.pdf Roweis stickers 1996] A sticker based model for DNA computation 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/9/93/Rothemund_2000.pdf Rothemund 2000] DNA computing by self-assembly 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/4/44/Benneson_2003.pdf Benneson 2003] DNA computer using restriction and ligation 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/4/45/Bonehetal_1996.pdf Boneh 1996] Review on the computational power of DNA 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/e/e3/Adleman_SciAm.pdf Adleman Scientific American] Good introduction to Adleman HPP experiment 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/f/fa/Adleman_Data_Encryption_Standard_1999.pdf Adleman Data Encryption Standard 1999] Proposal to use the Sticker Model to attack the US Data Encryption Standard 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/d/d5/Aspects_of_Biomolecular_Computing.pdf] An overview of Biomolecular computing including a summary of DNA computing and a section on the limitations of such computing 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/0/07/DNA_computing_in_vitro_and_in_vivo.pdf] DNA computing in vitro and in vivo. An overview illustrating the differences between in vitro and in vivo DNA computing. 2001.

[http://gcat.davidson.edu/mediawiki-1.15.0/images/7/77/DNA_Computing_on_surface.pdf] The principle of the technique has been demonstrated experimentally for a simple example of the Hamiltonian path problem 

[http://gcat.davidson.edu/mediawiki-1.15.0/images/6/6f/Ravinderjit_2000.pdf Ravinderjit 2000] Using a gel based DNA computer to solve a 6-variable 11-clause 3-SAT problem 

Molecular Computation by Hairpin Formation; [http://gcat.davidson.edu/GcatWiki/images/3/39/Sakamoto_DNA_computer_3SAT.pdf Sakamoto et al.]

Need full text from this paper: Solution of a 20-Variable Problem on a DNA Computer. Published in 2002 by Adleman. http://www.sciencemag.org/content/296/5567/499.short

Need full text from this paper: DNA-Based Computing of Strategic Assignment Problems, http://prl.aps.org/abstract/PRL/v106/i18/e188702

Criticism of DNA-Based Computing of Strategic Assignment Problems: http://arstechnica.com/science/news/2011/05/is-dna-computing-going-to-terminate-internet-banking.ars

File:DNA computing in vitro and in vivo.pdf

2011-06-02T17:56:17Z

Cbarta: