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DNA affinity capture and protein profiling by SELDI-TOF mass spectrometry: effect of DNA methylation
Thomas K Bane1, James F LeBlanc, Terry D Lee
1Division of Biology, Beckman Research Institute, The City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010, USA.
Abstract:
We report here that surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry, as performed on a Ciphergen Biosystems ProteinChip System, can be used in conjunction with DNA affinity capture (DACA) to study specific DNA-protein binding. Using DNA molecules bound to a surface, sequence-specific interactions can be detected as demonstrated by a mutation affecting the binding profile for TBP, a transcription factor. Also, a comparison between methylated and unmethylated promoter-containing DNA fragments shows numerous binding profile differences over a mass range extending to >60 kDa. The binding of several proteins is inhibited by methylation of the DNA.