Color imaging method for mapping stretched DNA hybridized with fluorescently labeled oligonucleotide probes

A method of identifying termination site-specific inhibitor drugs, comprising:

• a) incubating a permeabilized cell by pulse chase with a replication buffer comprising ATP, dATP, dGTP, dCTP, dTTP, detectably labeled dUTP and a drug suspected of site-specifically inhibiting replication termination to produce labeled DNA;
• b) isolating the labeled DNA from the cell;
• c) gravitationally stretching the labeled DNA;
• d) hybridizing the stretched DNA with a detectably labeled oligonucleotide probe that binds to said labeled DNA;
• and
• e) detecting the position of the labeled DNA wherein more than one site of labeled DNA is indicative of a drug that inhibits site specific termination.

A method of mapping DNA comprising:

• (a) extending DNA to a substantially linear form;
• (b) hybridizing a labeled probe to the substantially linear DNA;
• (c) generating a color image of the hybridized substantially linear DNA;
• (d) digitizing and storing the color image;
• (e) processing the stored color image to identify a midline of the hybridized substantially linear DNA;
• and
• (f) mapping the hybridized substantially linear DNA as a function of the identified midline.

A method for determining physical distances along a DNA segment comprising:

• (a) extending DNA to form a substantially linear molecule;
• (b) labeling the linear DNA at spaced locations along the linear DNA by hybridization with a plurality of fluorescently labeled oligonucleotide probes;
• (c) producing a color image of the hybridized linear DNA;
• (d) storing a pixelized version of the color image;
• and
• (e) for each color in the color image, processing the color image to determine a midline of the image;
• and
• (f) calculating the length of the midline based on evaluating a plurality of pixels for colors emanating from a starting point and distance each vector extends within the color image.