Reading dry chemical arrays

Details Reading dry chemical arrays Reading dry chemical arrays

2002-04-30

2004-09-14

Stafira, Michael P. (Department: 2877)

Optics: measuring and testing

Of light reflection

C422S082080, C435S808000

Reexamination Certificate

active

06791690

ABSTRACT:

FIELD OF THE INVENTION
This invention relates to arrays, particularly biopolymer arrays such as DNA or protein arrays, which are useful in diagnostic, screening, gene expression analysis, and other applications.
BACKGROUND OF THE INVENTION
Polynucleotide arrays (such as DNA or RNA arrays) and peptide array, are known and may be used, for example, as diagnostic or screening tools. Such arrays include regions (sometimes referenced as spots or features) of usually different sequence polynucleotides or peptides arranged in a predetermined configuration on a substrate. The array is “addressable” in that different features have different predetermined locations (“addresses”) on a substrate carrying the array.
Biopolymer arrays can be fabricated using in situ synthesis methods or deposition of the previously obtained biopolymers. The in situ fabrication methods include those described in U.S. Pat. No. 5,449,754 for synthesizing peptide arrays, and in U.S. Pat. No. 6,180,351 and WO 98/41531 and the references cited therein for polynucleotides. In situ methods also include photolithographic techniques such as described, for example, in WO 91/07087, WO 92/10587, WO 92/10588, and U.S. Pat. No. 5,143,854. The deposition methods basically involve depositing biopolymers at predetermined locations on a substrate which are suitably activated such that the biopolymers can link thereto. Biopolymers of different sequence may be deposited at different feature locations on the substrate to yield the completed array. Procedures known in the art for deposition of biopolymers, particularly DNA such as whole oligomers or cDNA, are described, for example, in U.S. Pat. No. 5,807,522 (touching drop dispensers to a substrate), and in PCT publications WO 95/25116 and WO 98/41531, and elsewhere (use of a pulse jet in the form of a piezoelectric inkjet head).
Further details of large scale fabrication of biopolymer arrays by depositing either previously obtained biopolymers or by the in situ method, are disclosed in U.S. Pat. No. 6,242,266, U.S. Pat. No. 6,232,072, U.S. Pat. No. 6,180,351, and U.S. Pat. No. 6,171,797.
In array fabrication, the quantities of DNA available for the array are usually very small and expensive. Sample quantities available for testing are usually also very small and it is therefore desirable to simultaneously test the same sample against a large number of different probes on an array. These conditions require the manufacture and use of arrays with large numbers of very small, closely spaced features.
The arrays, when exposed to a sample, will exhibit a binding pattern. The array can be read by observing this binding pattern by, for example, labeling all targets such as polynucleotide targets (for example, DNA), in the sample with a suitable label (such as a fluorescent compound), scanning an illuminating beam across the array and accurately detecting the fluorescent signal from the different features of the array. Assuming that the different sequence polynucleotides were correctly deposited in accordance with the predetermined configuration, then the observed binding pattern will be indicative of the presence and/or concentration of one or more polynucleotide components in the sample. Peptide or arrays of other chemical moieties can be used in a similar manner. Conventionally, the illuminating and detecting have been performed on a dry array from a forward direction facing a front surface of the array carrying the array features, so that the illuminating and detected light need not pass through the substrate. In an alternative known arrangement, a transparent substrate forms part of a chamber in a housing with the array on a front substrate surface facing inward to the chamber. After exposure to a liquid containing the sample, the chamber is flushed and again filled with a liquid and the liquid containing chamber positioned in the array reading apparatus. In this situation, aside from the flushing and re-filling of the chamber, care must be taken that liquid does not leak from the chamber while positioned in the reading apparatus. The illuminating and detecting in this case has, of necessity, been performed in a backward direction through the substrate and onto the array while it is immersed in the liquid.
Techniques and apparatus for scanning chemical arrays are described, for example, in U.S. Pat. No. 5,763,870 and U.S. Pat. No. 5,945,679. Apparatus which reads an array by scanning an illuminating beam by the foregoing technique are often referred to as scanners and the technique itself often referred to as scanning. Conventionally, such scanning has been done by illuminating array features on a front surface of the substrate one pixel at a time.
Array scanners typically use a laser beam as a light source, which is scanned over pixels covering the array features. A detector (typically a fluorescence detector) with a very high light sensitivity is normally desirable to achieve maximum signal-to-noise in detecting hybridized molecules, particularly in array scanners used for DNA sequencing or gene expression studies. At present, photomultiplier tubes (“PMTs”) are still the detector of choice although charge coupled devices (“CCDs”) and avalanche photodiodes (“APDs”) can also be used. PMTs and APDs are typically used for temporally sequential scanning of array features, while CCDs permit scanning many features in parallel (for example, one line of features simultaneously, in which case an illuminating line may be used).
When a sample component only weakly binds to an array feature (due to a low concentration of that component in the sample) the resulting fluorescence signal from that feature will be low. To be able to detect such low signal features, it is important to detect the resulting low signal with a high signal to noise ratio. It is also desirable to have a reading method where a liquid filled chamber containing the array is not positioned within the scanner.
SUMMARY OF THE INVENTION
One of the items recognized by the present invention is that when a dry array on a front surface of a substrate is interrogated or read from a forward position, the power density of the interrogating light or light emitted in response to the interrogating light, or both, can be reduced as a result of Fresnel reflection. This may consequently lead to a reduced detected signal from an array feature.
In one aspect then, the present invention provides a method of interrogating an addressable array unit having a substantially unreflective substrate with a front surface, and a dry array on the front surface having a plurality of different chemical features (for example, polynucleotide features of different sequence). In one configuration the method may include directing an interrogating light from a position forward of the front surface onto the chemical features of the dry array. In an additional or alternative configuration the method may include detecting light directed in a forward direction which is emitted from respective features in response to the interrogating light. The substrate may be substantially unreflective by virtue of there being no metallic or semi-metallic (for example, no silicon) coating present, and can also optionally be a transparent substrate.
In a first configuration, the detected light is emitted from locations of the features positioned within an ⅛ wavelength of an antinode resulting from either directly incident interrogating light (that is, directly incident on the emitting locations) and interrogating light reflected by the substrate (to the emitting locations), or from directly detected emitted light and emitted light reflected by the substrate. That is, the majority (or optionally at least 60%, 70%, 80%, 90% or 95%) of detected light is from such features. In a second configuration the substantially unreflective substrate may include a transparent layer extending between the front surface of the substrate and a next layer, and which transparent layer has a thickness t. This transparent layer may function as a spacer layer or anti-reflective layer, as discussed

Affiliated with

Also associated with

Rating

Reading dry chemical arrays does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Reading dry chemical arrays, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Reading dry chemical arrays will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-3258889