Difference between revisions of "CH391L/S13/DnaAssembly"

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The Registry of Standard Biological Parts is an attempt to create an annotated and characterized repository of biological parts. It is motivated in part because synthetic biologists rely 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. This page details how to create DNA from small (<60 nts) oligonucleotides to larger genes (~400 nts) to genome sized (~500 ,000 nts) biological units.
 
The Registry of Standard Biological Parts is an attempt to create an annotated and characterized repository of biological parts. It is motivated in part because synthetic biologists rely 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. This page details how to create DNA from small (<60 nts) oligonucleotides to larger genes (~400 nts) to genome sized (~500 ,000 nts) biological units.
  
==Gene Synthesis==
+
==DNA Synthesis==
 +
 
 +
===Oligonucleotide Synthesis===
 +
Oligonucleotides are [http://en.wikipedia.org/wiki/Oligonucleotide_synthesis chemically synthesized] from DNA phosphoramidite monomers. Briefly, activated phosphoramidite monomers are added in the 3' to 5' direction using a cyclical activation and blocking chemistry to obtain a DNA polymer linked by phosphodiester bonds.
 +
 
 +
[[Image:CH391L_S12_Phosphoramidite.png]]
 +
 
 +
Chemical synthesis is currently limited to oligonucleotides of about 200 nt in length.
 +
 
 +
===Gene Synthesis===
 +
<!--Regardless of the length of the eventual product, synthetic DNA constructs are built from some combination of short DNA oligonucleotides. These oligonucleotides are later assembled into a complementary DNA duplex, amplified and inserted into their final genetic context.-->
  
 
Gene synthesis, or [http://en.wikipedia.org/wiki/Artificial_gene_synthesis artificial gene synthesis], refers to the process of creating a nucleic acid template for a gene ''in vitro'', without the requirement of a preexisting DNA template. Soon after the elucidation of the genetic code and the description of the central dogma of molecular biology, there arose a need to synthesize genes ''de novo'' in order to study their biological function both in the test tube and in model organisms. Chemical synthesis of DNA has grown from an expensive and time-consuming process into a viable commercial industry capable of high-throughput manufacture of almost any scale of custom DNA molecules in almost any context. This allows species-specific gene optimization, creation of genes from rare or dangerous sources, and combinatorial assembly of any DNA sequence that can be chemically synthesized, even including non-traditional bases. The most advanced applications of gene synthesis have been applied to the recent creation of completely synthetic minimal genomes in prokaryotes.
 
Gene synthesis, or [http://en.wikipedia.org/wiki/Artificial_gene_synthesis artificial gene synthesis], refers to the process of creating a nucleic acid template for a gene ''in vitro'', without the requirement of a preexisting DNA template. Soon after the elucidation of the genetic code and the description of the central dogma of molecular biology, there arose a need to synthesize genes ''de novo'' in order to study their biological function both in the test tube and in model organisms. Chemical synthesis of DNA has grown from an expensive and time-consuming process into a viable commercial industry capable of high-throughput manufacture of almost any scale of custom DNA molecules in almost any context. This allows species-specific gene optimization, creation of genes from rare or dangerous sources, and combinatorial assembly of any DNA sequence that can be chemically synthesized, even including non-traditional bases. The most advanced applications of gene synthesis have been applied to the recent creation of completely synthetic minimal genomes in prokaryotes.
Line 17: Line 27:
 
===History of Gene Synthesis===
 
===History of Gene Synthesis===
 
Gene synthesis predates the invention of restriction enzymes and molecular cloning techniques by several years. The first gene to be completely synthesized ''in vitro'' was a 77-nt alanine transfer RNA by the laboratory of [http://en.wikipedia.org/wiki/Har_Gobind_Khorana Har Gobind Khorana] in 1972 <cite>Khorana1972</cite>. This was the result of nearly five years of work and resulted in a DNA template without promoter or transcriptional control sequences. The first peptide- and protein-producing synthetic genes were created in 1977 and 1979, respectively <cite>Itakura1977, Goeddell1979</cite>. Steady advancement has led to recent synthesis of complete gene clusters tens of thousands of nucleotides in length, and ultimately a bacterial genome approximately 1.2 million bases in length.
 
