DNA affinity capture and protein profiling by SELDI-TOF mass spectrometry: effect of DNA methylation.
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.
Bane
Thomas K
TK
Division of Biology, Beckman Research Institute, The City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010, USA.
LeBlanc
James F
JF
Lee
Terry D
TD
Riggs
Arthur D
AD
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D001667:Binding, Competitive; D002457:Cell Extracts; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006367:HeLa Cells; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000235:genetics; D012680:Sensitivity and Specificity; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D035181:TATA-Box Binding Protein; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D002457:Cell Extracts; D004268:DNA-Binding Proteins; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; C077885:XIST non-coding RNA; D004247:DNA