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| DNA methylation methods include: The methylation-sensitive single-nucleotide primer extension (Ms-SNuPE), combined bisulfite restriction analysis (COBRA), bisulfite treatment and PCR-single-strand conformation polymorphism analysis (Bisulfite-PCR-SSCP/BiPS), Methylation-specific PCR, Bisulfite sequencing. |
Analysis of DNA methylation using SNuPE
protocol
You treat your DNA with bisulphite and then anneal a primer which ends immediately before
the site of analysis. Then you perform two primer extension reactions, one with radiolabelled
dCTP (ddCTP) and another with dTTP (ddTTP). In this reactions only one nuc ...
Tag-Adapted Bisulfite Genomic Sequencing for Fine-Mapping of DNA Methylation
review
A new method for assaying methylation of cytosines at CpG dinucleotides has been developed. The PCR-based method allows for continuous, fine mapping of DNA methylation, without the need for prior knowledge of the methylation status of a CpG site, or requireme ...
Understanding DNA Methylation and Epigenetic Gene Silencing in Cancer
review
A open access book for continuing medical education (CME). The book can be downloaded as PDF file (1.5M). (Edited by Stephen Baylin, M.D.)
Recognize the distribution of CpG islands and gene promoters
* Describe the process of DNA methylation
* Explain w ...
A practical guide to DNA methylation
troubleshooting
Promega notes on DNA methylation guide (pdf file). It can be used as a troubleshooting guide. (by Tom Schoenfeld, Promega Corporation)
The pattern and extent of DNA methylation can significantly affect the success of restriction digestions or bacterial tran ...
DNA Methylation Database MethDB
database
The purpose of this database is to provide the scientific community with a resource to store DNA methylation data and to make these data readily available to the public. Descriptions of MethDB has been published in the database issues of Nucleic Acids Research ...
MethPrimer Database
database
DNA Methylation analysis PCR Primer Database maintained by University of Ghent, Belgium.
This is a public database holding PCR primers for popular DNA methylation analysis methods (Methylation-specific PCR, Bisulfite-PCR-SSCP, Methylation-sensitive single-n ...
More dna methylation protocols
(Curr Protoc Mol Biol. 2001 May;Chapter 12:Unit 12.3.)
Baldwin AS Jr, Oettinger M, Struhl K.
University of North Carolina, Chapel Hill, North Carolina, USA.
Interference assays identify specific residues in the DNA binding site that, when modified, interfere with binding of the protein. The protocols use end-labeled DNA probes that are modified at an average of one site per molecule of probe. These probes are incubated with the protein of interest, and protein-DNA complexes are separated from free probe by the mobility shift assay. A DNA probe that is modified at a position that interferes with binding will not be retarded in this assay; thus, the specific protein-DNA complex is depleted for DNA that contains modifications on bases important for binding. After gel purification, the bound and unbound DNA are specifically cleaved at the modified residues and the resulting products analyzed by electrophoresis on polyacrylamide sequencing gels and autoradiography. In the methylation interference protocol presented here, probes are generated by methylating guanines (at the N-7 position) and adenines (at the N-3 position) with DMS; these methylated bases are cleaved specifically by piperidine. In the uracil interference protocol, probes are generated by PCR amplification in the presence of a mixture of TTP and dUTP, thereby producing products in which thymine residues are replaced by deoxyuracil residues (which contains hydrogen in place of the thymine 5-methyl group). Uracil bases are specifically cleaved by uracil-N-glycosylase to generate apyrimidinic sites that are susceptible to piperidine. These procedures provide complementary information about the nucleotides involved in protein-DNA interactions.
Last update: 
11-May-2012 02:38 pm
