US 11,859,241 B2
Compositions and methods for pairwise sequencing
Sinan Arslan, San Diego, CA (US); Junhua Zhao, San Diego, CA (US); Molly He, San Diego, CA (US); Samantha Snow, San Diego, CA (US); William Light, Poway, CA (US); Matthew Kellinger, San Diego, CA (US); Michael Previte, San Diego, CA (US); Michael Kim, El Cajon, CA (US); Hua Yu, San Diego, CA (US); Yu-Hsien Hwang-Fu, San Diego, CA (US); Marco Tjioe, San Diego, CA (US); Andrew Boddicker, San Diego, CA (US); Mark Ambroso, Escondido, CA (US); Tyler Lopez, Winchester, CA (US); Michael Klein, Encinitas, CA (US); and Virginia Saade, San Diego, CA (US)
Assigned to Element Biosciences, Inc., San Diego, CA (US)
Filed by Element Biosciences, Inc., San Diego, CA (US)
Filed on Feb. 8, 2023, as Appl. No. 18/166,429.
Application 18/166,429 is a continuation in part of application No. 17/521,239, filed on Nov. 8, 2021.
Application 17/521,239 is a continuation of application No. 17/377,284, filed on Jul. 15, 2021, granted, now 11,220,707, issued on Jan. 11, 2022.
Claims priority of provisional application 63/212,059, filed on Jun. 17, 2021.
Prior Publication US 2023/0203564 A1, Jun. 29, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/68 (2018.01); C12P 19/34 (2006.01); C12Q 1/6806 (2018.01); C12Q 1/6834 (2018.01); C12Q 1/6874 (2018.01); G01N 21/64 (2006.01); C12Q 1/6853 (2018.01)
CPC C12Q 1/6806 (2013.01) [C12Q 1/6834 (2013.01); C12Q 1/6853 (2013.01); C12Q 1/6874 (2013.01); G01N 21/6428 (2013.01); G01N 21/6458 (2013.01); C12Q 2600/158 (2013.01)] 25 Claims
OG exemplary drawing
 
1. A method for pairwise sequencing, comprising:
a) providing a plurality of immobilized nucleic acid concatemer template molecules each comprising at least one uridine that can be enzymatically cleaved to generate an abasic site in the concatemer template molecule, wherein individual concatemer template molecules in the plurality are immobilized to a first surface primer that is immobilized to a support;
b) sequencing the plurality of immobilized concatemer template molecules with a plurality of soluble forward sequencing primers a plurality of sequencing polymerases, a plurality of multivalent molecules and a plurality of nucleotide analogs, thereby generating a plurality of extended forward sequencing primer strands, wherein individual immobilized concatemer template molecules have two or more extended forward sequencing primer strands hybridized thereon;
c) retaining the plurality of immobilized concatemer template molecules and replacing the plurality of extended forward sequencing primer strands with a plurality of forward extension strands that are hybridized to the retained immobilized single stranded nucleic acid concatemer template molecules by conducting a primer extension reaction;
d) removing the retained immobilized concatemer template molecules by generating abasic sites at the at least one uridine in the immobilized concatemer template molecules and generating gaps at the abasic sites to generate a plurality of gap-containing concatemer template molecules while retaining the plurality of forward extension strands and retaining the plurality of immobilized surface primers; and
e) sequencing the plurality of retained forward extension strands with a plurality of soluble reverse sequencing primers a plurality of sequencing polymerases, a plurality of multivalent molecules and a plurality of nucleotide analogs, thereby generating a plurality of extended reverse sequencing primer strands, wherein individual retained forward extension strands have two or more extended reverse sequencing primer strands hybridized thereon,
wherein individual multivalent molecules of the plurality of multivalent molecules of steps (b) and (e) comprise (1) a core; and (2) a plurality of nucleotide arms which comprise (i) a core attachment moiety, (ii) a spacer, (iii) a linker, and (iv) a nucleotide unit,
wherein the core is attached to the plurality of nucleotide arms via their core attachment moiety, and
wherein the spacer is attached to the linker, and wherein the linker is attached to the nucleotide unit.