DNA conformation (loop structures) in normal and abnormal gene expression
Method of detection or diagnosis of abnormal gene expression in an individual comprising determining in a sample from the individual the presence or absence of a chromosome structure in which two separate regions of the gene have been brought into close proximity, to thereby detect or diagnose whether the individual has abnormal gene expression.
1. A method of making and detecting a ligated DNA, wherein said ligated DNA is made from a DNA sample from an individual of a specific species, wherein the sequence of the ligated DNA can be predicted, and wherein said method comprises the steps of:
(a) identifying Checkpoint Charlie (CC) marker DNA sequences in the genome of the species by a pattern recognition algorithm that scans the genome's DNA sequence and calculates a reverse algorithmic score based on the weights assigned to each type of nucleotide present in the scanned sequence and the position of the nucleotide relative to a nucleotide in the CC marker, wherein said Checkpoint Charlie (CC) marker DNA sequences are capable of coming together to form a juxtaposition;
(b) cross-linking DNA sequences in the sample which have been brought together in a juxtaposition;
(c) cleaving the cross-linked DNA;
(d) ligating the cleaved DNA to create a ligated DNA not previously present in the sample, wherein the ligated DNA comprises sequence from both of the DNA sequences that formed the juxtaposition; and
(e) detecting the presence of the ligated DNA by identifying the presence of Checkpoint Charlies (CC markers) DNA sequences identified in step (a) in the ligated DNA.
2. A method according to claim 1 , wherein step (e) is carried out by amplifying the ligated DNA by PCR.
3. A method according to claim 1 wherein the DNA is eukaryotic DNA.
4. A method according to claim 1 wherein the DNA is plant, yeast, insect, marsupial, bird or mammalian DNA.
5. A method according to claim 1 wherein the DNA is human or rodent DNA.