Gene synthesis predates the invention of restriction enzymes and molecular cloning techniques by several years. The first gene to be completely synthesized ''in vitro'' was a 77-nt alanine transfer RNA by the laboratory of [http://en.wikipedia.org/wiki/Har_Gobind_Khorana Har Gobind Khorana] in 1972 <cite>Khorana1972</cite>. This was the result of nearly five years of work and resulted in a DNA template without promoter or transcriptional control sequences. The first peptide- and protein-producing synthetic genes were created in 1977 and 1979, respectively <cite>Itakura1977, Goeddell1979</cite>. Steady advancement has led to recent synthesis of complete gene clusters tens of thousands of nucleotides in length, and ultimately a bacterial genome approximately 1.2 million bases in length.
 
===Oligonucleotide Synthesis===
 
Regardless of the length of the eventual product, synthetic DNA constructs are built from some combination of short DNA oligonucleotides. These oligonucleotides are later assembled into a complementary DNA duplex, amplified and inserted into their final genetic context.
 
 
Oligonucleotides are [http://en.wikipedia.org/wiki/Oligonucleotide_synthesis chemically synthesized] from DNA phosphoramidite monomers. Briefly, activated phosphoramidite monomers are added in the 3' to 5' direction using a cyclical activation and blocking chemistry to obtain a DNA polymer linked by phosphodiester bonds.
 
 
[[Image:CH391L_S12_Phosphoramidite.png]]
 
 
Chemical synthesis is currently limited to oligonucleotides of about 200 nt in length.
 
  
 
===Cost Analysis===
 
===Cost Analysis===

Revision as of 19:40, 22 January 2013


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 acquire and assemble to facilitate the building of more complex biological devices. To learn more about the Registry and the biological parts known as BioBricks™, see the entry for the iGEM Registry.

The Registry of Standard Biological Parts is an attempt to create an annotated and characterized repository of biological parts. It is motivated in part because synthetic biologists rely 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. This page details how to create DNA from small (<60 nts) oligonucleotides to larger genes (~400 nts) to genome sized (~500 ,000 nts) biological units.

DNA Synthesis

Oligonucleotide Synthesis

Oligonucleotides are chemically synthesized from DNA phosphoramidite monomers. Briefly, activated phosphoramidite monomers are added in the 3' to 5' direction using a cyclical activation and blocking chemistry to obtain a DNA polymer linked by phosphodiester bonds.

CH391L S12 Phosphoramidite.png

Chemical synthesis is currently limited to oligonucleotides of about 200 nt in length.

Gene Synthesis

Gene synthesis, or artificial gene synthesis, refers to the process of creating a nucleic acid template for a gene in vitro, without the requirement of a preexisting DNA template. Soon after the elucidation of the genetic code and the description of the central dogma of molecular biology, there arose a need to synthesize genes de novo in order to study their biological function both in the test tube and in model organisms. Chemical synthesis of DNA has grown from an expensive and time-consuming process into a viable commercial industry capable of high-throughput manufacture of almost any scale of custom DNA molecules in almost any context. This allows species-specific gene optimization, creation of genes from rare or dangerous sources, and combinatorial assembly of any DNA sequence that can be chemically synthesized, even including non-traditional bases. The most advanced applications of gene synthesis have been applied to the recent creation of completely synthetic minimal genomes in prokaryotes.

Despite nearly four decades of progress in gene synthesis technologies, most DNA sequences used in modern molecular biology are assembled in part or in whole from naturally occurring templates. However this limits the scope and applications to previously existing genes and the results of large-scale genomic surveys of novel genes from nature. Modern gene synthesis relies heavily on advancements in chemical DNA oligonucleotide synthesis, with the primary challenges being scale, cost, fidelity and the eventual assembly of complete gene products.

A directory of commercial gene synthesis providers can be found at Genespace. The company biomatik is not included on this list.

History of Gene Synthesis

Gene synthesis predates the invention of restriction enzymes and molecular cloning techniques by several years. The first gene to be completely synthesized in vitro was a 77-nt alanine transfer RNA by the laboratory of Har Gobind Khorana in 1972 [1]. This was the result of nearly five years of work and resulted in a DNA template without promoter or transcriptional control sequences. The first peptide- and protein-producing synthetic genes were created in 1977 and 1979, respectively [2, 3]. Steady advancement has led to recent synthesis of complete gene clusters tens of thousands of nucleotides in length, and ultimately a bacterial genome approximately 1.2 million bases in length.

