Kerry B Gunning

US Patent:

8067164, Nov 29, 2011

Filed:

Aug 12, 2008

Appl. No.:

12/190446

Inventors:

Kerry B. Gunning - Coralville IA, US
Mark Aaron Behlke - Coralville IA, US

Assignee:

Integrated DNA Technologies, Inc. - Skokie IL

International Classification:

C12Q 1/68
C12P 19/34
C07H 21/02
C07H 19/04
C40B 40/06

US Classification:

435 6, 435 911, 435 912, 536 253, 536 266, 506 16

Abstract:

The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5′ end to prohibit degradation by a 5′-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface. The invention also provides hybridization and wash buffers and conditions to maximize hybridization specificity and signal intensity, and reduce hybridization times.

US Patent:

20090136916, May 28, 2009

Filed:

Aug 13, 2008

Appl. No.:

12/191132

Inventors:

David W. Brown - North Brookfield MA, US
John E. Herrmann - Northboro MA, US
Saul Tzipori - Shrewsbury MA, US
Kerry B. Gunning - Coralville IA, US

Assignee:

TRUSTEES OF TUFTS COLLEGE - Medford MA

International Classification:

C12Q 1/70
C40B 60/10
C07H 21/02
C07H 21/04
C40B 50/14

US Classification:

435 5, 506 38, 536 2372, 536 2432, 506 30

Abstract:

The present invention relates to methods, microarrays and kits for detecting one or more human astrovirus serotypes in a sample (e.g., a fecal sample) from an individual. The method includes amplifying nucleic acid molecules of the sample with one or more primers, to thereby obtain an amplified nucleic acid product; contacting the amplified nucleic acid product with one or more serotype specific probes having a nucleic acid sequence that is specific for only one astrovirus serotype in the group of astroviruses being assessed, wherein the nucleic acid sequence includes between about 9 and 25 nucleic acid bases (e.g., SEQ ID NO: 5-24); and detecting the hybridization complex. The presence of hybridization complexes with a serotype specific probe indicates the presence of one or more specific astrovirus serotypes, and the absence of hybridization complexes with a serotype specific probe indicates the absence of the specific astrovirus serotype. Identification of the astrovirus serotypes allows for one to diagnose an individual infected with the serotype. The present invention further includes microarrays having any one of the astrovirus specific probe, or kits having microarrays and reagents for carrying out the assay.

US Patent:

20120077191, Mar 29, 2012

Filed:

Aug 11, 2011

Appl. No.:

13/208310

Inventors:

KERRY GUNNING - CORALVILLE IA, US
KURT A. KRUMMEL - SAN DIEGO CA, US
RUSSEL BALDOCCHI - ENCINITAS CA, US
YI ZHANG - SAN DIEGO CA, US
RAMA GHATTI - SAN DIEGO CA, US
HAICHUAN ZHANG - SAN DIEGO CA, US
EUGENE TU - SAN DIEGO CA, US
ANDREW S. KATZ - LA JOLLA CA, US

Assignee:

CELULA, INC. - SAN DIEGO CA

International Classification:

C12Q 1/68
C07H 21/04

US Classification:

435 611, 536 2431

Abstract:

Described herein are compositions and methods useful for the detection of nucleic acid variations. Ligation within a probe or between probes is used to distinguish between probes perfectly complementary to a target and those containing a mismatch. Nucleotide fill-in/extension steps are optionally applied according to the type of assay performed. A circularization and relinearization step can be applied to create a template for further amplification and detection. In certain aspects, portions of a target sequence or its complement are not amplified.

US Patent:

20120077712, Mar 29, 2012

Filed:

Nov 11, 2011

Appl. No.:

13/294792

Inventors:

Kerry B. Gunning - Coralville IA, US
Mark Aaron Behlke - Coralville IA, US

International Classification:

C40B 40/06
C40B 50/18

US Classification:

506 16, 506 32

Abstract:

The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5′ end to prohibit degradation by a 5′-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface. The invention also provides hybridization and wash buffers and conditions to maximize hybridization specificity and signal intensity, and reduce hybridization times.

US Patent:

20130040860, Feb 14, 2013

Filed:

Oct 11, 2012

Appl. No.:

13/650087

Inventors:

Kerry B. Gunning - San Diego CA, US
Mark Aaron Behike - Coralville IA, US

International Classification:

C40B 50/18
C40B 40/06

US Classification:

506 16, 506 32

Abstract:

The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5′ end to prohibit degradation by a 5′-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface. The invention also provides hybridization and wash buffers and conditions to maximize hybridization specificity and signal intensity, and reduce hybridization times.

US Patent:

20130316927, Nov 28, 2013

Filed:

Jun 6, 2013

Appl. No.:

13/911971

Inventors:

Kerry B. Gunning - San Diego CA, US
Mark Aaron Behlke - Coralville IA, US

International Classification:

C12Q 1/68

US Classification:

506 9, 506 43

Abstract:

The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5′ end to prohibit degradation by a 5′-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface. The invention also provides hybridization and wash buffers and conditions to maximize hybridization specificity and signal intensity, and reduce hybridization times.

US Patent:

20220282398, Sep 8, 2022

Filed:

Mar 7, 2022

Appl. No.:

17/688062

Inventors:

- Austin TX, US
Kerry Gunning - Austin TX, US

International Classification:

C40B 30/04
C12Q 1/6806
C12Q 1/6853
C12Q 1/6832
C40B 40/08

Abstract:

Sets of hybridization blockers, kits include at least one set of hybridization blockers, and methods of use thereof in massively parallel nucleic acid sequencing, are provided according to aspects of the present disclosure, each of the hybridization blockers comprising at least one Tm increasing nucleotide, the set of hybridization blockers for use in massively parallel sequencing of a plurality of nucleic acid sequencing library molecules, wherein the set of hybridization blockers efficiently blocks the complementary strand interactions between the adapter regions of different library molecules and is therefore effective to reduce the capture of non-target sequences during a capture enrichment hybridization to maximize the efficiency of the massively parallel sequencing techniques.

US Patent:

20210261952, Aug 26, 2021

Filed:

Feb 22, 2021

Appl. No.:

17/181947

Inventors:

- Austin TX, US
Kerry Gunning - Austin TX, US

International Classification:

C12N 15/10
C12Q 1/6876

Abstract:

Oligonucleotide primers and methods of use in producing sequencing libraries are provided according to aspects of the present disclosure which include, from 5′ to 3′, a homopolymer-hybridizing region, and an anchor region comprising 5′-(λ)N-3′, wherein the homopolymer-hybridizing region is a contiguous sequence of 5 to 20 elements, wherein the elements are nucleotides or Tincreasing nucleotide analogs, wherein at least 4 of the elements are Tincreasing nucleotide analogs, wherein the homopolymer-hybridizing region hybridizes to a complementary homopolymer tract of a target nucleic acid, wherein the complementary homopolymer tract comprises a contiguous sequence of complementary elements, wherein λ is any nucleotide or nucleotide analog with the proviso that λ is not a nucleotide or nucleotide analog complementary to a complementary element of the complementary homopolymer tract, and wherein N is any nucleotide or nucleotide analog.