US 6,284,465 B1 · Apparatus, systems and method for locating nucleic acids bound to surfaces

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.

Claims34

Dependent claims

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.

3 more elements

A system for 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;
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.

3 more elements

A method for locating nucleic acid positions on a substrate comprising the steps of:

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.

3 more elements

Dependencies are inferred from the claim text.

Apparatus, systems and method for locating nucleic acids bound to surfaces

Life of this patent

Apparatus, systems and method for locating nucleic acids bound to surfaces

Life of this patent

Abstract

Claims34