Cost Analysis

Carlson longest sDNA 2010-thumb-500x457.png
Carlson cost per base june 2011.png
Cost per genome 20130122.jpg


References
Cost
Time

Molecular Cloning

Restriction Enzyme

BioBricks
BglBricks
list of BioBrick Foundation Standards

Polymerase Chain Reaction

TOPO TA cloning (invitrogen)
SOE (splice by overlap extension) pcr
PCA

Ligation

Recombination/Homology

j5 from Nathan Hillson

-In-Fusion (Clontech) poxvirus DNA polymerase with 3′–5′ exonuclease activity
-In-Fusion BioBrick Assembly
-cold fusion (SBI)

-golden gate
-MoClo [4]
-GoldenBraid

-SLIC sequence and ligation independent cloning T4 DNA polymerase (exonuclease)
-Gibson T5 exonuclease, Phusion polymerase, Taq ligase
-CPEC circular polymerase extension cloning

-SLiCE (Seamless Ligation Cloning Extract) in vitro homologous recombination

Uncategorized
-Fast Seamless Cloning (Dogene)
-CloneEZ kit (Genescript)
-GENEART
-lic
-gateway
-lambda red

Transformation

  • e coli
  • s. cerevisiae

Bacterial Mating

MAGIC

More cloning strategies found here

References

  1. Weber E, Engler C, Gruetzner R, Werner S, and Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS One. 2011 Feb 18;6(2):e16765. DOI:10.1371/journal.pone.0016765 | PubMed ID:21364738 | HubMed [Weber2011]
    MoClo
  2. Hughes RA, Miklos AE, and Ellington AD. Gene synthesis: methods and applications. Methods Enzymol. 2011;498:277-309. DOI:10.1016/B978-0-12-385120-8.00012-7 | PubMed ID:21601682 | HubMed [Hughes2011]
    Gene Synthesis Review
  3. Werner S, Engler C, Weber E, Gruetzner R, and Marillonnet S. Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioeng Bugs. 2012 Jan 1;3(1):38-43. DOI:10.4161/bbug.3.1.18223 | PubMed ID:22126803 | HubMed [Werner2012]
    MoClo
  4. Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, and Orzaez D. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One. 2011;6(7):e21622. DOI:10.1371/journal.pone.0021622 | PubMed ID:21750718 | HubMed [SarrionPerdigones2011]
    GoldenBraid
  5. Engler C, Kandzia R, and Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One. 2008;3(11):e3647. DOI:10.1371/journal.pone.0003647 | PubMed ID:18985154 | HubMed [Engler2008]
    GoldenGate
  6. Quan J and Tian J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One. 2009 Jul 30;4(7):e6441. DOI:10.1371/journal.pone.0006441 | PubMed ID:19649325 | HubMed [Quan2009]
    CPEC
  7. 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. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008 Feb 29;319(5867):1215-20. DOI:10.1126/science.1151721 | PubMed ID:18218864 | HubMed [Gibson2008]
  8. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, and Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009 May;6(5):343-5. DOI:10.1038/nmeth.1318 | PubMed ID:19363495 | HubMed [Gibson2009]
    T5 exonuclease recombination
  9. Li MZ and Elledge SJ. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods. 2007 Mar;4(3):251-6. DOI:10.1038/nmeth1010 | PubMed ID:17293868 | HubMed [Li2007]
    SLIC
  10. Li MZ and Elledge SJ. SLIC: a method for sequence- and ligation-independent cloning. Methods Mol Biol. 2012;852:51-9. DOI:10.1007/978-1-61779-564-0_5 | PubMed ID:22328425 | HubMed [Li2012]
    SLIC
  11. Sleight SC, Bartley BA, Lieviant JA, and Sauro HM. In-Fusion BioBrick assembly and re-engineering. Nucleic Acids Res. 2010 May;38(8):2624-36. DOI:10.1093/nar/gkq179 | PubMed ID:20385581 | HubMed [Sleight2010]
    In-Fusion biobrick
  12. Zhu B, Cai G, Hall EO, and Freeman GJ. In-fusion assembly: seamless engineering of multidomain fusion proteins, modular vectors, and mutations. Biotechniques. 2007 Sep;43(3):354-9. PubMed ID:17907578 | HubMed [Zhu2007]
