IP Library › Granted Patent US 12,577,607
Granted Patent B2
US 12,577,607 · App. 18/190,455 · Granted Mar 17, 2026

High intensity labeled reactant compositions and methods for sequencing

Inventors: Jonathan M. Rothberg (Miami Beach, FL); Jeremy Lackey (Foster City, CA); Brian Reed (Madison, CT); Xinghua Shi (Madison, CT); Haidong Huang (Madison, CT); David Dodd (Guilford, CT)
Assignee: Quantum-Si Incorporated
C12Q1/6818C12Q1/6869G01N21/6428G01N2021/6439G01N2458/00
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Quick Facts
Patent No.
US 12,577,607
App. No.
18/190,455
Granted
Mar 17, 2026
Kind
B2
Abstract

Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Claims (15)

1 . A labeled molecule comprising a FRET label that comprises at least three luminescent molecules, including at least one donor molecule and at least one acceptor molecule, wherein the FRET label comprises a donor molecule to acceptor molecule ratio of greater than 1:1 or an acceptor molecule to donor molecule ratio of greater than 1:1, and wherein each donor molecule and acceptor molecule are separated by about 1-3 nm.

2 . The labeled molecule of claim 1 , wherein the FRET label comprises a donor molecule to acceptor molecule ratio of greater than 1.5:1, greater than 2:1, greater than 2.5:1, greater than 3:1, greater than 3.5:1, or greater than 4:1.

3 . The labeled molecule of claim 1 , wherein the FRET label comprises an acceptor molecule to donor molecule ratio of greater than 1.5:1, greater than 2:1, greater than 2.5:1, greater than 3:1, greater than 3.5:1, or greater than 4:1.

4 . The labeled molecule of claim 1 , wherein the FRET label comprises at least two donor molecules and at least one acceptor molecule.

5 . The labeled molecule of claim 1 , wherein the FRET label comprises at least one donor molecule and at least two acceptor molecules.

6 . The labeled molecule of claim 1 , wherein each donor molecule and acceptor molecule have a FRET efficiency of at least 85%.

7 . The labeled molecule of claim 1 , wherein one or more luminescent molecules are integrated into the molecule.

8 . The labeled molecule of claim 1 , wherein any of the luminescent molecules is a fluorescent dye, optionally wherein the fluorescent dye is a rhodamine dye, a boron-dipyrromethene dye, or a cyanine dye.

9 . The labeled molecule of claim 1 , wherein the molecule is separated from any of the luminescent molecules by between approximately 1 and 10 nm.

10 . A labeled molecule comprising a FRET label that comprises at least three luminescent molecules, including at least one donor molecule and at least one acceptor molecule, wherein the FRET label comprises an acceptor molecule to donor molecule ratio of at least 2:1, and wherein each donor molecule and acceptor molecule are separated by about 1-3 nm.

11 . The labeled molecule of claim 10 , wherein the FRET label comprises an acceptor molecule to donor molecule ratio of at least 2.5:1, at least 3:1, at least 3.5:1, or at least 4:1.

12 . The labeled molecule of claim 10 , wherein each donor molecule and acceptor molecule have a FRET efficiency of at least 85%.

13 . The labeled molecule of claim 10 , wherein one or more luminescent molecules are integrated into the molecule.

14 . The labeled molecule of claim 10 , wherein any of the luminescent molecules is a fluorescent dye, optionally wherein the fluorescent dye is a rhodamine dye, a boron-dipyrromethene dye, or a cyanine dye.

