Analysis of DNA-protein interactions: from nitrocellulose filter binding assays to microarray studies.
Determination of the sequence of the human genome and knowledge of the genetic code have allowed rapid progress in the identification of mammalian proteins. However, far less is known about the molecular mechanisms that control expression of human genes and about the variations in gene expression that underlie many pathological states, including cancer. This is caused in part by lack of information about the binding specificities of DNA-binding proteins and particularly regulative important molecules such as transcription factors. It is consequently crucial to develop new technologies or improve existing ones for the analysis of DNA-protein interaction in order to identify and characterise DNA response elements and the related transcription factors or other DNA-binding proteins. The techniques that are currently available vary with respect to the type of result that can be expected from the assay: a mere qualitative demonstration of binding; the identification of response element sequences at high throughput; or a quantitative characterisation of affinities. This article gives an overview of early and recent methodologies applied to such ends.
Helwa
Reham
R
Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. r.helwa@dkfz.de
Hoheisel
Jörg D
JD
D001665:Binding Sites; D003101:Collodion / Q000737:chemistry*; D004247:DNA / Q000032:analysis* / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000032:analysis* / Q000378:metabolism; D006801:Humans; D046228:Microarray Analysis / Q000295:instrumentation / Q000379:methods*; D011485:Protein Binding
D004268:DNA-Binding Proteins; D003101:Collodion; D004247:DNA