Optical analysis of molecules

• US 7,313,308 B2
• Filed: 01/24/2007
• Issued: 12/25/2007
• Est. Priority Date: 09/17/2004
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Turner, Stephen, Korlach, Jonas
• Primary Examiner(s): Wells, Nikita
• Application Number:
  US11/626,610
• Publication Number:
  US 20070206189A1
• Time in Patent Office: 335 Days
• Field of Search: None
• US Class Current: 385/129
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• CPC Class Codes: G01N 2021/6463 Optics
• CPC Class Codes: G01N 2021/7786 Fluorescence
• CPC Class Codes: G01N 21/00 Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light G01N3/00 - G01N19/00 take precedence
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/645 Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/648 using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
• CPC Class Codes: G01N 21/77 by observing the effect on a chemical indicator
• CPC Class Codes: G01N 2201/06113 Coherent sources; lasers

Abstract

The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughout and low-cost single-molecular analysis.

Claims

1. An array of optical confinements for characterizing molecules and/or monitoring a chemical reaction, said array having a surface density exceeding 4×

10⁴ confinements per mm², wherein individual confinement in the array permits resolution of individual molecules present at a concentration higher than about 1 micromolar.

2. An array of optical confinements for characterizing molecules and/or monitoring a chemical reaction, said array having a surface density exceeding 4×

10⁴ confinements per mm², wherein individual confinement in the array provides an effective observation volume less than about 1000 zeptoliters.

3. A method of detecting interactions among a plurality of molecules, comprising:

placing the plurality of molecules in close proximity to an array of zero-mode waveguides, wherein individual waveguides in the array are separated by a distance sufficient to yield detectable intensities of diffractive scattering at multiple diffracted orders upon illuminating the array with an incident wavelength;

illuminating the array of zero-mode waveguides with an incident wavelength; and

detecting a change in the intensities of diffractive scattering of the incident wavelength at the multiple diffracted orders, thereby detecting the interactions among a plurality of molecules.

4. A method of reducing diffractive scattering upon illuminating an array of optical confinement with an incident wavelength, wherein the array comprises at least a first optical confinement and a second confinement, said method comprising:

forming the array of optical confinements wherein the first zero-mode waveguide is separated from the second zero-mode waveguide by a distance such that upon illumination with the incident wavelength, intensity of diffractive scattering resulting from the first zero-mode waveguide at a given angle is less than that if the first zero-mode waveguide were illuminated with the same incident wavelength in the absence of the second zero-mode waveguide.

5. A method of fabricating an array of optical confinements that exhibits a minimal intensity of diffractive scattering of an incident wavelength, comprising:

providing a substrate; and

forming the array of optical confinements on the substrate such that individual confinements in the array are separated from each other at a distance less than one half of the wavelength.

6. A method of creating a plurality of optical confinements having a surface density exceeding 4×

10⁴ confinements per mm², wherein individual confinement in the array permits resolution of individual molecules present at a concentration higher than at least about 1 micromolar, comprising;

providing a substrate;

forming an array of optical confinements having a surface density exceeding 4×

10⁴ confinements per mm², wherein the individual confinement comprises a zero-mode waveguide comprising;

a cladding surrounding a core, wherein said cladding is configured to preclude propagation of electromagnetic energy of a frequency less than a cutoff frequency longitudinally through the core of the zero-mode waveguide; and

illuminating the array with an electromagnetic radiation of a frequency less than the cutoff frequency, thereby creating a plurality of optical confinements.