John D Lyle

US Patent:

8388982, Mar 5, 2013

Filed:

Nov 19, 2009

Appl. No.:

12/622375

Inventors:

Xiangxu Kong - Foster City CA, US
Gene Shen - Santa Clara CA, US
Andrei Fedorov - San Mateo CA, US
John Lyle - Fremont CA, US
Grace Lee - San Ramon CA, US
Lubomir Sebo - Redwood City CA, US
Duc Do - San Jose CA, US
Robert Weber - Mountain View CA, US
Stephen Dudek - San Francisco CA, US

Assignee:

Pacific Biosciences of California, Inc. - Menlo Park CA

International Classification:

A61K 9/00
A61K 8/00
A61F 13/00
C12Q 1/68
C12Q 1/48
C12Q 1/02

US Classification:

424400, 424 59, 424422, 435 61, 435 15, 435 29

Abstract:

Compositions, devices, systems and methods for reducing and/or preventing photo-induced damage of one or more reactants in an illuminated analytical reaction by addition of one or more photo-induced damage mitigating agents to the reaction mixture and allowing the reaction to proceed for a period that is less than a photo-induced damage threshold period.

US Patent:

20020164348, Nov 7, 2002

Filed:

May 22, 2001

Appl. No.:

09/863841

Inventors:

Karla Kirkegaard - Palo Alto CA, US
Kathy Richmond - Mountain View CA, US
John Lyle - Palo Alto CA, US
Steve Schultz - Tsaile AZ, US
Scott Hobson - Schriesheim, DE

International Classification:

A61K039/12
C12Q001/70

US Classification:

424/186100, 530/388300, 435/005000

Abstract:

The present invention provides a viral RNA-dependent RNA polymerase pharmacophore which is characterized by binding to a conserved interface binding surfaces of a viral RNA-dependent RNA polymerase.

US Patent:

20130316916, Nov 28, 2013

Filed:

Jun 28, 2013

Appl. No.:

13/930178

Inventors:

Stephen Turner - Menlo Park CA, US
Jessica Lee - Cupertino CA, US
Lei Jia - North Potomac MD, US
Jonas Korlach - Newark CA, US
Jon Sorenson - Alameda CA, US
Dale Webster - San Mateo CA, US
John Lyle - Fremont CA, US
Kevin Travers - Menlo Park CA, US
Jeremiah Hanes - Menlo Park CA, US
Joseph Puglisi - Stanford CA, US

International Classification:

C12Q 1/68

US Classification:

506 2, 435 611

Abstract:

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

US Patent:

20210147465, May 20, 2021

Filed:

Aug 28, 2020

Appl. No.:

17/006638

Inventors:

- Menlo Park CA, US
Jeremiah HANES - Menlo Park CA, US
Gene SHEN - Santa Clara CA, US
Louis BROGLEY - Santa Cruz CA, US
Stephen YUE - Eugene OR, US
Frank ZHENG - Fremont CA, US
Yuri LAPIN - Newark CA, US
John LYLE - Fremont CA, US
Honey OSUNA - San Francisco CA, US
Andrei FEDOROV - San Bruno CA, US

Assignee:

Pacific Biosciences of California, Inc. - Menlo Park CA

International Classification:

C07H 19/10
C07F 9/6558
C07F 9/6561
C09B 23/06
C09B 23/08
C09B 69/10

Abstract:

Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.

US Patent:

20190309171, Oct 10, 2019

Filed:

Dec 4, 2018

Appl. No.:

16/209916

Inventors:

- Menlo Park CA, US
Jeremiah HANES - Menlo Park CA, US
Gene SHEN - Santa Clara CA, US
Louis BROGLEY - Santa Cruz CA, US
Stephen YUE - Eugene OR, US
Yuri LAPIN - Newark CA, US
John LYLE - Fremont CA, US
Honey OSUNA - San Francisco CA, US
Andrei FEDOROV - San Bruno CA, US
Lubomir SEBO - Redwood City CA, US

Assignee:

Pacific Biosciences of California, Inc. - Menlo Park CA

International Classification:

C09B 69/10
G01N 33/533
C09B 23/10
C09B 23/06
C09B 69/00

Abstract:

Multimeric protected fluorescent reagents and their methods of synthesis are provided. The reagents are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The reagents contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements. The reagents also contain coupling elements connect monomeric compounds into multimeric forms, thereby increasing brightness.

US Patent:

20190194741, Jun 27, 2019

Filed:

Dec 12, 2018

Appl. No.:

16/218280

Inventors:

- Menlo Park CA, US
John Lyle - Fremont CA, US
Keith Bjornson - Fremont CA, US
Jeremiah Hanes - Woodside CA, US

International Classification:

C12Q 1/6869

Abstract:

Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.

US Patent:

20180346507, Dec 6, 2018

Filed:

Apr 30, 2018

Appl. No.:

15/966334

Inventors:

- Menlo Park CA, US
Jeremiah HANES - Menlo Park CA, US
Gene SHEN - Santa Clara CA, US
Louis BROGLEY - Santa Cruz CA, US
Stephen YUE - Eugene OR, US
Frank ZHENG - Fremont CA, US
Yuri LAPIN - Newark CA, US
John LYLE - Fremont CA, US
Honey OSUNA - San Francisco CA, US
Andrei FEDOROV - San Bruno CA, US

International Classification:

C07H 19/10
C09B 69/10
C09B 23/08
C07F 9/6558
C07F 9/6561
C09B 23/06

Abstract:

Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.

US Patent:

20180237757, Aug 23, 2018

Filed:

Feb 12, 2018

Appl. No.:

15/894157

Inventors:

- Menlo Park CA, US
Paul S. Peluso - Newark CA, US
David K. Hanzel - Palo Alto CA, US
Geoff Otto - Brookline MA, US
Thang Pham - Mountain View CA, US
Fred Christians - Los Altos Hills CA, US
Arekadiusz Bibillo - Cupertino CA, US
Insil Park - Fremont CA, US
Sonya Clark - Oakland CA, US
John Lyle - Fremont CA, US

International Classification:

C12N 9/12
C12Q 1/6869

Abstract:

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.