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REVIEW: Analysis of chromatin structure by ligation-mediated PCR.
- G P Pfeifer
Genome Res. November 1992 2: 107-111; doi:10.1101/gr.2.2.107
.... , Riggs. A.D. Pfeifer, G.P., Steigerwald, S.D. Mueller, P.R. Wold, B. and Riggs. A.D. 1989 . Genomic sequencing and methylation analysis by ligation mediated PCR. Science 246 : 810 – 813 . 6.. Garrity, P.A. , Wold. B.A. Garrity, P.A. and Wold. B.A. 1992 . Effects of different DNA polymerases...
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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...reveals the overall extent of nicks and other alkali-labile sites (such as abasic sites) when compared with the results of a neutral comet assay, but does not provide information about the locations of breaks in s (Collins 2004). Ligation-mediated PCR has been used to generate and amplify DNA fragments...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...of interest by PCR. For example, ligation-mediated PCR (LM-PCR) maps nucleobase modifications by ligating PCR-competent adaptors to the ends of cDNA created by termination of polymerase elongation in vitro when it encounters nicks and single base gaps introduced by DNA modification (Sugasawa 2010; Yan et al...
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ARTICLE: Capture PCR: efficient amplification of DNA fragments adjacent to a known sequence in human and YAC DNA.
- M Lagerström,
- J Parik,
- H Malmgren,
- J Stewart,
- U Pettersson,
- and U Landegren
Genome Res. November 1991 1: 111-119; doi:10.1101/gr.1.2.111
...be designed so that a complement for the general primer is formed only after a molecule has been copied from a specific primer hybridizing internal to the fragment. This is done to avoid amplification of all DNA sequences surrounded by oligomers. For instance, in the vectorette strategy, or bubble PCR, (8...
REVIEW: The ligase chain reaction in a PCR world.
- F Barany
Genome Res. August 1991 1: 5-16; doi:10.1101/gr.1.1.5
...amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230 : 1350 – 1354 . 3. Erlich, H.A., ed. 1989. PCR technology: Principles and applications for DNA amplification . Stockton Press, New York. 4. Innis, M.A., D.H. Gelfand, J.J. Sninsky, and T...
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Methods: DNA amplification method tolerant to sample degradation
- Gang Wang,
- Elizabeth Maher,
- Cameron Brennan,
- Lynda Chin,
- Christopher Leo,
- Manjit Kaur,
- Penny Zhu,
- Martha Rook,
- Jia Liu Wolfe,
- and G. Mike Makrigiorgos
Genome Res. November 2004 14: 2357-2366; doi:10.1101/gr.2813404
...for developing RCA–RCA was precipitated by several observations: (1) Ligation-mediated PCR approaches for whole amplification, such as SCOMP ( Nelson et al. 1989 ; Klein et al. 1999 ) or balanced-PCR ( Makrigiorgos et al. 2002 ; Wang et al. 2004 ), are efficient in amplification of modestly degraded DNA...
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REVIEW: RNA fingerprinting by arbitrarily primed PCR.
- M McClelland and
- J Welsh
Genome Res. August 1994 4: S66-S81
...fingerprinting with AP-PCR using pairwise combinations of primers: Application to genetic mapping of the mouse. Nucleic Acids Res. 19 : 5275 – 5279 . 28.. Garrity, P.A. , Wold. B.J. Garrity, P.A. and Wold. B.J. 1992 . Effects of different DNA polymerases in ligation-mediated PCR: Enhanced genomic sequencing...
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ARTICLE: Use of a simplified single-site PCR to facilitate cloning of genomic DNA sequences flanking a transgene integration site.
- G R MacGregor and
- P A Overbeek
Genome Res. November 1991 1: 129-135; doi:10.1101/gr.1.2.129
...restriction fragment, finally synthesizing a complement of the ligated oligonucleotide sequence. Subsequently, a PCR is initiated which uses primers specific for the transgenic DNA and the newly synthesized DNA complementary to the ligated oligonucleotide. The only prerequisite data are sequence information...
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Letter: Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity
- Christian Schmidl,
- Maja Klug,
- Tina J. Boeld,
- Reinhard Andreesen,
- Petra Hoffmann,
- Matthias Edinger,
- and Michael Rehli
Genome Res. July 2009 19: 1165-1174; Published in Advance June 3, 2009, doi:10.1101/gr.091470.109
.... Ligation-mediated PCR (LM-PCR) ChIP and input DNAwere blunted and phosphorylated for 30min at 20°C in 50-mL reactions containing 103 T4 DNA ligase buffer, 2 mL of dNTP mix (10 mM each), 3 U of T4 DNA polymerase, 10 U of T4 polynucleotide kinase, and 1 U of Klenow DNA polymerase. Purification using...
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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
...II restriction enzyme. An oligonucleotide adaptor containing a recognition site for Mme I, a type IIS restriction enzyme, is then used to release 21-bp tags from fixed positions in the DNA relative to the sites recognized by the fragmenting enzyme. These tags are PCR-amplified, purified, concatenated...

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