Compositions for chromosome-specific staining

• US 5,756,696 A
• Filed: 12/23/1994
• Issued: 05/26/1998
• Est. Priority Date: 01/16/1986
• Status: Expired due to Term

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Pinkel, Daniel, Gray, Joe W.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/364,400
• Time in Patent Office: 1,250 Days
• Field of Search: 435/5, 435/6, 435/810, 436/501, 536/23.1, 536/24.1, 536/24.3-24.33, 935/77, 935/78
• US Class Current: 536/23.1
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6879 for sex determination
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Claims

1. Nucleic acid probes for use in in situ hybridization comprising a heterogeneous mixture that contains labeled nucleic acid fragments that are substantially complementary to unique nucleic acid segments, wherein said mixture comprises blocking nucleic acid having nucleic acid fragments which are substantially complementary to repetitive segments in the labeled nucleic acid, produced by the process of:

(a) obtaining chromosome-specific DNA fragments;

(b) amplifying said chromosome-specific DNA fragments;

(c) labeling said chromosome-specific DNA fragments with a fluorescent or affinity label; and

(d) adding sufficient blocking nucleic acid to prevent substantial binding of the labeled nucleic acid sequences to repetitive nucleic acid sequences in a target DNA.

2. Nucleic acid probes according to claim 1, wherein said step (b) of amplifying said chromosome-specific DNA fragments is performed by using a PCR process.

3. Nucleic acid probes according to claim 1, wherein said probes have a combined complexity of greater than about 40 kb.

4. Nucleic acid probes according to claim 3, wherein said probes have a combined complexity of between about 40 and about 100 kb.

5. Nucleic acid probes according to claim 1, wherein said probes have a combined complexity of greater than about 50 kb.

6. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled by direct attachment of a fluorochrome.

7. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are immunochemically labeled.

8. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled with biotin.

9. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled by direct attachment of an enzyme.

10. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled by modification with N-acetoxy-N-2-acetylaminofluorene.

11. Nucleic acid probes according to claim 1, wherein said labeled nucleic acid fragments are complementary to the total genomic complement of chromosomes, fragments complementary to a single chromosome, fragments complementary to a subset of chromosomes, or fragments complementary to a subregion of a single chromosome.

12. Nucleic acid probes according to claim 11, wherein said labeled nucleic acid fragments are selected from the nucleic acid of normal human chromosomes 1 through 22, X and Y.

13. Nucleic acid probes according to claim 12, wherein said labeled nucleic acid fragments are selected from the nucleic acid of chromosome 21.