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Apparatus and method for analysis of nucleic acids hybridization on high density NA chips.

a nucleic acid hybridization and high density technology, applied in the field of new gene probe biosensors, can solve the problems of short shelf life of common labels and the safety hazards associated with the use of radioactive compounds, and achieve the effect of improving spectral sensitivity

Inactive Publication Date: 2002-09-05
POPONIN VLADIMIR
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Benefits of technology

[0017] The applicant has surprisingly and unexpectedly discovered, using a novel analytic technique, coupling near-field optics with SERS techniques, that each hybridization member in a hybridized pair of molecules (e.g., hybridized DNA fragments) has a unique spectrum of low frequency (lattice-type) vibrations. The novel analytic technique presented herein is employed in the novel spectroscopic instrument of the present invention, which is useful for detecting molecular hybridization. The novel instrument and methods presented herein enable vastly improved spectral sensitivity as compared to known methods.
[0018] One object of the present invention is to provide a more efficient, reliable, faster and more accurate method for direct detection of nucleic acid hybridization on high density nucleic acid chips. The invention provides direct spectroscopic detection of DNA-DNA, DNA-RNA, and RNA-RNA hybridization.
[0019] Among the many advantages of the apparatus and method of the present invention, are the ability to eliminate the need for labeling (by fluorescent or other labels) as is required in currently used methods. Furthermore, the apparatus and method of the present invention enable high throughput screening of DNA without the necessity for PCR amplification.

Problems solved by technology

A variety of disadvantages are associated with the use of radioactive labels, including the short shelf life of common labels and the safety hazards associated with the use of radioactive compounds.

Method used

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  • Apparatus and method for analysis of nucleic acids hybridization on high density NA chips.
  • Apparatus and method for analysis of nucleic acids hybridization on high density NA chips.

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third embodiment

[0041] In a third embodiment, random array technology may be used in combination with a fiber optic sensor (e.g., a sensor arrangement of the type disclosed in U.S. Pat. Nos. 5,244,636 and 5,244,813 ). In this embodiment, ultimate spatial resolution is 5 microns per pixel, enabling the speed at which the chip can be read to be reduced to microseconds. Optical IR fiber employed in the practice of the present invention may be single-mode fiber or a multi-mode fiber bundle. Multi-mode fiber bundles, which commonly have up to 2000 fibers in one bundle, may be used in multichannel recording.

[0042] A fiber coupler may be used to transfer illuminating and scattered optical signals into large aperture beams and vice versa. A splitter can be used to send reflected light through wide-field or confocal optics into the Raman spectrograph.

[0043] The preferred source of illuminating radiation is an argon ion laser, although other suitable radiation sources may be usefully employed in the general ...

first embodiment

[0045] Where the SNOM is employed (first embodiment above), a signal from the piezo scanning device 30 is transferred to the control electronics system.

[0046] The spectral range of Raman spectra used in the near field SERS molecular hybridization detection system of the present invention is preferably in the range of about 0 to about 1700 sm.sup.-1 with the preferred spectral interval ranging from about 0 to about 300 sm.sup.-1. It is anticipated that the best results will be in a spectral interval which ranges from 10 to about 150 sm.sup.-1.

[0047] The present invention also provides a method for detecting hybridization of molecules using the near field SERS technology of the present invention. The method is enabled by the fundamental property that single stranded and double stranded fragments of nucleic acids have different characteristic frequencies in Raman spectra. In fact, each complimentary fragment of DNA from a set of double stranded DNA fragments has an intrinsic low freque...

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Abstract

The invention generally relates to a new gene probe biosensor employing near field surface enhanced Raman scattering (NFSERS) for direct spectroscopic detection of hybridized molecules (such as hybridized DNA) without the need for labels, and the invention also relates to methods for using the biosensor.

Description

1. FIELD OF THE INVENTION[0001] 1.1 Brief Description of the Invention[0002] The invention disclosed herein relates to a new gene probe biosensor employing near field surface enhanced Raman scattering (NFSERS) for direct spectroscopic detection of DNA hybridization without the need for labels, and the invention also relates to methods for using the biosensor.[0003] 1.2 Background of the invention[0004] In 1928, C. V. Raman and his collaborator, K. S. Krishnan, established that the spectrum of inelastically scattered light can provide a unique fingerprint of molecular structure. Since this initial discovery, Raman spectroscopy has advanced dramatically. Many Raman-related analytical instruments have been developed, some of which have applicability to proteins and nucleic acids. Recent developments have enabled the use of Raman spectroscopy to obtain information such as conformation and / or orientation of molecules and some molecular groups, local hydrogen bonding interactions, and tim...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68
CPCC12Q1/6825C12Q2565/632
Inventor POPONIN, VLADIMIR
Owner POPONIN VLADIMIR
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