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High resolution DNA detection methods and devices

a dna detection and high-resolution technology, applied in the field of high-resolution dna detection methods and devices, can solve the problems of high system costs, and ineffective gene chip systems

Inactive Publication Date: 2005-12-29
CONNOLLY DENNIS MICHAEL
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0006]FIG. 2 is a variation on the method shown in FIG. 1 using a ligase method to distinguish a single base variation. The variation is identified by the asterisk. After step D, a ligase is used. Only those targets which have an exact match at the ends

Problems solved by technology

Such a system is expensive to use and is not amenable to a portable system for biological sample detection and identification.
Furthermore, the hybridization reactions take up to two hours.
For many potential uses, such as detecting biological warfare agents, the gene chip system is simply not effective.

Method used

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  • High resolution DNA detection methods and devices
  • High resolution DNA detection methods and devices

Examples

Experimental program
Comparison scheme
Effect test

example 1

Preparation of a Sample to Detect Pathogens

[0082] A sample to be tested is isolated. A common sample would be a blood sample from a patient. The sample is injected into the device. The sample moves into a chamber where it is treated chemically, with detergents, and enzymatically, with proteases to free nucleic acid molecules from cells in the sample. Heat treatment is also used to facilitate the release of the nucleic acid molecules. For that reason, proteins used in the present invention are preferably thermostable. The mixture may then pass though a filter on the chip to partially purify the nucleic acid molecules.

example 2

Preparation of Oligonucleotide Probe Sets

[0083] Each oligonucleotide probe set is selected so that the two probes are complimentary to a portion of the target nucleic acid molecule and so that the two portions of the target nucleic acid molecule are located sufficiently far apart that the nucleic acid molecule can bridge the gap between the two probes on the device when they are both bound. The complimentary sequences will be chosen such that there is some additional length to allow the target nucleic acid molecule to move freely when bound by one probe, so that it may access the second probe. Preferably the molecule will not be much longer than needed to easily bridge the gap. As the length of the molecule increases the chance of it locating the second probe decreases, because the effective concentration of the binding site on the target molecule decreases as the volume in which it can move increases.

[0084] Each probe set will be attached to a substrate so that they are positione...

example 3

Testing for the Presence of the Target Nucleic Acid Molecule

[0085] The probe sets will be contacted with the nucleic acid molecules. The test chamber has a small volume to facilitate binding of the target to the probe. To increase the chance of binding, the sample is circulated multiple times through the test chamber. The sample will flow through a test chamber containing the probe sets, at a flow rate sufficiently low to allow the target nucleic acid molecules to bind to a probe. Conditions are determined by the length and sequence of the probe.

[0086] The conditions will be set at a level where the stringency is sufficient to eliminate non-specific binding to the probes. The target nucleic acid molecule is contacted with the probes under stringent conditions. The stringent conditions for hybridization are by the nucleic acid, salt, and temperature. These conditions are well known in the art and may be-altered in order to identify or detect identical or related polynucleotide sequ...

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Abstract

The present invention provides methods and devices for detecting a target nucleic acid molecule. A set of oligonucleotide probes integrated into an electric circuit, where the oligonucleotide probes are positioned such that they can not come into contact with one another, are contacted with a sample. If the sample contains a target nucleic acid molecule, one which has sequences complimentary to both probes, the target nucleic acid molecule can bridge the gap between the probes. The resulting bridge can then carry electrical current between the two probes, indicating the presence of the target nucleic acid molecule.

Description

BACKGROUND OF THE INVENTION [0001] DNA identification technology has numerous uses including identification of pathogenic organisms, genetic testing, and forensics. Advances have been made to allow for automated screening of thousands of sequences concurrently. Gene chip technologies exist where DNA probes are immobilized on a substrate such as a glass or silicon chip. A sample containing nucleic acid molecules is applied to the chip and the nucleic acid molecules within the sample are allowed to hybridize to the probe DNA on the chip. Fluorescence detection is typically used to identify double stranded nucleic acid molecule products. The advantage of the system is the ability to screen hundreds or thousands of sequences using automated systems. [0002] Hybridization screening with fluorescence detection is a powerful technique for detecting nucleic acid sequences. However, in order to detect target DNA molecules, the target must first be amplified by PCR to get a reliable signal. Th...

Claims

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Application Information

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IPC IPC(8): G01N33/53C12M1/00C12M1/34C12N15/09C12Q1/25C12Q1/37C12Q1/68C12Q1/6816C12Q1/6825C12Q1/689C12Q1/70C40B40/06G01N1/02G01N33/569G01N37/00H01L51/30
CPCB01J2219/00529C12Q1/6883B01J2219/00722B82Y10/00C12Q1/6816C12Q1/6825C12Q1/689C12Q1/70C40B40/06G01N2001/021H01L51/0093B01J2219/00653Y10S436/806Y10S436/807C12Q2565/607C12Q2523/313C12Q2565/543H10K85/761
Inventor CONNOLLY, DENNIS MICHAEL
Owner CONNOLLY DENNIS MICHAEL
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