US 11,939,628 B2
Compositions and methods for analyzing modified nucleotides
Romualdas Vaisvila, Ipswich, MA (US); Theodore B. Davis, Boxford, MA (US); Shengxi Guan, Stoneham, MA (US); Zhiyi Sun, Gloucester, MA (US); Laurence Ettwiller, Beverly, MA (US); and Lana Saleh, Hamilton, MA (US)
Assigned to New England Biolabs, Inc., Ipswich, MA (US)
Filed by New England Biolabs, Inc., Ipswich, MA (US)
Filed on Feb. 22, 2021, as Appl. No. 17/181,351.
Application 17/181,351 is a continuation of application No. 16/287,604, filed on Feb. 27, 2019, granted, now 11,001,876.
Application 16/287,604 is a continuation of application No. 15/893,373, filed on Feb. 9, 2018, granted, now 10,260,088, issued on Apr. 16, 2019.
Application 15/893,373 is a continuation in part of application No. 15/441,431, filed on Feb. 24, 2017, granted, now 10,227,646, issued on Mar. 12, 2019.
Application 15/441,431 is a continuation in part of application No. PCT/US2016/059447, filed on Oct. 28, 2016.
Claims priority of provisional application 62/325,626, filed on Apr. 21, 2016.
Claims priority of provisional application 62/300,396, filed on Feb. 26, 2016.
Claims priority of provisional application 62/271,679, filed on Dec. 28, 2015.
Claims priority of provisional application 62/257,284, filed on Nov. 19, 2015.
Claims priority of provisional application 62/248,872, filed on Oct. 30, 2015.
Prior Publication US 2021/0207200 A1, Jul. 8, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6827 (2018.01); C12N 9/02 (2006.01); C12N 9/78 (2006.01); C12Q 1/6806 (2018.01)
CPC C12Q 1/6827 (2013.01) [C12N 9/0071 (2013.01); C12N 9/78 (2013.01); C12Q 1/6806 (2013.01); C12Y 114/11 (2013.01); C12Y 305/04005 (2013.01)] 4 Claims
OG exemplary drawing
 
1. A method, comprising:
(a) reacting 5-hydroxymethylcytosine (5hmC) in a nucleic acid sample with a glucosyl transferase in the absence of a Tet enzyme to form a nucleic acid product with a modified hmC;
(b) converting cytosine (C) to uracil and 5-methyl cytosine (5mC) to thymidine in the nucleic acid product from (a) with a protein that has at least 90% sequence homology to apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (Apobec);
(c) optionally amplifying the reaction product from (b); and
(d) hybridizing and/or sequencing the product from (b) or amplicon thereof.