Rubicon Genomics, Inc.

Takara Bio USA, Inc.

Brendan J Tarrier

Vladimir L Makarov

Emmanuel Kamberov

Eric Bruening

Takao Kurihara

Tong Sun

Tim Tesmer

Joseph M'Mwirichia

Jonathon H Pinter

Jonathan H Pinter

Eric E Bruening

Joseph M M'mwirichia

Joseph M M'Mwirichia

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Compositions including a double stranded nucleic acid molecule and a stem-loop oligonucleotide

Kits including stem-loop oligonucleotides for use in preparing nucleic acid molecules

The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries. In particular, the method employs preparation of a DNA molecule by digesting the DNA molecule with at least one methylation-sensitive restriction enzyme; incorporating a nucleic acid molecule into at least some of the digested DNA molecules by either (1) incorporating at least one primer from a plurality of primers that have a 5' constant sequence and a 3&#x2032; variable sequence, wherein the primers are substantially non-self-complementary and substantially non-complementary to other primers in the plurality; or (2) incorporating an oligonucleotide having an inverted repeat and a loop under conditions wherein the oligonucleotide becomes blunt-end ligated to one strand of the digested DNA molecule, followed by polymerization from a 3&#x2032; hydroxyl group present in a nick in the oligonucleotide-linked molecule; and amplifying one or more of the DNA molecules.

Methods and compositions for generating and amplifying DNA libraries for sensitive detection and analysis of DNA methylation

The present invention is directed generally to the use of stem-loop oligonucleotides comprising an inverted repeat, a loop, and at least one degradable site or site capable of becoming a degradable site in the preparation of DNA molecules, such as a library. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Methods for processing and amplifying nucleic acids

The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.

Methods for preparing amplifiable DNA molecules

Attaching a stem-loop oligonucleotide to a double stranded DNA molecule

Isolation of CpG islands by thermal segregation and enzymatic selection-amplification method

Use of stem-loop oligonucleotides in the preparation of nucleic acid molecules

Methods for producing and using stem-loop oligonucleotides

Methods of producing nucleic acid molecules comprising stem loop oligonucleotides

Growing community of inventors

Belleville, MI, United States of America

Brendan J Tarrier