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.