Methods and compositions related to target analysis
AssigneePresident and Fellows of Harvard College
InventorsHuy Quoc NGUYEN, Shyamtanu CHATTORAJ, George M. CHURCH, Chao-ting WU
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Abstract
The technology described herein is directed to methods, systems, and compositions for analyzing, detecting, and/or visualizing target molecules. Described herein are compositions and systems comprising oligonucleotide tags comprising barcoded cassettes. Also described herein are methods for analyzing target molecules, the method comprising contacting a sample with at least one oligonucleotide tag, contacting the sample with at least two readout molecules, and detecting the relative spatial order of the readout molecules.
Claims21
A method of analyzing at least one target molecule in a sample, the method comprising:
- (a) contacting the sample with at least one oligonucleotide tag, each oligonucleotide tag comprising:
- (i) a recognition domain that binds specifically to a target molecule to be analyzed, and
- (ii) at least one street comprising at least one cassette, each cassette comprising:
- (1) a barcode region comprising at least 1 nucleotide, flanked on at least one side by an anchor region;
- wherein each oligonucleotide tag's street is unique from the streets of the other oligonucleotide tags of step (a) at least in that (A) the spatial order of the cassettes within the street differs or (B) that the sequence of the barcode region differs from the barcode regions of the other oligonucleotide tags of step (a);
- (b) contacting the sample with at least two readout molecules, wherein each readout molecule comprises:
- (i) an oligonucleotide that hybridizes specifically with a cassette of at least one oligonucleotide tag used in step (a);
- and
- (ii) a detection molecule;
- wherein the at least two readout molecules collectively comprise at least two distinguishable detection molecules;
- and
- (c) detecting the relative spatial order of the detection molecules hybridized to at least one oligonucleotide tag, wherein the at least one oligonucleotide tag is hybridized to the at least one target molecule, whereby the relative spatial order of the detection molecules permits identification of which oligonucleotide tag is hybridized to the target molecule at that location.
(canceled)
A system for analyzing at least one target molecule in a sample, the system comprising:
- (a) a detector that can detect at least two detectable molecules;
- (b) at least one oligonucleotide tag, each oligonucleotide tag comprising:
- (i) a recognition domain that binds specifically to a target molecule to be analyzed, and
- (ii) a street comprising at least one cassette, each cassette comprising:
- (1) a barcode region comprising at least 1 nucleotide, flanked on at least one side by an anchor region;
- wherein each oligonucleotide tag's street is unique from the streets of the other oligonucleotide tags of (b) at least in that (A) the spatial order of the cassettes within the street differs or (B) that the sequence of the barcode region differs from the barcode regions of the other oligonucleotide tags of (b);
- and
- (c) at least two readout molecules, wherein each readout molecule comprises:
- (i) an oligonucleotide that hybridizes specifically with a cassette of at least one oligonucleotide tag used in (b);
- and
- (ii) a detection molecule;
- wherein the at least two readout molecules collectively comprise at least two distinguishable detection molecules;
- and
- wherein a sample is contacted with the at least one oligonucleotide tag and the at least two readout molecules, and the relative spatial order of the detection molecules hybridized to at least one oligonucleotide tag is detected, wherein the at least one oligonucleotide tag is hybridized to the at least one target molecule, whereby the relative spatial order of the detection molecules permits identification of which oligonucleotide tag is hybridized to the target molecule at that location.
Dependencies are inferred from the claim text.