Reverse detection for identification and/or quantification of nucleotide target sequences on biochips

• US 20030157528A1
• Filed: 12/13/2002
• Published: 08/21/2003
• Est. Priority Date: 06/14/2000
• Status: Abandoned Application

• Current Assignee: Eppendorf Array Technologies SA (Eppendorf Se)
• Original Assignee: Eppendorf Array Technologies SA (Eppendorf Se)
• Inventors: Art, Muriel, Remacle, Jose, Zammatteo, Nathalie, Lockman, Laurence
• Application Number:
  US10/311,195
• Publication Number:
  US 20030157528A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence

Abstract

The present invention relates to a method for the identification and/or the quantification of one or more target nucleotide sequences (3) present homologous to each other and being possibly present in a sample and discrimination from possibly homologous sequences, by using two sets of nucleotide sequences (1 and 2), wherein a first set of nucleotide sequences possibly labelled (1) bind specifically to said target nucleotide sequences (3) in a first step and are detected and/or quantified through hybridisation with a second set of capture nucleotide sequences (2) having at least a part of sequence complementary to the possibly labelled nucleotide sequence (1) of the first set of nucleotide sequences, said capture nucleotide sequence (2) being immobilised upon the surface (4) of a solid support according to an array of at least 4 discrete regions/cm², each of said discrete regions being bonded with one species of capture nucleotide sequences (2), and wherein the identification and quantification of the binding between the possibly labelled nucleotide sequence (1) and their corresponding capture nucleotide sequence (2) is correlated with the identification and the quantification of a target nucleotide sequence (3) present in the sample.

Claims

1. Method for the identification and/or the quantification of one or more target nucleotide sequences (3) present homologous to each other and being possibly present in a sample and discrimination from possibly homologous sequences, by using two sets of nucleotide sequences (1 and 2), wherein a first set of nucleotide sequences possibly labelled (1) bind specifically to said target nucleotide sequences (3) in a first step and are detected and/or quantified through hybridisation with a

second set of capture nucleotide sequences (2) having at least a part of sequence complementary to the possibly labelled nucleotide sequence (1) of the first set of nucleotide sequences, said capture nucleotide sequence (2) being immobilised upon the surface (4) of a solid support according to an array of at least 4 discrete regions/cm², each of said discrete regions being bonded with one species of capture nucleotide sequences (2), and wherein the identification and quantification of the binding between the possibly labelled nucleotide sequence (1) and their corresponding capture nucleotide sequence (2) is correlated with the identification and the quantification of a target nucleotide sequence (3) present in the sample.

2. The method according to claim 1, wherein between the first step and the second step, the possibly labelled sequence of the first set of nucleotide sequences which are not bound to the target nucleotide sequence (3) are removed and the possibly labelled sequences (1) of the first set of nucleotide sequences bound to the target nucleotide sequence (3) are deshybridised from each other before their reuse in the second step.

3. The method according to claim 1 or 2, wherein the target nucleotide sequences (3) are firstly bound upon the solid support (4), preferably by covalent binding before its hybridisation binding with one or more possibly labelled sequences (1) of the first set of nucleotide sequences.

4. The method according to claim 1 or 2, wherein the binding between the target nucleotide sequences (3) and the possibly labelled sequences (1) of the first set of nucleotide sequences occurs in solution.

5. The method according to any of the preceding claims 1 to 4, wherein the possibly labelled sequences (1) of the first set of nucleotide sequences have a length which is essentially identical or similar (preferably higher than 80% similar) to the length of the capture nucleotide sequences (2) of the second set of nucleotide sequences.

6. The method according to any of the preceding claims, wherein the target nucleotide sequences (3) to be identified and/or quantified present an homology with homologous sequences present in the sample higher than 30%, preferably higher than 60%, more preferably higher than 80%.

7. The method according to any of the preceding claims, wherein the target nucleotide sequences (3) to be identified and/or quantified differ from homologous sequences by only one base.

8. The method according to any of the preceding claims, wherein the possibly labelled nucleotide sequences (1) contain a part of a portion of their sequences comprised between 10 and 60 bases, a sequence which is specific to the target nucleotide sequence (3).

9. The method according to any of the preceding claims, wherein the capture nucleotide sequences of the second set of nucleotide sequences present a sequence which is complementary to the possibly labelled nucleotide sequences (1).

10. The method according to the claim 9, wherein the capture nucleotide sequences (2) of the second set of claims have a sequence which is complementary to the possibly labelled nucleotide sequences (1) of the first set of nucleotide sequences upon their complete sequence or have a sequence which is bound to the solid support through spacers having a length comprised between 10 and 200 bases.

11. The method according to any of the preceding claims, wherein the possibly labelled nucleotide sequences (1) contain part of their sequence being not specific of the target but specific of their capture probes.

12. The method according to any of the preceding claims, wherein the labelled nucleotide sequences (1) contain a mixture of two or more labelled sequences terminated by a different nucleotide which binds to the target sequence adjacent to the possible SNP, one of the end nucleotide being perfectly matched to the SNP, and another annexed probe which will bind to the other site of the SNP target, the perfectly matched probe being ligated to this probe by a ligase before detected on the capture probe array.

13. The method according to any of the preceding claims, wherein the labelled nucleotide sequences (1) contain a mixture of probes each one differing in at least one base located at the SNP site and treated with a specific nuclease before being detected on the capture probe array.

14. The method according to any of the preceding claims, wherein the one or more target nucleotide sequences (3) to be detected and/or quantified are rRNAs, preferably selected from the group consisting of 16S, 23S, 18S and 25S rRNAs.

15. The method according to any of the preceding claims 1 to 14, wherein the one or more target nucleotide sequences (3) to be detected and/or quantified are mRNAs, preferably a mRNA retrotranscripted into a cDNA by a consensus sequence.

16. The method according to any of the preceding claims, wherein the solid support is selected from the group consisting of glass, electronic device, silicon support, plastic support, compact disc, filter, metallic support, polylysine coated surfaces or a mixture thereof.

17. A diagnostic and/or quantification apparatus of one or more homologous target nucleotide sequences possibly present in a sample, which comprises means to perform the method according to any of the preceding claims.

18. Apparatus according to claim 17, characterised in that it comprises two separate chambers (5 and 6), each being dedicated to one of the step performed in the method according to any of the preceding claims 1 to 16.

19. The apparatus according to claim 17 or 18, wherein the chamber comprises a solid support upon which capture nucleotide sequences (2) are immobilised upon its surface according to an array of at least 4 discrete regions/cm², each of said discrete regions being bound with one species of nucleotide sequences.

20. A machine or automate for performing the various steps of the method according to any of the preceding claims 1 to 16 upon an apparatus according to claims 17 to 19.