The inventive subject matter described herein is related to the subject matter described in the following U.S. Patents and Published Patent Applications invented by Drs. Holger Schmidt and Aaron Hawkins. These patent documents enable novel devices and methods in the fields of integrated optofluidics (e.g., based on micron-scale liquid-core optical waveguides where light and fluids are guided on a chip, enabling novel methods for on-chip detection and manipulation of single particles for a new class of portable biomedical analytic instruments); nanopores in optofluidic devices (e.g., nanoscopic openings in membranes are used as electrical single molecule detectors using optofluidic devices to combine both electrical and optical detection on a single chip); and single-photon nonlinear optics (e.g., atomic vapor cells on an integrated optical waveguide chip enable the guiding of light through small volumes of rubidium vapor, which in turn enables the study of quantum interference effects on a chip, including induced transparency, slow light and single photon nonlinearities):                Publication Number: U.S. Pat. No. 8,005,332B2        Title: Integrated optical vapor cell apparatus for precision spectroscopy        Publication Date: 2011 Aug. 23        Publication Number: U.S. Pat. No. 7,995,890B2        Title: Device for light-based particle manipulation on waveguides        Publication Date: 2011 Aug. 9        Publication Number: U.S. Pat. No. 7,444,053B2        Title: Integrated electrical and optical sensor for biomolecule analysis with single molecule sensitivity        Publication Date: 2008 Oct. 28        Publication Number: U.S. Pat. No. 7,391,949B2        Title: Low loss hollow core optical waveguide        Publication Date: 2008 Jun. 24        Publication Number: U.S. Pat. No. 7,248,771B2        Title: Integrated sensor with electrical and optical single molecule sensitivity        Publication Date: 2007 Jul. 24        Publication Number: U.S. Pat. No. 7,149,396B2        Title: Apparatus for optical measurements on low-index non-solid materials based on arrow waveguides        Publication Date: 2006 Dec. 12        Publication Number: U.S. Pat. No. 7,127,146B2        Title: Apparatus for optical measurements on low-index non-solid materials based on arrow waveguides        Publication Date: 2006 Oct. 24        Publication Number: US20110253295A1        Title: Integrated Optical Vapor Cell Apparatus for Precision Spectroscopy        Publication Date: 2011 Oct. 20        Publication Number: US20090175586A1        Title: DEVICE FOR LIGHT-BASED PARTICLE MANIPULATION ON WAVEGUIDES        Publication Date: 2009 Jul. 9        Publication Number: US20080278710A1        Title: Integrated Optical Vapor Cell Apparatus for Precision Spectroscopy        Publication Date: 2008 Nov. 13        Publication Number: US20070122097A1        Title: Low loss hollow core optical waveguide        Publication Date: 2007 May 31        Publication Number: US20060251371A1        Title: Integrated electrical and optical sensor for biomolecule analysis with single molecule sensitivity        Publication Date: 2006 Nov. 9        Publication Number: US20060098927A1        Title: Integrated sensor with electrical and optical single molecule sensitivity        Application Date: 2005 Oct. 14        Publication Date: 2006 May 11        Publication Number: US20060008227A1        Title: Apparatus for optical measurements on low-index non-solid materials based on arrow waveguides        Publication Date: 2006 Jan. 12        Publication Number: US20040252957A1        Title: Apparatus for optical measurements on low-index non-solid materials based on arrow waveguides        Publication Date: 2004 Dec. 16        
FIG. 1a shows a planar optofluidic platform the inventors have developed for ultrasensitive fluorescence detection. (This platform is described in detail in the above-cited US patent documents.) Liquid-core antiresonant reflecting optical waveguides (ARROWS) with typical core dimensions of 5×12 μm (see SEM, bottom center, with super-imposed image of the guided mode) are interfaced with solid-core waveguides (see SEM in bottom right) at different points of the liquid core [26] (bracketed numerals refer to the literary references cited below). The devices are fabricated on a silicon chip using standard microfabrication techniques involving deposition of dielectric layers in combination with sacrificial layer etching [28-33]. Excitation light enters the liquid core through an orthogonally intersecting solid-core ARROW. Fluorescence from molecules in the core is collected perpendicularly in the chip plane and guided along the liquid-core channels [34]. This arrangement enables single particle sensitivity by creating femtoliter optical excitation volumes [35,36]. Fluidic reservoirs at the channel ends allow for channel filling and insertion of electrodes to induce electrokinetic particle movement. The photograph in the bottom left of FIG. 1 illustrates the optofluidic chip under test. This platform has successfully been used for fluorescence analysis of a variety of particles, including microbeads [37-39], single dye molecules [35,36], liposomes [40] and ribosomes, and virus capsids [41].
FIG. 1b shows the molecular beacon approach that can be used for specific detection of nucleic acids. Beacon detection is both highly sensitive and specific [42-44]. FIG. 1c shows the on-chip detection of single HPV-18 (human papillomavirus) DNA molecules as they flow by the excitation spot. This shows that amplification-free detection of pathogen nucleic acids is possible on a small optofluidic chip.
Integrated biosensing platforms are a topic of intense current research interest. With a wide range of biological targets (cells to molecular biomarkers), sensing mechanisms (optical, electrical, magnetic etc.), and deployment locations (clinical research labs to point-of-care), a unified description is virtually impossible. There is, however, widespread agreement over the fact that emerging molecular diagnostic instruments need to be compact, inexpensive, and simple in construction and use, while featuring high sensitivity and specificity. Simultaneous detection of multiple targets (“multiplexing”) is a valuable feature of such platforms.
Multiplex detection has been applied to different diagnostic targets, including nucleic acids (e.g. DNA microarrays [1,2], multiplex polymerase chain reaction (PCR) [3,4]), proteins (protein microarrays [5,6]) and others (e.g. ELISAs (enzyme-linked immunosorbent assays [7,8]). Detection is typically accomplished using optical fluorescence which bears the potential of both spatial (multiple detection locations) and spectral (multiple wavelengths) multiplexing and possible combinations of both. PCR methods are excellent examples for the significance of multiplexing. They are the current gold standard for molecular diagnostics, and the underlying nucleic acid detection is ideally suited for next generation genome-based analysis with a broad range of applications, including pathogen detection [9-11], mutation analysis [12,13], cancer detection [14-16], disease monitoring [17,18], and forensic studies [19-21]. Commercially available kits (e.g. Qiagen) allow for up to ˜16× multiplexing in 1000 parallel reactions, while research platforms such as the Virochip have demonstrated parallel amplification of up to 1,000 targets [22-24]. However, multiplex PCR is complex and slow [22] and requires a target amplification step with several drawbacks [10]. Therefore, an on-chip approach for molecular diagnostics that provides 10-100× target multiplexing without the need for target amplification is highly significant.