CH391L/S13/DnaAssembly
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| - | ==Oligonucleotide Synthesis== | + | [[Category:CH391L_S13]] |
| + | |||
| + | ==Introduction== | ||
| + | |||
| + | A large number of parts have been made by the synthetic biology community. Many can be found as part of the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]. These modular genetic components are designed to be easy to assemble to facilitate the building of more complex biological devices. To learn more about the Registry and BioBricks™, see [[CH391L/S12/iGEM Registry | last year's]] wiki page. | ||
| + | |||
| + | Synthetic biology relies on the ability to make testable biological units. This means that the ability to gather, manipulate, or even create genetic material is vital for "doing" synthetic biology. The techniques employed by synthetic biologists include oligonucleotide synthesis, restriction enzyme digestion, ligase, pcr, and recombination (homology). | ||
| + | |||
| + | Trying to get from genes to genomes. | ||
| + | |||
| + | ==DNA Synthesis== | ||
| + | ===Oligonucleotide Synthesis=== | ||
[http://en.wikipedia.org/wiki/Oligonucleotide_synthesis from wikipedia] <br> | [http://en.wikipedia.org/wiki/Oligonucleotide_synthesis from wikipedia] <br> | ||
| - | ==Gene Synthesis== | + | ===Gene Synthesis=== |
| - | + | IDT Gene Blocks <br> | |
| + | DNA2.0 <br> | ||
| + | invitrogen (life technologies, geneart) <br> | ||
| + | genscript <br> | ||
| + | celtek <br> | ||
| + | biobasic <br> | ||
| + | sigma? <br> | ||
| + | GENEWIZ <br> | ||
| + | biomatik <br> | ||
| + | OriGene (blue heron) <br> | ||
| + | Epoch Life Science <br> | ||
| - | + | References <br> | |
| + | Cost <br> | ||
| + | Time <br> | ||
| - | + | ==Molecular Cloning== | |
| - | + | ||
| - | + | ||
| + | ===Restriction Enzyme=== | ||
| + | BioBricks <br> | ||
| + | BglBricks <br> | ||
| + | [[The_BioBricks_Foundation:Standards/Technical/Formats | list]] of BioBrick Foundation Standards <br> | ||
| - | + | ===Polymerase Chain Reaction=== | |
| - | + | TOPO TA cloning (invitrogen) <br> | |
| - | + | ||
| + | ===Ligase=== | ||
| + | ===Recombination/Homology=== | ||
| + | [http://j5.jbei.org j5] from [[User:Nathan_J._Hillson | Nathan Hillson]] <br> | ||
| - | |||
| - | |||
-cold fusion <br> | -cold fusion <br> | ||
-in fusion <br> | -in fusion <br> | ||
| - | - | + | -lambda red <br> |
-golden gate <br> | -golden gate <br> | ||
| - | - | + | -lic <br> |
| - | - | + | |
| - | + | -SLIC/[http://openwetware.org/wiki/Gibson_Assembly Gibson]/CPEC/SLiCE <br> | |
| - | + | ||
| + | ===Transformation=== | ||
| + | *e coli <br> | ||
| + | *s. cerevisiae <br> | ||
| + | |||
| + | ===Bacterial Mating=== | ||
| + | |||
| + | |||
-MoClo <cite>Weber2011</cite> | -MoClo <cite>Weber2011</cite> | ||
| + | -mage <br> | ||
== References == | == References == | ||
<biblio> | <biblio> | ||
| + | #Hughes2011 pmid=21601682 | ||
| + | //Gene Synthesis Review | ||
#Weber2011 pmid=21364738 | #Weber2011 pmid=21364738 | ||
//MoClo | //MoClo | ||
| Line 44: | Line 79: | ||
#Quan2009 pmid=19649325 | #Quan2009 pmid=19649325 | ||
//CPEC | //CPEC | ||
| + | #Gibson2008 pmid=18218864 | ||
| + | // | ||
#Gibson2009 pmid=19363495 | #Gibson2009 pmid=19363495 | ||
//T5 exonuclease recombination | //T5 exonuclease recombination | ||
| Line 62: | Line 99: | ||
#Horton2009 pmid=2357375 | #Horton2009 pmid=2357375 | ||
//SOEing | //SOEing | ||
| - | + | #Czar2009 pmid=19111926 | |
| + | //review | ||
| + | #Stemmer1995 pmid=7590320 | ||
| + | //PCA | ||
| + | #Aslanidis1990 pmid=2235490 | ||
| + | //LIC | ||
| + | #Aslanidis1994 pmid=7580902 | ||
| + | //LIC | ||
| + | #Li1997 pmid=9321675 | ||
| + | //LIC | ||
| + | #Angrand1999 pmid=10446259 | ||
| + | //lambda Red recombinase | ||
| + | #Hartley2000 pmid=11076863 | ||
| + | //Gateway lambda Int | ||
| + | #Khalil2007 pmid=17702758 | ||
| + | //Gateway lambda Cre | ||
| + | #Larionov1996 pmid=8552668 | ||
| + | //Transformation-associated recombination (TAR) cloning | ||
| + | #Hillson2012 j5 DNA Assembly Design Automation Software [[doi: 10.1021/sb2000116]] | ||
| + | #Gibson2010 pmid=20488990 | ||
| + | //genome replacement | ||
| + | #Li2005 pmid=15731760 | ||
| + | //MAGIC, bacterial mating approach | ||
</biblio> | </biblio> | ||
Revision as of 00:57, 22 January 2013
Contents |
Introduction
A large number of parts have been made by the synthetic biology community. Many can be found as part of the Registry of Standard Biological Parts. These modular genetic components are designed to be easy to assemble to facilitate the building of more complex biological devices. To learn more about the Registry and BioBricks™, see last year's wiki page.
