Janice J Chen

US Patent:

20220364159, Nov 17, 2022

Filed:

Jul 22, 2020

Appl. No.:

17/629895

Inventors:

- Brisbane CA, US
Janice Sha Chen - San Francisco CA, US
Lucas Benjamin Harrington - Berkeley CA, US

International Classification:

C12Q 1/6816
C12N 9/22

Abstract:

Described herein are methods and systems for direct detection of DNA nucleic acids using a DNA-activated programmable RNA nuclease.

US Patent:

20210388437, Dec 16, 2021

Filed:

Jul 29, 2021

Appl. No.:

17/388321

Inventors:

- Oakland CA, US
Janice S. Chen - Berkeley CA, US
Lucas Benjamin Harrington - Berkeley CA, US
Enbo Ma - Moraga CA, US

International Classification:

C12Q 1/6876
C12N 15/11
C12N 9/22
C12Q 1/6823

Abstract:

Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a “single stranded detector DNA”) and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.

US Patent:

20210317527, Oct 14, 2021

Filed:

Aug 26, 2019

Appl. No.:

17/270215

Inventors:

- Oakland CA, US
Janice S. Chen - Berkeley CA, US
Lucas Benjamin Harrington - Berkeley CA, US

International Classification:

C12Q 1/6876
C12N 15/11
C12N 9/22
C12Q 1/6816

Abstract:

The present disclosure provides labeled single stranded detector DNA molecules that provide a sensitive readout for detection of a target DNA. The present disclosure provides compositions, systems, and kits comprising a labeled single stranded detector DNA of the present disclosure. The present disclosure further provides methods of detecting a target DNA (double stranded or single stranded) in a sample.

US Patent:

20210269858, Sep 2, 2021

Filed:

May 13, 2021

Appl. No.:

17/319907

Inventors:

- Oakland CA, US
Andrea Granados - San Francisco CA, US
Jennifer A. Doudna - Berkeley CA, US
Lucas B. Harrington - Berkeley CA, US
Janice S. Chen - Berkeley CA, US
Xianding Deng - San Francisco CA, US

International Classification:

C12Q 1/6806
C12Q 1/70
C12Q 1/689
C12Q 1/6893
C12Q 1/6895
C12Q 1/6888

Abstract:

The present disclosure provides methods for characterizing a target DNA present in a sample. The methods involve contacting the sample with a type V CRISPR/Cas effector protein and one or more guide RNAs, where the contacting generates a cleavage product comprising a 5′ overhang; and ligating a double-stranded nucleic acid adapter to the cleavage product, to generate a ligation product. The ligation product includes the target DNA, which can be sequenced. The sample can be subjected to one or more amplification steps prior to the contacting step, with primers that provide for amplification of nucleic acids of, e.g., specific pathogens, categories of pathogens, two or more different pathogens, or two or more different categories of pathogens.

US Patent:

20210214697, Jul 15, 2021

Filed:

Oct 31, 2018

Appl. No.:

16/755535

Inventors:

Jillian F. BANFIELD - Berkeley CA, US
- Oaland CA, US
Janice S. Chen - Berkeley CA, US
Lucas B. Harrington - Berkeley CA, US
Jillian F. Banfield - Berkeley CA, US

International Classification:

C12N 9/22
C12N 15/11

Abstract:

Provided are compositions and methods that include one or more of: (1) a Class 2 CRISPR/Cas effector protein, a nucleic acid encoding the effector protein, and/or a modified host cell comprising the effector protein (and/or a nucleic acid encoding the same); (2) a CRISPR/Cas guide RNA that binds to and provides sequence specificity to the Class 2 CRISPR/Cas effector protein, a nucleic acid encoding the CRISPR/Cas guide RNA, and/or a modified host cell comprising the CRISPR/Cas guide RNA (and/or a nucleic acid encoding the same); and (3) a CRISPR/Cas transactivating noncoding RNA (trancRNA), a nucleic acid encoding the CRISPR/Cas trancRNA, and/or a modified host cell comprising the CRISPR/Cas trancRNA (and/or a nucleic acid encoding the same).

US Patent:

20210017508, Jan 21, 2021

Filed:

Sep 25, 2020

Appl. No.:

17/032521

Inventors:

- Oakland CA, US
David Burstein - Berkeley CA, US
Janice S. Chen - Berkeley CA, US
Lucas B. Harrington - Berkeley CA, US
Jillian F. Banfield - Berkeley CA, US

International Classification:

C12N 9/22
C12N 15/11
C12N 15/113

Abstract:

Provided are compositions and methods that include one or more of: (1) a “CasZ” protein (also referred to as a CasZ polypeptide), a nucleic acid encoding the CasZ protein, and/or a modified host cell comprising the CasZ protein (and/or a nucleic acid encoding the same); (2) a CasZ guide RNA that binds to and provides sequence specificity to the CasZ protein, a nucleic acid encoding the CasZ guide RNA, and/or a modified host cell comprising the CasZ guide RNA (and/or a nucleic acid encoding the same); and (3) a CasZ transactivating noncoding RNA (trancRNA) (referred to herein as a “CasZ trancRNA”), a nucleic acid encoding the CasZ trancRNA, and/or a modified host cell comprising the CasZ trancRNA (and/or a nucleic acid encoding the same).

US Patent:

20210009974, Jan 14, 2021

Filed:

Sep 29, 2020

Appl. No.:

17/037620

Inventors:

- South San Francisco CA, US
Janice Sha CHEN - San Francisco CA, US
James Paul BROUGHTON - San Francisco CA, US
Pedro Patrick Draper GALARZA - Oakland CA, US
Isaac Paterson WITTE - Walnut Creek CA, US
Jasmeet SINGH - Santa Clara CA, US

International Classification:

C12N 9/22
C12N 15/113
C12Q 1/6886
C12Q 1/70

Abstract:

Disclosed herein are compositions, kits, and methods related to improved Cas activity. Through compositions and kits disclosed herein and practice of methods disclosed herein, one attains improved Cas activity such as Cas12 activity relative to Cas proteins in the art such as LbCas12. Further described herein are methods to detect target nucleic acid using a programmable nuclease system. Often, the target nucleic acids are present in at low frequency in the sample. Provided herein are methods for enriching these target nucleic acids for detection. Also described herein are methods to insert a PAM sequence into a target sequence of interest for use in a detection comprising a programmable nuclease.

US Patent:

20200399697, Dec 24, 2020

Filed:

Jul 13, 2020

Appl. No.:

16/927351

Inventors:

- Oakland CA, US
Janice S. Chen - Berkeley CA, US
Lucas Benjamin Harrington - Berkeley CA, US
Enbo Ma - Moraga CA, US

International Classification:

C12Q 1/6876
C12Q 1/6823
C12N 9/22
C12N 15/11

Abstract:

Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a “single stranded detector DNA”) and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.