Samuel Levy

20100311602, Dec 9, 2010

Oct 15, 2007

12/311780

Samuel Levy - Rockville MD, US
Susanne Goldberg - Germantown MD, US
Karen Beeson - Rockville MD, US

J. Craig Venter Institute, Inc. - Rockville MD

C40B 30/04
C12P 19/34
C07H 21/04

506 9, 435 915, 435 912, 536 231

The present invention relates, e.g., to a method for isolating a DNA molecule of interest in a form suitable for sequencing at least a portion of the DNA by a high throughput sequencing method, comprising (a) digesting a double-stranded (ds) DNA molecule with two different restriction enzymes, A and B, to generate a ds form of the DNA molecule of interest, which is bounded by the two restriction enzyme cleavage products, and (b) attaching to each end of the DNA molecule of interest an adaptor molecule which comprises at one end a restriction enzyme cleavage site that is compatible with the restriction enzyme A or the restriction enzyme B cleavage product, and which also comprises a sequence and/or element that allows the DNA of interest to be sequenced with a high throughput sequencing apparatus. The method can be adapted for sequencing DNA with a variety of high throughput sequencing apparatuses, including machines manufactured by the 454, Illumina (Solexa Sequencing technology) and ABI (SOLiD™ Sequencing technology) companies. A method is also described for sequencing regulatory elements within a cell, comprising subjecting a collection of ds DNA molecules that are enriched for regulatory elements and that are generated by digestion with two restriction enzymes, A and B, which generate sticky ends, to an isolation method of the invention, and sequencing the collection of ds DNA molecules with a high throughput sequencing apparatus.