Patents by Inventor Sriharsa Pradhan
Sriharsa Pradhan has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11840741Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.Type: GrantFiled: November 9, 2021Date of Patent: December 12, 2023Assignee: New England Biolabs, Inc.Inventors: Chaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
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Publication number: 20230123635Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.Type: ApplicationFiled: June 8, 2021Publication date: April 20, 2023Applicant: New England Biolabs, Inc.Inventors: Sriharsa Pradhan, Hang Gyeong Chin, George R. Feehery, Shuang-Yong Xu, Vishnu Udayakumaran Nair Sunitha Kumary, Julie Beaulieu
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Publication number: 20230089237Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.Type: ApplicationFiled: September 21, 2022Publication date: March 23, 2023Applicant: New England Biolabs, Inc.Inventors: Sriharsa Pradhan, Hang Gyeong Chin, George R. Feehery, Shuang-Yong Xu, Vishnu Udayakumaran Nair Sunitha Kumary, Julie Beaulieu, Pierre O. Esteve
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Patent number: 11492667Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.Type: GrantFiled: June 8, 2021Date of Patent: November 8, 2022Assignee: New England Biolabs, Inc.Inventors: Sriharsa Pradhan, Hang Gyeong Chin, George R. Feehery, Shuang-Yong Xu, Vishnu Udayakumaran Nair Sunitha Kumary, Julie Beaulieu, Pierre O. Esteve
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Publication number: 20220056537Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.Type: ApplicationFiled: November 9, 2021Publication date: February 24, 2022Applicant: New England Biolabs, Inc.Inventors: Chaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
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Publication number: 20210388434Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.Type: ApplicationFiled: June 8, 2021Publication date: December 16, 2021Applicant: New England Biolabs, Inc.Inventors: Sriharsa Pradhan, Hang Gyeong Chin, George R. Feehery, Shuang-Yong Xu, Vishnu Udayakumaran Nair Sunitha Kumary, Julie Beaulieu, Pierre O. Esteve
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Patent number: 11198910Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.Type: GrantFiled: August 31, 2017Date of Patent: December 14, 2021Assignee: New England Biolabs, Inc.Inventors: Chaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
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Publication number: 20190211404Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.Type: ApplicationFiled: August 31, 2017Publication date: July 11, 2019Applicant: New England Biolabs, Inc.Inventors: Chaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
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Patent number: 9963705Abstract: RNA molecules inhibiting a DNMT and methods and compositions incorporating or generating the RNA molecules are described.Type: GrantFiled: November 10, 2014Date of Patent: May 8, 2018Assignee: New England Biolabs, Inc.Inventors: Sriharsa Pradhan, Pierre O. Esteve, Guoqiang Zhang
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Publication number: 20160272977Abstract: RNA molecules inhibiting a DNMT and methods and compositions incorporating or generating the RNA molecules are described.Type: ApplicationFiled: November 10, 2014Publication date: September 22, 2016Applicant: New England Biolabs, Inc.Inventors: Sriharsa Pradhan, Pierre O. Esteve, Guoqiang Zhang
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Compositions and Methods for the Transfer of a Hexosamine to a Modified Nucleotide in a Nucleic Acid
Publication number: 20160046981Abstract: Nucleic acids comprising ?-glucosaminyloxy-5-methylcytosine; compositions, kits and methods of producing the nucleic acids using a glycosyltransferase; and methods of using the nucleic acids are described.Type: ApplicationFiled: October 29, 2015Publication date: February 18, 2016Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Ivan R. Correa, JR., Nan Dai, Jurate Bitinaite, Sriharsa Pradhan, Hang-Gyeong Chin -
Publication number: 20160032362Abstract: Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.Type: ApplicationFiled: February 10, 2015Publication date: February 4, 2016Inventors: George R. Feehery, Sriharsa Pradhan
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Compositions and methods for the transfer of a hexosamine to a modified nucleotide in a nucleic acid
Patent number: 9200260Abstract: Nucleic acids comprising ?-glucosaminyloxy-5-methylcytosine; compositions, kits and methods of producing the nucleic acids using a glycosyltransferase; and methods of using the nucleic acids are described.Type: GrantFiled: March 14, 2013Date of Patent: December 1, 2015Assignee: New England Biolabs, Inc.Inventors: Ivan R. Correa, Jr., Nan Dai, Jurate Bitinaite, Sriharsa Pradhan, Hang-Gyeong Chin -
