Apparatus, systems and method for locating nucleic acids bound to surfaces
First Claim
1. An apparatus with self-locating nucleic acid positions in an array comprising:
- a substrate having a surface;
a first plurality of nucleotide sequences bound to the surface of the substrate;
regions on the substrate surface that are devoid of the first plurality of nucleotide sequences, wherein the first plurality of nucleotide sequences comprise a first optically detectable contrast from the regions; and
a second plurality of nucleotide sequences hybridized to complementary nucleotide sequences of the first plurality of nucleotide sequences, the second plurality of nucleotide sequences comprising a second optically detectable contrast distinguishable from the first optically detectable contrast, wherein the first optically detectable contrast comprises a first optical signal and the second optically detectable contrast comprises a second optical signal when scanned with an optical scanner, the first optical signal being independent of the second optical signal, such that the first optical signal indicates the location of the first plurality of nucleotide sequences in the array independently of the hybridization by the second plurality of nucleotide sequences.
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Abstract
An apparatus, systems and method for locating nucleic acids in an array on a substrate have self-locating nucleic acid features. The nucleic acid features produce nucleotide-dependent location signals or optically detectable contrast between nucleotide-bound regions and non-nucleotide-bound regions of the substrate when scanned by an optical scanner. When used as analytical tools for monitoring gene expression and mutations in gene sequences, the nucleotide features are hybridized with nucleic acids of known or unknown sequences. The apparatus, systems and method locate both weakly and strongly hybridized nucleotide features on the substrate for identification of target nucleic acid sequences. The nucleotide feature signals or contrast are independent of the optical signals conventionally produced by the hybridized nucleotides. Therefore, the apparatus, systems and method locate all of the nucleotide features, hybridized or not, independently of the extent of hybridization. The present invention advantageously self-locates both bright and dim hybridized features on an array substrate and is therefore, independent of the random and systematic errors associated with the manufacturing equipment and processes. Moreover, the present invention provides a powerful quality control tool to the in situ synthesis process. The present invention provides information about what part or percentage of each feature contains full-length probes. The present optical scanning system detects optical signals from the nucleotide features independently of the signals from the hybridized nucleotides using essentially conventional scanning technology. The independently detected signals are processed such that all features are located and the hybridized features are accurately detected and analyzed.
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Citations
34 Claims
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1. An apparatus with self-locating nucleic acid positions in an array comprising:
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a substrate having a surface;
a first plurality of nucleotide sequences bound to the surface of the substrate;
regions on the substrate surface that are devoid of the first plurality of nucleotide sequences, wherein the first plurality of nucleotide sequences comprise a first optically detectable contrast from the regions; and
a second plurality of nucleotide sequences hybridized to complementary nucleotide sequences of the first plurality of nucleotide sequences, the second plurality of nucleotide sequences comprising a second optically detectable contrast distinguishable from the first optically detectable contrast, wherein the first optically detectable contrast comprises a first optical signal and the second optically detectable contrast comprises a second optical signal when scanned with an optical scanner, the first optical signal being independent of the second optical signal, such that the first optical signal indicates the location of the first plurality of nucleotide sequences in the array independently of the hybridization by the second plurality of nucleotide sequences. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A system for locating nucleic acid positions in an array comprising:
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a substrate having a surface;
a first plurality of nucleotide sequences bound to the surface of the substrate;
regions on the substrate surface that are devoid of the first plurality of nucleotide sequences, wherein the first plurality of nucleotide sequences comprise a first optically detectable contrast from the regions;
a second plurality of nucleotide sequences hybridized to at least some sequences of the first plurality of nucleotide sequences, the second plurality of nucleotide sequences comprising a second optically detectable contrast distinguishable from the first optically detectable contrast; and
an optical system for optically scanning the surface of the substrate, such that the first optically detectable contrast comprises a first optical signal and the second optically detectable contrast comprises a second optical signal independently of the first optical signal, for detecting the first optical signal independently of the second optical signal, for analyzing the first optical signal to locate the first plurality of nucleotide sequences, and independently for analyzing the second optical signal for hybridization by the second plurality of nucleotide sequences on the substrate. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19)
a first detection subsystem for detecting the first optical signal having a first input and a first output; a second detection subsystem for detecting the second optical signal independently of the first detection subsystem and having a second input and a second output; and
an analysis subsystem having inputs and outputs, wherein the first output from the first detection subsystem and second output from the second detection subsystem are received by the inputs of the analysis subsystem, and wherein the outputs of the analysis subsystem comprise the location of the first plurality of nucleotide sequences and the location of the second plurality of nucleotide sequences on the substrate.
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18. The system of claim 17, wherein the optical scanning system further comprises a signal filtering device and a full reflector, the signal filtering device comprising one or more of a dichroic reflector, an interference filter and a monochrometer, wherein the signal filtering device filters the first optical signal from the second optical signal and the full reflector directs the first optical signal into the first detection subsystem.
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19. The system of claim 17, wherein the optical scanning system further comprises a partial reflecting device for reflecting the first optical signal into the first detection subsystem and for reflecting signal noise absorbing device.
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20. A method for locating nucleic acid positions on a substrate comprising the steps of:
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providing a first plurality of nucleotide sequences on a substrate surface in a pattern such that there are regions on the substrate surface that are devoid of the first plurality of nucleotide sequences, the first plurality of nucleotide sequences comprising a first optically detectable contrast from the regions;
hybridizing at least some of the first plurality of nucleotide sequences with a second plurality of nucleotide sequences, the second plurality of nucleotide sequences comprising a second optically detectable contrast distinguishable from the first optically detectable contrast;
optically scanning the substrate surface such that the first optically detectable contrast comprises a first optical signal and the second optically detectable contrast comprises a second optical signal;
independently detecting the first optical signal and the second optical signal; and
determining the locations of the first plurality of nucleotide sequences and the second plurality of nucleotide sequences on the substrate based on the detected first optical signal and the detected second optical signal. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
a plurality of sequential steps of adding a nucleotide to a single end of each polynucleotide sequence; and
after the last step of adding, the step of labeling a last nucleotide of the full-length polynucleotide sequences with a member of a signal producing system.
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30. The method of claim 29, wherein the step of labeling comprises the step of adding a label as the member of the signal producing system to the last nucleotide of the full-length polynucleotide sequences and wherein the step of determining comprises further determining what percentage of the first plurality of nucleotide sequences contains the full-length polynucleotide sequences from the first optical signal produced by the member.
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31. The method of claim 30, wherein the step of adding a label comprises adding a member of a specific binding pair to the last nucleotide of the full-length polynucleotide sequences.
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32. The method of claim 31, wherein the step of hybridizing comprises the step of adding a complementary member to the member of the specific binding pair on the last nucleotide of the full-length polynucleotide sequences.
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33. The method of claim 31, further comprising, after the step of hybridizing, the step of adding a complementary member to the member of the specific binding pair on the last nucleotide of the full-length polynucleotide sequences.
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34. The method of claim 20, wherein the steps of determining comprises the step of identifying the locations of the first plurality of nucleotide sequences regardless of the extent of hybridization by the second plurality of nucleotide sequences.
Specification