    in-fusion
  13. Benoit RM, Wilhelm RN, Scherer-Becker D, and Ostermeier C. An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids. Protein Expr Purif. 2006 Jan;45(1):66-71. DOI:10.1016/j.pep.2005.09.022 | PubMed ID:16289702 | HubMed [Benoit2006]
    in-fusion
  14. Geu-Flores F, Nour-Eldin HH, Nielsen MT, and Halkier BA. USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 2007;35(7):e55. DOI:10.1093/nar/gkm106 | PubMed ID:17389646 | HubMed [GeuFlores2007]
    USER
  15. Gibson DG. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res. 2009 Nov;37(20):6984-90. DOI:10.1093/nar/gkp687 | PubMed ID:19745056 | HubMed [Gibson2009-2]
    oligonucleotide assembly
  16. Horton RM, Cai ZL, Ho SN, and Pease LR. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques. 1990 May;8(5):528-35. PubMed ID:2357375 | HubMed [Horton2009]
    SOEing
  17. Czar MJ, Anderson JC, Bader JS, and Peccoud J. Gene synthesis demystified. Trends Biotechnol. 2009 Feb;27(2):63-72. DOI:10.1016/j.tibtech.2008.10.007 | PubMed ID:19111926 | HubMed [Czar2009]
    review
  18. Stemmer WP, Crameri A, Ha KD, Brennan TM, and Heyneker HL. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. 1995 Oct 16;164(1):49-53. PubMed ID:7590320 | HubMed [Stemmer1995]
    PCA
  19. Aslanidis C and de Jong PJ. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 1990 Oct 25;18(20):6069-74. PubMed ID:2235490 | HubMed [Aslanidis1990]
    LIC
  20. Aslanidis C, de Jong PJ, and Schmitz G. Minimal length requirement of the single-stranded tails for ligation-independent cloning (LIC) of PCR products. PCR Methods Appl. 1994 Dec;4(3):172-7. PubMed ID:7580902 | HubMed [Aslanidis1994]
    LIC
  21. Li C and Evans RM. Ligation independent cloning irrespective of restriction site compatibility. Nucleic Acids Res. 1997 Oct 15;25(20):4165-6. PubMed ID:9321675 | HubMed [Li1997]
    LIC
  22. Angrand PO, Daigle N, van der Hoeven F, Schöler HR, and Stewart AF. Simplified generation of targeting constructs using ET recombination. Nucleic Acids Res. 1999 Sep 1;27(17):e16. PubMed ID:10446259 | HubMed [Angrand1999]
    lambda Red recombinase
  23. Hartley JL, Temple GF, and Brasch MA. DNA cloning using in vitro site-specific recombination. Genome Res. 2000 Nov;10(11):1788-95. PubMed ID:11076863 | HubMed [Hartley2000]
    Gateway lambda Int
  24. Khalil AM, Julius JA, and Bachant J. One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning. Nucleic Acids Res. 2007;35(16):e104. DOI:10.1093/nar/gkm583 | PubMed ID:17702758 | HubMed [Khalil2007]
    Gateway lambda Cre
  25. Larionov V, Kouprina N, Graves J, Chen XN, Korenberg JR, and Resnick MA. Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):491-6. PubMed ID:8552668 | HubMed [Larionov1996]
    Transformation-associated recombination (TAR) cloning
  26. j5 DNA Assembly Design Automation Software doi: 10.1021/sb2000116 [Hillson2012]
  27. 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. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 2010 Jul 2;329(5987):52-6. DOI:10.1126/science.1190719 | PubMed ID:20488990 | HubMed [Gibson2010]
    genome replacement
  28. Li MZ and Elledge SJ. MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules. Nat Genet. 2005 Mar;37(3):311-9. DOI:10.1038/ng1505 | PubMed ID:15731760 | HubMed [Li2005]
    MAGIC, bacterial mating approach
  29. Zhang Y, Werling U, and Edelmann W. SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res. 2012 Apr;40(8):e55. DOI:10.1093/nar/gkr1288 | PubMed ID:22241772 | HubMed [Zhang2012]
    SLiCe
All Medline abstracts: PubMed | HubMed