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REVIEW: Sequencing of PCR-amplified DNA.
- I S Bevan,
- R Rapley,
- and M R Walker
Genome Res. May 1992 1: 222-228; doi:10.1101/gr.1.4.222
...: 6545 – 6551 . 23. Gould, S.J., , Subramani, S. , Scheffler. I.E. Gould, S.J., Subramani, S. and Scheffler. I.E. 1989 . Use of the DNA polymerase chain reaction for homology probing: Isolation of partial DNA or genomic clones encoding the iron-sulphur protein of succinate dehydrogenase from several...
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Method: Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
- Eric E. Schadt,
- Onureena Banerjee,
- Gang Fang,
- Zhixing Feng,
- Wing H. Wong,
- Xuegong Zhang,
- Andrey Kislyuk,
- Tyson A. Clark,
- Khai Luong,
- Alona Keren-Paz,
- Andrew Chess,
- Vipin Kumar,
- Alice Chen-Plotkin,
- Neal Sondheimer,
- Jonas Korlach,
- and Andrew Kasarskis
Genome Res. January 2013 23: 129-141; Published in Advance October 23, 2012, doi:10.1101/gr.136739.111
...-strand breaks at oxidatively modified positions. The samples were PCR amplified before and after treatment to demonstrate the degree of modification. First-derivative plots of the amplification are shown. Schadt et al. 136 Genome Research www..org Identification of putative 8-oxoG events in mtDNA To determine...
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Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
- Thomas O. Auer,
- Karine Duroure,
- Anne De Cian,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
...of a sequence of interest. Among these, zinc finger and TALE nucleases (TALENs) are fusions of artificial DNA binding domains—arrays of zinc fingers and TALE effector repeats, respectively—to the endonuclease domain of the FokI restriction enzyme. The latter is only active as a dimer and therefore needs...
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Research: LSH and G9a/GLP complex are required for developmentally programmed DNA methylation
- Kevin Myant,
- Ausma Termanis,
- Arvind Y.M. Sundaram,
- Tristin Boe,
- Chao Li,
- Cara Merusi,
- Joe Burrage,
- Jose I. de Las Heras,
- and Irina Stancheva
Genome Res. January 2011 21: 83-94; Published in Advance December 13, 2010, doi:10.1101/gr.108498.110
...and expressed in trophectoderm (Oda et al. 2006). In our experiments, we observed partial loss of DNA methylation from the promoter of the Gm9 gene, located immediately upstream of the Rhox cluster, and complete loss of DNAmethylation from the promoters of 15 out of 22Rhox genes represented on the arrays...
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METHODS: Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA
- John J. Dunn,
- Sean R. McCorkle,
- Laura A. Praissman,
- Geoffrey Hind,
- Daniel van der Lelie,
- Wadie F. Bahou,
- Dmitri V. Gnatenko,
- and Maureen K. Krause
Genome Res. November 1, 2002 12: 1756-1765; doi:10.1101/gr.306102
...partially overlaps the Nla III site of the bound DNA, the released fragments contain 21 bases of sequence information from the starting DNA. These products are recovered and ligated with an adaptor having a 16-fold degenerate 3′ overhang ( Spinella et al. 1999 ) which renders it compatible with all possible...
REVIEW: Amplifying DNA with arbitrary oligonucleotide primers.
- G Caetano-Anollés
Genome Res. October 1993 3: 85-94; doi:10.1101/gr.3.2.85
...of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease digested DNA: Identification of markers linked to the supernodulation locus in soybean. Mol. &amp; Gen. Genet 241 : 57 – 64 . 74. Caetano-Anollés, G., B.J. Bassam, and P.M. Gresshoff. 1992c. DNA amplification fingerprinting with very...
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Methods: Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones
- David L. Cheo,
- Steven A. Titus,
- Devon R.N. Byrd,
- James L. Hartley,
- Gary F. Temple,
- and Michael A. Brasch
Genome Res. October 15, 2004 14: 2111-2120; doi:10.1101/gr.2512204
...al. 2002 ) and STE 2 ( Hagen et al.1991 ) were PCR amplified from yeast genomic DNA using att B-containing promoter-specific oligonucleotides, such that the products were flanked by 5′ att B4 sites and 3′ att B1.1R sites. Reaction of these B4-B1.1R PCR products to pDONR-P4-P1R generated L4-promoter...
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ARTICLES: Use of vectorette and subvectorette PCR to isolate transgene flanking DNA.
- M J Allen,
- A Collick,
- and A J Jeffreys
Genome Res. October 1994 4: 71-75
...this single- copy transgene to have intact 3' MS32 human flanking DNA but no 5' flanking sequences. The mouse flanking DNA se- quences again showed an unusual lack of most restriction sites other than for Avail. AvaII was again chosen to con- struct a vectorette library using partially digested 102B genomic...
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ARTICLES: PCR regimen for enhanced specificity and yield of targeted genomic DNA sequences: ras and p53.
- D J Phillips,
- J M Benson,
- J M Pruckler,
- and W C Hooper
Genome Res. August 1992 2: 45-50; doi:10.1101/gr.2.1.45
.... , Itakura. M. Iwahana, H., Yoshimoto, K. and Itakura. M. 1992 . Detection of point mutations by SSCP of PCR-amplified DNA after endonuclease digestion. BioTechniques 12 : 64 – 66 . 16.. Saiki, R.K., , Gelfand, D.H. , Stoffel, S. , Scharf, S.J. , Higuchi, R. , Horn, G.T. , Mullis, K.B. , Erlich. H.A. Saiki...
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ARTICLES: PCR with end trimming and cassette ligation: a rapid method to clone exon-intron boundaries and a 5'-upstream sequence of genomic DNA based on a cDNA sequence.
- H Iwahana,
- T Tsujisawa,
- R Katashima,
- K Yoshimoto,
- and M Itakura
Genome Res. August 1994 4: 19-25
...I and partially filled with dCTP using Klenow fragment of DNA polymerase I. C2 cassette was ligated to the BlnI-digested and end- trimmed DNA. The initial PCR was performed using oRB183, an outer primer annealing to the rat ATase gene, and oRB404, an outer primer annealing to cassette, oRB183 can work as a primer...

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