# US 2010/0167944 A1 · Compositions and Methods for the Detection of Topoisomerase II Complexes with DNA

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- Number: US 2010/0167944 A1
- Document ID: US20100167944A1
- Status: Published application
- Kind: A1
- Application number: 12/487,789
- Filed: 2009-06-19
- Published: 2010-07-01
- Earliest claimed: 2004-09-09
- Assignees: The Children's Hospital of Philadelphia
- Inventors: Carolyn A. Felix; Donald A. Baldwin
- Web page: https://patentgrep.com/patent/US20100167944A1

## CPC

- C12Q 1/6876: Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q 2600/142: Toxicological screening, e.g. expression profiles which identify toxicity
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

Compositions, methods, and kits for detecting DNA topoisomerase II-DNA complexes are disclosed.

## Claims

### Claim 1

A method for identifying DNA sequences present in topoisomerase II-DNA complexes in cells, comprising:
a) isolating topoisomerase II-DNA complexes from the cell;
b) amplifying the DNA present in said isolated topoisomerase II-DNA complexes via polymerase chain reaction; and
c) identifying the sequences present in said amplified DNA, thereby identifying the sequences present in said topoisomerase II-DNA complexes.

### Claim 2 (depends on 1)

The method of claim 1, wherein the DNA in said topoisomerase II-DNA complexes is genomic DNA.

### Claim 3 (depends on 1)

The method of claim 1, wherein the identification of the DNA sequences in step c) comprises further amplifying the amplified DNA from step b) with gene specific primers.

### Claim 4 (depends on 1)

The method of claim 1, wherein the identification of the sequences in step c) comprises further amplifying the amplified DNA from step b) by real-time PCR.

### Claim 5 (depends on 1)

The method of claim 1, wherein the identification of the sequences in step c) comprises hybridizing the amplified DNA from step b) with a microarray.

### Claim 6 (depends on 1)

The method of claim 1, wherein said cells are CD34+ cells.

### Claim 7 (depends on 1)

The method of claim 1, wherein said amplified DNA of step b) comprises sequences from the myeloid lymphoid leukemia (MLL) gene.

### Claim 8 (depends on 1)

The method of claim 1, wherein said cells are exposed to an agent suspected of modulating formation of topoisomerase cleavage complexes.

### Claim 9 (depends on 5)

The method of claim 5, wherein said microarray comprises myeloid lymphoid leukemia (MLL) breakpoint cluster region (bcr) oligonucleotide sequences.

### Claim 10 (depends on 9)

The method of claim 9, wherein said MLL bcr oligonucleotide sequences hybridize to non-repetitive MLL bcr sequences.

### Claim 11 (depends on 9)

The method of claim 9, wherein said microarray further comprises oligonucleotide sequences from the Alu region between nucleotide positions 663-1779 in the MLL bcr.

### Claim 12 (depends on 9)

The method of claim 9, wherein said microarray further comprises control sequences which are not involved in MLL translocations.

### Claim 13

(canceled)

### Claim 14 (depends on 9)

The method of claim 9, wherein said microarray further comprises oligonucleotide sequences from MLL partner genes.

### Claim 15

(canceled)

### Claim 16 (depends on 5)

The method of claim 5, wherein said microarray comprises oligonucleotide sequences from myeloid lymphoid leukemia (MLL) partner genes.

### Claim at position 17

17-19. (canceled)

### Claim 20 (depends on 1)

The method of claim 1, wherein said isolating of topoisomerase II-DNA complexes of step a) comprises lysing said cells and immunoprecipitating said topoisomerase II-DNA complexes.

### Claim at position 19

21-33. (canceled)

### Claim 34 (depends on 1)

The method of claim 1, wherein said cells are obtained from a human.

### Claim 35 (depends on 9)

The method of claim 9, wherein said MLL bcr oligonucleotide sequences specifically hybridize to the MLL bcr under very high stringency conditions and wherein said bcr of the MLL gene is 8.3 kilobases between exons 5-11 of the MLL gene at chromosome band 11q23.

### Claim 36 (depends on 1)

The method of claim 1, wherein the identification of MLL sequences in the topoisomerase II-DNA complexes indicates the potential to develop MLL translocations.