Certain transcription factors (enhancer binding proteins) significantly increase
transcription rates from genes by nicking a single DNA strand in the vicinity of
their DNA binding sites, thereby allowing RNA polymerase to gain access to the
transcribed DNA strand by a process of "threading". DNA template nicking is a detectable
and quantifiable byproduct indicative of transcriptional activation that can be
used to design practical assays. These assays are used to determine which transcription
factors (enhancer binding proteins) are actively catalyzing the transcription of
a gene in any cell type, or in any cell in response to any drug or treatment. This
group of transcription factors have a predictable molecular biological activity
in addition to transcription activation, namely site-specific DNA strand cleavage.
