In vitro footprinting of promoter regions within supercoiled plasmid DNA.

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11 Scopus citations


Polypurine/polypyrimidine (pPu/pPy) tracts, which exist in the promoter regions of many growth-related genes, have been proposed to be very dynamic in their conformation. In this chapter, we describe a detailed protocol for DNase I and S1 nuclease footprinting experiments with supercoiled plasmid DNA containing the promoter regions to probe whether there are conformational transitions to B-type DNA, melted DNA, and G-quadruplex structures within this tract. This is demonstrated with the proximal promoter region of the human vascular endothelial growth factor (VEGF) gene, which also contains multiple binding sites for Sp1 and Egr-1 transcription factors.

Original languageEnglish (US)
Pages (from-to)223-233
Number of pages11
JournalMethods in molecular biology (Clifton, N.J.)
StatePublished - 2010

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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