FIG. 5.
Theoretical approach for determining the extent of the actual domain. (A) The diagrammed situation contains an actual domain of 1 bp (X) located at position 0 (shown within a region that extends from −400 to +400). Horizontal lines below the coordinate scale indicate 400-bp chromosomal DNA fragments that contain position 0; there are 400 such fragments. The subset of DNA fragments that are detectable as 300-bp PCR fragments (defined by the central position of the PCR fragment) are indicated by the shaded boxes. (B) The graphs represent various situations in which the length of the chromosomal fragments (350 to 550 bp) is indicated; in all cases, the PCR fragments are 300 bp. The number of distinct chromosomal DNA fragments containing position 0 that can be detected by 300-bp PCR fragments (y axis) is shown as a function of the central position of the PCR fragment (x axis). For any PCR fragment (as defined by the location of the central base pair), the number of distinct chromosomal DNA fragments is directly related to the expected experimental signal. This approach assumes that chromosomal fragmentation is random with respect to nucleotide position.