Harvard College

Other

Chao-ting Wu

George M Church

Brian Beliveau

Son C Nguyen

Evan R Daugharthy

Benjamin Richard Williams

Sonny C Nguyen

The present invention relates to a method of identifying a target genomic nucleic acid sequence including hybridizing a set of probes to the target genomic nucleic acid sequence, wherein the set of probes has a unique associated barcode sequence for identification of the target genomic nucleic acid sequence, wherein each probe of the set includes (1) a complementary sequence complementary to a first strand of the target genomic nucleic acid sequence and (2) the associated barcode sequence or a portion of the associated barcode sequence, sequencing the associated barcode sequence from probes hybridized to the target genomic nucleic acid sequence using a fluorescence-based sequencing method, and identifying the target genomic nucleic acid sequence by the sequenced barcode sequence.

Methods for detecting and identifying genomic nucleic acids

Novel methods for making high resolution oligonucleotide paints are provided. Novel, high resolution oligonucleotide paints are also provided.

Oligonucleotide paints

The present invention relates to a method of covalently attaching a chromosome within a cell to a matrix including modifying a plurality of nucleotides within the chromosome to include a matrix attachment moiety wherein the chromosome contacts the matrix, and attaching the matrix attachment moiety of the plurality of nucleotides to the matrix, thereby attaching the chromosome to the matrix.

Methods for attaching cellular constituents to a matrix

Novel methods and compositions for identifying one or more factors associated with a nucleic acid sequence (e.g., DNA and/or RNA) of interest are provided.

Oligonucleotide trapping

The present invention relates to methods of elongating chromosomes. Embodiments of the present disclosure are directed to methods of elongating DNA by immobilizing or attaching the DNA to a substrate. According to one aspect, naturally occurring DNA includes a nucleic acid and one or more factors bound thereto, and may be referred to herein as 'starting DNA'.

Methods of elongating DNA

The present invention relates to methods of making linear nucleic acid probes using rolling circle amplification methods.

Methods of making oligonucleotide probes

The present invention relates to methods of hybridizing nucleic acid probes to genomic DNA.

Methods of identifying homologous genes using FISH

Methods and compositions for determining the nucleic acid sequence of polynucleotides that are at least 1500 nucleotides in length are provided.

Methods for sequencing nucleic acid molecules

The present invention relates to methods of making linear nucleic acid probes using rolling circle amplification methods. In one aspect, an oligonucleotide template sequence is contacrted with one or more first primers, a first polymerase and first nucleotides under conditions that extend one or more hybridize primers to make a strand complementary to the oligonucleotide template sequence thereby forming a double stranded oligonucleotide. The double stranded oligonucleotide is circularized. A rolling circle template is obtained from the circularized double stranded oligonucleotide. The rolling circle template is contacted with one or more second primers, a second polymerase and second nucleotides under conditions that form a single stranded nucleic acid, and the single stranded nucleic acid is cleaved to form the plurality of nucleic acid probes.

Growing community of inventors

Brookline, MA, United States of America

Chao-ting Wu