Single nucleotide polymorphic discrimination by electronic dot blot assay on semiconductor microchips

• US 20040058317A1
• Filed: 11/30/2000
• Published: 03/25/2004
• Est. Priority Date: 03/30/1999
• Status: Abandoned Application

• Current Assignee: Nanogen, Inc., United States Secretary of Health and Human Services is the head of the United States Department of Health and Human Services
• Original Assignee: Nanogen, Inc.
• Inventors: Wu, David J., Chanock, Stephen J., Foster, Charles B., Gilles, Patrick N., Dillon, Patrick J.
• Application Number:
  US09/727,030
• Publication Number:
  US 20040058317A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence

Abstract

A rapid assay for single nucleotide polymorphism (SNP) detection that utilizes electronic circuitry on silicon microchips is disclosed. The method provides accurate discrimination of amplified DNA samples following electronic assisted transport, concentration, and attachment of DNA to selected electrodes (test sites). The test sites make up organized arrays of samples that are distinguished by using internal controls of dual labeled reporters comprising wild-type and mismatched sequences to validate the SNP genotype. This method has been used to discriminate the complex quadra-allelic SNP of mannose binding protein.

Claims

1. A method for detecting at least one single nucleotide polymorphism in at least one patient nucleic acid containing sample using an electronically addressable microchip having a plurality of test sites, wherein each test site comprises an individually controllable electrode covered by a permeation layer, the method comprising:

i. providing at least one sample nucleic acid containing at least one target nucleic acid sequence of interest that contains at least one single nucleotide polymorphism locus;

ii. electronically biasing one or more specified test sites on the microchip in order to concentrate the sample nucleic acid at the specified test sites;

iii. immobilizing the sample nucleic acid onto the test sites;

iv. electronically hybridizing a mixture comprising first and second differently labeled nucleic acid probes to the immobilized sample nucleic acid to form hybridized complexes, wherein the first probe contains a sequence specific for one allele of the single nucleotide polymorphism of the locus, and the second probe contains a sequence differing from the first sequence by a single base;

v. performing electronic stringency on said hybridized complexes to destabilize hybridization complexes comprising at least one mismatch between the immobilized sample nucleic acid and the hybridized probe; and

vi. detecting hybridization complexes that remain following the electronic stringency step (v) by detecting the hybridized labeled probes.

2. The method of claim 1, further comprising the step of subjecting the sample nucleic acid containing the target nucleic acid sequence in the patient sample to an amplification reaction whereby the amount of sample nucleic acid containing the target nucleic acid sequence is increased.

3. The method of claim 1 wherein the single nucleotide polymorphism locus is bi-allelic.

4. The method of claim 1 wherein the single nucleotide polymorphism locus is multi-allelic.

5. The method of claim 1 wherein at least one target nucleic acid sequence of interest is selected from the group consisting of whole or partial naturally occurring nucleic acid sequences encoding (1) mannose binding protein, (2) Fc-gamma receptors, (3) major histocompatibility complex proteins, (4) Interleukin 1β

, (5) lymphotoxin, and (6) tumor necrosis factor α

.

6. The method of claim 1 further comprising providing at least one control target nucleic acid, wherein the control target nucleic acid contains a sequence specific for an allele of the single nucleotide polymorphism locus, and wherein the control target nucleic acid is immobilized at a selected test site.

7. The method of claim 2 wherein the sample nucleic acid further comprises a biotin moiety, and the sample nucleic acid is immobilized on the selected test sites by a biotin-streptavidin interaction.

8. The method of claim 1 wherein the electronic stringency step (v) is carried out until the detectable signal from hybridization complexes comprising at least one mismatch between the immobilized target nucleic sequence and the hybridized probe is significantly reduced as compared to the detectable signal from hybridization complexes without any mismatch between the immobilized target nucleic sequence and the hybridized probe.

9. The method of claim 8 wherein the electronic stringency step (v) is carried out until the detectable signal from hybridization complexes comprising at least one mismatch between the immobilized target nucleic sequence and the hybridized probe is approximately the same as a background signal.

10. The method of claim 8 further comprising monitoring the detectable signal from the from hybridization complexes between the immobilized target nucleic sequence and the hybridized probes with a monitoring device in real time various stages of electronic hybridization and electronic stringency in order to determine when the detectable signal from hybridization complexes comprising at least one mismatch between the immobilized target nucleic sequence and the hybridized probe is significantly reduced.

11. The method of claim 10 wherein a controller for the power level or length of time of the electronic stringency applied in step (v) is functionally connected to a microprocessor which is functionally connected to the monitoring device, whereby the extent of the electronic stringency applied in step (v) is reduced or ceased in response to the detection of a significantly reduced detectable signal.

12. The method of claim 1 wherein the first and second nucleic acid probes both contain a sequence specific for an allele of the single nucleotide polymorphism locus.

13. The method of claim 1 wherein the first and second nucleic acid probes are differently labeled with different fluorophores.

14. The method of claim 13 wherein the different fluorophores are Cy3 and Cy5.

15. The method of claim 1 wherein a plurality of sample nucleic acids from each patient sample are immobilized on one test site, and wherein each sample nucleic acid contains a target nucleic acid sequence containing a different single nucleotide polymorphism locus.

16. The method of claim 1 wherein a plurality of sample nucleic acids from each patient sample are immobilized on a selected group of test sites, wherein each sample nucleic acid is immobilized on at least one separate test site, and wherein each sample nucleic acid contains a target nucleic acid sequence containing a different single nucleotide polymorphism locus.

17. The method of claim 1 wherein a plurality of patient samples are provided and immobilized on the microchip, and wherein sample nucleic acids from each patient sample are immobilized on a different set of selected test sites on the microchip during steps (iv) through (vi).

18. The method claim 17 wherein said patient sample nucleic acids are sequentially immobilized onto the test sites by repeating steps (ii) and (iii) for each patient sample.

19. The method of claim 1 wherein step (iv) is repeated with at least one additional mixture of first and second probes.

20. The method of claim 1 further comprising the steps of:

(a) stripping all hybridized probes from the immobilized sample nucleic acids using a method selected from the group consisting of electronic denaturing, chemical denaturing, thermal denaturing, and combinations thereof; and

(b) repeating steps (iv) through (vi) with at least one additional mixture of first and second probes.

21. The method of claim 20 wherein the patient'"'"'s genotype for more than one single nucleotide polymorphism locus is determined from the data gathered in the multiple steps (vi).