DNA segment method
To achieve plausible docking, it was necessary for us to make two types
of conformation changes to the DNA before presenting it for docking. The
first type, called “DNA segment method,” involved making adjustments
at the base-pair level by using experimentally-determined structures for
DNA segments about 4-5 bp in length. The I1 sequence was divided
into six overlapping segments, for example, TAGC, GCATT, TTTTT, etc. For
each segment, a search for the sequence was performed in the RCSB
database and at least four examples were chosen. The geometric
parameters of the sequence were calculated using Web 3DNA (see below).
After averaging the parameter values for the desired region of the DNA
over the four example sequences, a table was constructed with the
geometric parameters of the entire I1 sequence. Web 3DNA was then
used to rebuild the I1 structure from the geometric parameters.
The same procedure was followed for I2 and the spacer betweenI1 and I2 . Over 52 experimental structures for DNA were
used to build the I1-spacer-I2 sequence.