15 . The labeled molecule of claim 10 , wherein the molecule is separated from any of the luminescent molecules by between approximately 1 and 10 nm.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jul 3, 2024
From: ROTHBERG, JONATHAN M.; LACKEY, JEREMY; REED, BRIAN; SHI, XINGHUA; HUANG, HAIDONG; DODD, DAVID
To: QUANTUM-SI INCORPORATED
Reel/Frame 068106/0533 →
Continuity (3)
Continuation 16751138 · Jan 23, 2020
Provisional Application 62795932 · Jan 23, 2019
Related Publication 20240124918A1 · Apr 18, 2024
References Cited (195)
US 5210015A · Gelfand et al. · 1993 [cited by applicant]
US 5487972A · Gelfand et al. · 1996 [cited by applicant]
US 5594117A · Urdea et al. · 1997 [cited by applicant]
US 5707804A · Mathies et al. · 1998 [cited by applicant]
US 5851840A · Sluka et al. · 1998 [cited by applicant]
US 6133445A · Waggoner et al. · 2000 [cited by applicant]
US 6153442A · Pirio et al. · 2000 [cited by applicant]
US 6248518B1 · Parkhurst et al. · 2001 [cited by applicant]
US 6255083B1 · Williams · 2001 [cited by applicant]
US 6399335B1 · Kao et al. · 2002 [cited by applicant]
US 6444682B1 · Simmonds et al. · 2002 [cited by applicant]
US 6627748B1 · Ju · 2003 [cited by examiner]
US 6762048B2 · Williams · 2004 [cited by applicant]
US 6787308B2 · Balasubramanian et al. · 2004 [cited by applicant]
US 6846638B2 · Shipwash · 2005 [cited by applicant]
US 6869764B2 · Williams et al. · 2005 [cited by applicant]
US 6936702B2 · Williams et al. · 2005 [cited by applicant]
US 7041812B2 · Kumar et al. · 2006 [cited by applicant]
US 7052847B2 · Korlach et al. · 2006 [cited by applicant]
US 7056661B2 · Korlach et al. · 2006 [cited by applicant]
US 7057026B2 · Barnes et al. · 2006 [cited by applicant]
US 7229799B2 · Williams · 2007 [cited by applicant]
US 7361466B2 · Korlach et al. · 2008 [cited by applicant]
US 7405281B2 · Xu et al. · 2008 [cited by applicant]
US 7625701B2 · Williams et al. · 2009 [cited by applicant]
US 7968702B2 · Wegener et al. · 2011 [cited by applicant]
US 7973146B2 · Shen et al. · 2011 [cited by applicant]
US 8034623B2 · Oh et al. · 2011 [cited by applicant]
US 8084734B2 · Vertes et al. · 2011 [cited by applicant]
US 8133702B2 · Shen et al. · 2012 [cited by applicant]
US 8148516B2 · Williams et al. · 2012 [cited by applicant]
US 8153375B2 · Travers et al. · 2012 [cited by applicant]
US 8192961B2 · Williams · 2012 [cited by applicant]
US 8252910B2 · Korlach et al. · 2012 [cited by applicant]
US 8257954B2 · Clark et al. · 2012 [cited by applicant]
US 8309330B2 · Travers et al. · 2012 [cited by applicant]
US 8354252B2 · Wegener et al. · 2013 [cited by applicant]
US 8383791B1 · McDowell et al. · 2013 [cited by applicant]
US 8420366B2 · Clark et al. · 2013 [cited by applicant]
US 8455193B2 · Travers et al. · 2013 [cited by applicant]
US 8530154B2 · Williams · 2013 [cited by applicant]
US 8581179B2 · Franzen · 2013 [cited by applicant]
US 8846881B2 · Korlach et al. · 2014 [cited by applicant]
US 8906614B2 · Wegener et al. · 2014 [cited by applicant]
US 8927212B2 · Kong et al. · 2015 [cited by applicant]
US 8980584B2 · Williams · 2015 [cited by applicant]
US 9062091B2 · Bjornson et al. · 2015 [cited by applicant]
US 9404146B2 · Travers et al. · 2016 [cited by applicant]
