Difference between revisions of "Part:BBa K2457004:Design"

(→‎Design Notes)
 
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===References===
 
===References===
 +
 +
BAE, T. & SCHNEEWIND, O. Allelic replacement in Staphylococcus aureus with inducible counter-selection. Plasmid p. 55, 58–63, 2006.
 +
 +
BENZINGER R, ENQUIST LW, SKALKA A. Transfection of Escherichia coli spheroplasts. V. Activity of recBC nuclease in rec+ and rec minus spheroplasts measured with different forms of bacteriophage DNA. J Virol.; v. 15, n. 4, p. 861–871, 1975.
 +
 +
BIKARD, David; JIANG, Wenyan; SAMAI, Poulami; HOCHSCHILD, Ann; ZHANG, Feng; MARRAFFINI, Luciano A.  Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Research. V. 41, n. 15, p. 7429-7437, 2013.
 +
 +
BROUNS, S.J. ET AL. SMALL CRISPR RNAs guide antiviral defense in prokaryotes. Science V. 321, p. 960–964, 2008.
 +
 +
COHEN, S. N.; CHANG, A. C. Y.; HSU, L. Nonchromosomal Antibiotic Resistance in Bacteria: Genetic Transformation of Escherichia coli by R-Factor DNA. Proc. Nat. Acad. Sci. Vol. 69. USA, 1972.
 +
 +
DOUDNA, Jeniffer A.; CHARPENTIER, Emanuelle The new frontier of genome engeineering with CRISPR-Cas9. SCIENCIE V. 346, p. 1258096-1 – 12580966-9. Nov. 2014
 +
 +
DUDÁS, Andrej; CHOVANEC, Miroslav. DNA double-strand break repair by homologous recombination. Reviews in Mutation Research. V. 566, p. 131-167, 2004.
 +
 +
GREEN, M.R. e SAMBROOK, J. Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Laboratory Press, 4ª Ed. Cold Spring Harbour, USA, 2012.
 +
 +
JIANG W, BIKARD D, COX D, ZHANG F, MARRAFFINI LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. V. 31, n. 3, p. 233 – 239,  2013.
 +
 +
JIANG Y, CHEN B, DUAN C, SUN B, YANG J, YANG S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol. V. 81, n. 7, p. 2506 – 2514, 2015.
 +
 +
JIANG, Wenyan; BIKARD, David; COX, David; ZHANG, Feng & MARRAFFIN, Luciano A. RNA-guided editing of bacterial genomes using crisPr-cas systems. Nature biotechnology. V. 31, n. 3, p. 233 – 241, março, 2013.
 +
 +
KHORANA, H. G; AGARWALS, K. L.; BESMER, P. et al. Total Synthesis of the Structural Gene for the Precursor of a Tyrosine Suppressor Transfer RNA from Escherichia coli. The Journal Of Biological Chemistry. Vol 251. Cambrigde, MT, 1975.
 +
 +
LI Y, LIN Z, HUANG C, ZHANG Y, WANG Z, TANG YJ, CHEN T, ZHAO X. Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng. V. 31, p. 13 – 21, 2015.
 +
 +
LIANG X, POTTER J, KUMAR S, ZOU Y, QUINTANILLA R, SRIDHARAN M, CARTE J, CHEN W, ROARK N, RANGANATHAN S, RAVINDER N, CHESNUT JD. Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection. J Biotechnol. 2015.
 +
 +
PYNE ME, MOO-YOUNG M, CHUNG DA, CHOU CP. Coupling the CRISPR/Cas9 system to lambda Red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl Environ Microbiol. V.81, n. 15, p. 5103 – 5114, 2015.
 +
 +
SHARAN, S.K., THOMASON, L.C., KUZNETSOV, S.G. & COURT, D.L. Recombineering:  a homologous recombination-based method of genetic engineering. Nat. Protoc. V. 4, p. 206–223, 2009.
 +
 +
SHETTY, R. P.; ENDY, D.; KNIGHT, T. F. Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering. Cambridge, MA, USA, 2008.
 +
 +
SUNG, C.K., LI, H., CLAVERYS, J.P. & MORRISON, D.A. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl. Environ. Microbiol. V. 67, p.  5190–5196, 2001.
 +
 +
TERNS, M.P. & TERNS, R.M. CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. V. 14, p. 321–327, 2011.
 +
URNOV, F.D., REBAR, E.J., HOLMES, M.C., ZHANG, H.S. & GREGORY, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. Vol. 11, p. 636–646, 2010.
 +
 +
VAN DER OOST, J., JORE, M.M., WESTRA, E.R., LUNDGREN, M. & BROUNS, S.J. CRISPRbased adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. V. 34, p. 401–407, 2009.
 +
 +
WU Y, LIANG D, WANG Y, BAI M, TANG W, BAO S, YAN Z, LI D, LI J. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. V. 13, n. 6, p.