Synthetic biology relies on the ability to make testable biological units. This means that the ability to gather, manipulate, or even create genetic material is vital for "doing" synthetic biology. The techniques employed by synthetic biologists include oligonucleotide synthesis, restriction enzyme digestion, ligase, pcr, and recombination (homology).
Trying to get from genes to genomes.
DNA Synthesis
Oligonucleotide Synthesis
Gene Synthesis
IDT Gene Blocks
DNA2.0
invitrogen (life technologies, geneart)
genscript
celtek
biobasic
sigma?
GENEWIZ
biomatik
OriGene (blue heron)
Epoch Life Science
References
Cost
Time
Molecular Cloning
Restriction Enzyme
BioBricks
BglBricks
list of BioBrick Foundation Standards
Polymerase Chain Reaction
TOPO TA cloning (invitrogen)
Ligase
Recombination/Homology
j5 from Nathan Hillson
-cold fusion
-in fusion
-lambda red
-golden gate
-lic
-SLIC/Gibson/CPEC/SLiCE
Transformation
- e coli
- s. cerevisiae
Bacterial Mating
-MoClo [1]
-mage
References
- Weber E, Engler C, Gruetzner R, Werner S, and Marillonnet S. . pmid:21364738.
MoClo - Hughes RA, Miklos AE, and Ellington AD. . pmid:21601682.
Gene Synthesis Review - Werner S, Engler C, Weber E, Gruetzner R, and Marillonnet S. . pmid:22126803.
MoClo - Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, and Orzaez D. . pmid:21750718.
GoldenBraid - Engler C, Kandzia R, and Marillonnet S. . pmid:18985154.
GoldenGate - Quan J and Tian J. . pmid:19649325.
CPEC - Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:18218864.
- Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:19363495.
T5 exonuclease recombination - Li MZ and Elledge SJ. . pmid:17293868.
SLIC - Li MZ and Elledge SJ. . pmid:22328425.
SLIC - Sleight SC, Bartley BA, Lieviant JA, and Sauro HM. . pmid:20385581.
In-Fusion biobrick - Zhu B, Cai G, Hall EO, and Freeman GJ. . pmid:17907578.
in-fusion - Benoit RM, Wilhelm RN, Scherer-Becker D, and Ostermeier C. . pmid:16289702.
in-fusion - Geu-Flores F, Nour-Eldin HH, Nielsen MT, and Halkier BA. . pmid:17389646.
USER - Gibson DG. . pmid:19745056.
oligonucleotide assembly - Horton RM, Cai ZL, Ho SN, and Pease LR. . pmid:2357375.
SOEing - Czar MJ, Anderson JC, Bader JS, and Peccoud J. . pmid:19111926.
review - Stemmer WP, Crameri A, Ha KD, Brennan TM, and Heyneker HL. . pmid:7590320.
PCA - Aslanidis C and de Jong PJ. . pmid:2235490.
LIC - Aslanidis C, de Jong PJ, and Schmitz G. . pmid:7580902.
LIC - Li C and Evans RM. . pmid:9321675.
LIC - Angrand PO, Daigle N, van der Hoeven F, Schöler HR, and Stewart AF. . pmid:10446259.
lambda Red recombinase - Hartley JL, Temple GF, and Brasch MA. . pmid:11076863.
Gateway lambda Int - Khalil AM, Julius JA, and Bachant J. . pmid:17702758.
Gateway lambda Cre - Larionov V, Kouprina N, Graves J, Chen XN, Korenberg JR, and Resnick MA. . pmid:8552668.
Transformation-associated recombination (TAR) cloning - j5 DNA Assembly Design Automation Software doi: 10.1021/sb2000116
- Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. . pmid:20488990.
genome replacement - Li MZ and Elledge SJ. . pmid:15731760.
MAGIC, bacterial mating approach
