Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
Type:
Grant
Filed:
March 3, 2010
Date of Patent:
June 26, 2012
Assignee:
Rubicon Genomics, Inc.
Inventors:
Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
Abstract: 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.
Type:
Application
Filed:
November 1, 2011
Publication date:
June 7, 2012
Applicant:
Rubicon Genomics, Inc.
Inventors:
VLADIMIR L. MAKAROV, Emmanuel Kamberov, Brendan J. Tarrier
Abstract: 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.
Type:
Grant
Filed:
September 28, 2010
Date of Patent:
December 6, 2011
Assignee:
Rubicon Genomics, Inc.
Inventors:
Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
Abstract: 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.
Type:
Application
Filed:
September 28, 2010
Publication date:
April 7, 2011
Applicant:
Rubicon Genomics, Inc.
Inventors:
Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
Abstract: 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.
Type:
Grant
Filed:
November 13, 2008
Date of Patent:
September 28, 2010
Assignee:
Rubicon Genomics, Inc.
Inventors:
Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
Type:
Application
Filed:
February 1, 2010
Publication date:
June 10, 2010
Applicant:
RUBICON GENOMICS, INC.
Inventors:
Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
Type:
Grant
Filed:
March 8, 2004
Date of Patent:
May 18, 2010
Assignee:
Rubicon Genomics, Inc.
Inventors:
Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
Type:
Grant
Filed:
November 13, 2002
Date of Patent:
February 2, 2010
Assignee:
Rubicon Genomics, Inc.
Inventors:
Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
Abstract: 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.
Type:
Application
Filed:
March 2, 2006
Publication date:
February 8, 2007
Applicant:
Rubicon Genomics, Inc.
Inventors:
Vladimir Makarov, Emmanuel Kamberov, Brendan Tarrier
Abstract: 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.
Type:
Application
Filed:
March 2, 2006
Publication date:
February 8, 2007
Applicant:
Rubicon Genomics, Inc.
Inventors:
Vladimir Makarov, Emmanuel Kamberov, Brendan Tarrier
Abstract: The present invention regards a variety of methods and compositions for whole genome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome in a non-biased manner utilizing adaptor-attached randomly generated fragments following modification of the DNA ends prior to the adaptor attachment. In an additional aspect of the present invention, there are methods and compositions for whole genome amplification regarding a one-step endonuclease cleavage and linker ligation reaction.
Type:
Application
Filed:
March 8, 2004
Publication date:
October 21, 2004
Applicant:
RUBICON GENOMICS, INC.
Inventors:
Jonathon H. Pinter, Takao Kurihara, Irina Sleptsova, Eric Bruening, William Ziehler, Vladimir L. Makarov
Abstract: Improved methods and reagents for chromosome walking of nucleic acid are discussed herein. A library of amplifiable nick translation molecules is generated, and a chromosome walk is initiated from a known sequence in the nucleic acid by producing at least one nick translate molecule, sequencing part of the nick translate molecule, and producing a second nick translate molecule by initiating the primer extension from the region of the obtained sequence of the prior nick translate molecule.
Type:
Grant
Filed:
November 15, 2001
Date of Patent:
August 17, 2004
Assignee:
Rubicon Genomics, Inc.
Inventors:
Vladimir L. Makarov, Emmanuel Kamberov, Irina Sleptsova
Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
Type:
Application
Filed:
November 13, 2002
Publication date:
July 31, 2003
Applicant:
RUBICON GENOMICS INC.
Inventors:
Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening