Pacific Biosciences of California, Inc.

University of California

Thang Pham

Jonas Korlach

Stephen Wilson Turner

Tyson A Clark

Paul S Peluso

David R Rank

David Kagen Hanzel

Arunashree Bhamidipati

Kevin Travers

John Lyle

Fred C Christians

Geoff Otto

Insil Park

Sonya Clark

Yu-Chih Tsai

Eric Olivares

Arekadiusz Bibillo

Gene W Shen

Lei Sun

Natasha Popovich

Alexander K Zettl

Adrian Nielsen Fehr

Jeremy Gray

Geoffrey Alan Otto

William E Mickelson

Arek Bibillo

Devon Murphy

Paul Mitsis

Aidin Fathalizadeh

Paul Hagerman

Aj Chmura

Albert James Chmura

William Mickelson

David Hanzel

David K Hanzel

This disclosure provides systems, methods, and apparatus related to boron nitride nanomaterials. In one aspect, a method includes generating a directed flow of plasma. A boron-containing species is introduced to the directed flow of the plasma. Boron nitride nanostructures are formed in a chamber. In another aspect, a method includes generating a directed flow of plasma using nitrogen gas. A boron-containing species is introduced to the directed flow of the plasma. The boron-containing species can consist of boron powder, boron nitride powder, and/or boron oxide powder. Boron nitride nanostructures are formed in a chamber, with a pressure in the chamber being about 3 atmospheres or greater.

System and methods for fabricating boron nitride nanostructures

Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.

Methods for isolating nucleic acids

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Compositions and methods for selection of nucleic acids

Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.

Polymerases for nucleotide analogue incorporation

Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.

Loading extended polymerase-nucleic acid complexes

The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution.

Methods and compositions for single molecule composition loading

Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.

Isolation of polymerase-nucleic acid complexes

Compositions that include polymerases with features for improving entry of nucleotide analogs into active site regions and for coordinating with the nucleotide analogs in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.

Growing community of inventors

Mountain View, CA, United States of America

Thang Pham