Patent number: 9145580Abstract: Compositions and methods are provided for enriching mitochondrial DNA and optionally chloroplast DNA from eukaryotic cells in a simple rapid method that provides greater than 100 fold enrichment. Affinity protein-coated substrate in a buffer is used to efficiently bind chromosomal DNA and thereby remove it from the buffer. Mitochondrial sequencing reads reveal that non-biased sequence selection providing representation of a substantial proportion of mitochondrial DNA in the eukaryotic cells analyzed.Type: GrantFiled: March 15, 2013Date of Patent: September 29, 2015Assignee: New England Biolabs, Inc.Inventors: George R. Feehery, Fiona Stewart, James McFarland, Sriharsa Pradhan
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Publication number: 20150240310Abstract: Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modifying enzymes together with site-specific endonucleases to detect the hmNs.Type: ApplicationFiled: April 14, 2015Publication date: August 27, 2015Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Jurate Bitinaite, Romualdas Vaisvila, Sriharsa Pradhan, Yu Zheng, Richard J. Roberts, Hang-Gyeong Chin, Devora Cohen-Karni, Christopher Noren, Elisabeth A. Raleigh, Geoffrey Wilson
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Patent number: 9034597Abstract: Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modifying enzymes together with site-specific endonucleases to detect the hmNs.Type: GrantFiled: August 25, 2010Date of Patent: May 19, 2015Assignee: New England Biolabs, Inc.Inventors: Jurate Bitinaite, Romualdas Vaisvila, Sriharsa Pradhan, Yu Zheng, Richard J. Roberts, Devora Cohen-Karni, Christopher Noren, Elisabeth A. Raleigh, Geoffrey Wilson, Hang-Gyeong Chin
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Patent number: 8980553Abstract: Compositions and methods are provided for enriching non-target polynucleotides from a mixture of non-target and target polynucleotides where differences between the target polynucleotides and the non-target polynucleotides include the extent of modified bases that are present in a greater density in the target polynucleotides than in the non-target polynucleotides. This permits the target polynucleotides to be selectively and rapidly bound to an affinity matrix such as affinity protein-coated magnetic beads providing enrichment of the non-target polynucleotides in the supernatant. One use of this enrichment is to remove human genomic DNA from a mixture of DNAs obtained from human tissue samples to enrich for polynucleotides in a microbiome so as to characterize the microbiome by DNA sequencing.Type: GrantFiled: March 30, 2012Date of Patent: March 17, 2015Assignee: New England Biolabs, Inc.Inventors: George R. Feehery, Fiona Stewart, James McFarland, Sriharsa Pradhan
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Compositions and Methods for the Transfer of a Hexosamine to a Modified Nucleotide in a Nucleic Acid
Publication number: 20140127677Abstract: Nucleic acids comprising ?-glucosaminyloxy-5-methylcytosine; compositions, kits and methods of producing the nucleic acids using a glycosyltransferase; and methods of using the nucleic acids are described.Type: ApplicationFiled: March 14, 2013Publication date: May 8, 2014Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Ivan R. Correa, JR., Nan Dai, Jurate Bitinaite, Sriharsa Pradhan, Hang-Gyeong Chin -
Patent number: 8367331Abstract: Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.Type: GrantFiled: October 29, 2009Date of Patent: February 5, 2013Assignee: New England Biolabs, Inc.Inventors: George R. Feehery, Sriharsa Pradhan
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Publication number: 20120252009Abstract: Compositions and methods are provided for enriching non-target polynucleotides from a mixture of non-target and target polynucleotides where differences between the target polynucleotides and the non-target polynucleotides include the extent of modified bases that are present in a greater density in the target polynucleotides than in the non-target polynucleotides. This permits the target polynucleotides to be selectively and rapidly bound to an affinity matrix such as affinity protein-coated magnetic beads providing enrichment of the non-target polynucleotides in the supernatant. One use of this enrichment is to remove human genomic DNA from a mixture of DNAs obtained from human tissue samples to enrich for polynucleotides in a microbiome so as to characterize the microbiome by DNA sequencing.Type: ApplicationFiled: March 30, 2012Publication date: October 4, 2012Applicant: NEW ENGLAND BIOLABS, INC.Inventors: George R. Feehery, Fiona Stewart, James McFarland, Sriharsa Pradhan