Latest revision as of 02:32, 2 November 2017


Donor DNA for HDR into LacZ


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 321
    Illegal NheI site found at 1164
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


References

BAE, T. & SCHNEEWIND, O. Allelic replacement in Staphylococcus aureus with inducible counter-selection. Plasmid p. 55, 58–63, 2006.

BENZINGER R, ENQUIST LW, SKALKA A. Transfection of Escherichia coli spheroplasts. V. Activity of recBC nuclease in rec+ and rec minus spheroplasts measured with different forms of bacteriophage DNA. J Virol.; v. 15, n. 4, p. 861–871, 1975.

BIKARD, David; JIANG, Wenyan; SAMAI, Poulami; HOCHSCHILD, Ann; ZHANG, Feng; MARRAFFINI, Luciano A. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Research. V. 41, n. 15, p. 7429-7437, 2013.

BROUNS, S.J. ET AL. SMALL CRISPR RNAs guide antiviral defense in prokaryotes. Science V. 321, p. 960–964, 2008.

COHEN, S. N.; CHANG, A. C. Y.; HSU, L. Nonchromosomal Antibiotic Resistance in Bacteria: Genetic Transformation of Escherichia coli by R-Factor DNA. Proc. Nat. Acad. Sci. Vol. 69. USA, 1972.

DOUDNA, Jeniffer A.; CHARPENTIER, Emanuelle The new frontier of genome engeineering with CRISPR-Cas9. SCIENCIE V. 346, p. 1258096-1 – 12580966-9. Nov. 2014

DUDÁS, Andrej; CHOVANEC, Miroslav. DNA double-strand break repair by homologous recombination. Reviews in Mutation Research. V. 566, p. 131-167, 2004.

GREEN, M.R. e SAMBROOK, J. Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Laboratory Press, 4ª Ed. Cold Spring Harbour, USA, 2012.

JIANG W, BIKARD D, COX D, ZHANG F, MARRAFFINI LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. V. 31, n. 3, p. 233 – 239, 2013.

JIANG Y, CHEN B, DUAN C, SUN B, YANG J, YANG S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol. V. 81, n. 7, p. 2506 – 2514, 2015.

JIANG, Wenyan; BIKARD, David; COX, David; ZHANG, Feng & MARRAFFIN, Luciano A. RNA-guided editing of bacterial genomes using crisPr-cas systems. Nature biotechnology. V. 31, n. 3, p. 233 – 241, março, 2013.

KHORANA, H. G; AGARWALS, K. L.; BESMER, P. et al. Total Synthesis of the Structural Gene for the Precursor of a Tyrosine Suppressor Transfer RNA from Escherichia coli. The Journal Of Biological Chemistry. Vol 251. Cambrigde, MT, 1975.

LI Y, LIN Z, HUANG C, ZHANG Y, WANG Z, TANG YJ, CHEN T, ZHAO X. Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng. V. 31, p. 13 – 21, 2015.

LIANG X, POTTER J, KUMAR S, ZOU Y, QUINTANILLA R, SRIDHARAN M, CARTE J, CHEN W, ROARK N, RANGANATHAN S, RAVINDER N, CHESNUT JD. Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection. J Biotechnol. 2015.

PYNE ME, MOO-YOUNG M, CHUNG DA, CHOU CP. Coupling the CRISPR/Cas9 system to lambda Red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl Environ Microbiol. V.81, n. 15, p. 5103 – 5114, 2015.

SHARAN, S.K., THOMASON, L.C., KUZNETSOV, S.G. & COURT, D.L. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. V. 4, p. 206–223, 2009.

SHETTY, R. P.; ENDY, D.; KNIGHT, T. F. Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering. Cambridge, MA, USA, 2008.

SUNG, C.K., LI, H., CLAVERYS, J.P. & MORRISON, D.A. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl. Environ. Microbiol. V. 67, p. 5190–5196, 2001.

TERNS, M.P. & TERNS, R.M. CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. V. 14, p. 321–327, 2011. URNOV, F.D., REBAR, E.J., HOLMES, M.C., ZHANG, H.S. & GREGORY, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. Vol. 11, p. 636–646, 2010.

VAN DER OOST, J., JORE, M.M., WESTRA, E.R., LUNDGREN, M. & BROUNS, S.J. CRISPRbased adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. V. 34, p. 401–407, 2009.

WU Y, LIANG D, WANG Y, BAI M, TANG W, BAO S, YAN Z, LI D, LI J. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. V. 13, n. 6, p.