US 9435810B2 · Havranek et al. · 2016 [cited by applicant]
US 9464107B2 · Wegener et al. · 2016 [cited by applicant]
US 9542527B2 · Travers et al. · 2017 [cited by applicant]
US 9551031B2 · Korlach et al. · 2017 [cited by applicant]
US 9551660B2 · Kong et al. · 2017 [cited by applicant]
US 9566335B1 · Emili et al. · 2017 [cited by applicant]
US 9582640B2 · Travers et al. · 2017 [cited by applicant]
US 9600626B2 · Travers et al. · 2017 [cited by applicant]
US 9678080B2 · Miller et al. · 2017 [cited by applicant]
US 9719073B2 · Emig et al. · 2017 [cited by applicant]
US 9845501B2 · Williams · 2017 [cited by applicant]
US 9879319B2 · Korlach et al. · 2018 [cited by applicant]
US 9910956B2 · Travers et al. · 2018 [cited by applicant]
US 9957291B2 · Sebo et al. · 2018 [cited by applicant]
US 10023605B2 · Bjornson et al. · 2018 [cited by applicant]
US 10066258B2 · Kong et al. · 2018 [cited by applicant]
US 10150872B2 · Zheng et al. · 2018 [cited by applicant]
US 10161002B2 · Korlach et al. · 2018 [cited by applicant]
US 10174363B2 · Rothberg et al. · 2019 [cited by applicant]
US 10481162B2 · Emili et al. · 2019 [cited by applicant]
US 10544449B2 · Shen et al. · 2020 [cited by applicant]
US 10545153B2 · Marcotte et al. · 2020 [cited by applicant]
US 10570445B2 · Kong et al. · 2020 [cited by applicant]
US 10676788B2 · Shen et al. · 2020 [cited by applicant]
US 10745750B2 · Korlach et al. · 2020 [cited by applicant]
US 10787573B2 · Zheng et al. · 2020 [cited by applicant]
US 11001875B2 · Rothberg et al. · 2021 [cited by applicant]
US 11613772B2 · Rothberg · 2023 [cited by examiner]
US 20020182625A1 · McGall et al. · 2002 [cited by applicant]
US 20030138809A1 · Williams et al. · 2003 [cited by applicant]
US 20030143591A1 · Davies et al. · 2003 [cited by applicant]
US 20050014154A1 · Weizenegger · 2005 [cited by applicant]
US 20050042633A1 · Williams · 2005 [cited by applicant]
US 20050266456A1 · Williams et al. · 2005 [cited by applicant]
US 20070072196A1 · Xu et al. · 2007 [cited by applicant]
US 20070219367A1 · Shchepinov et al. · 2007 [cited by applicant]
US 20090068645A1 · Sibson · 2009 [cited by applicant]
US 20090104614A1 · Tsourkas et al. · 2009 [cited by applicant]
US 20090117540A1 · Sorge · 2009 [cited by applicant]
US 20090233302A1 · Wegener et al. · 2009 [cited by applicant]
US 20090263802A1 · Drmanac · 2009 [cited by applicant]
US 20100009872A1 · Eid et al. · 2010 [cited by applicant]
US 20100029494A1 · Cherkasov et al. · 2010 [cited by applicant]
US 20100034750A1 · Perfect et al. · 2010 [cited by applicant]
US 20100035254A1 · Williams · 2010 [cited by applicant]
US 20100093553A1 · Park et al. · 2010 [cited by applicant]
US 20100129822A1 · Siva et al. · 2010 [cited by applicant]
US 20100152424A1 · Korlach et al. · 2010 [cited by applicant]
US 20100317005A1 · Hardin et al. · 2010 [cited by applicant]
US 20110003343A1 · Nikiforov et al. · 2011 [cited by applicant]
US 20110165652A1 · Hardin et al. · 2011 [cited by applicant]
US 20110212437A1 · Emig et al. · 2011 [cited by applicant]
US 20110256549A1 · Gaylord et al. · 2011 [cited by applicant]
US 20110281776A1 · Eshoo et al. · 2011 [cited by applicant]
US 20120322692A1 · Pham et al. · 2012 [cited by applicant]
US 20130240359A1 · Turner et al. · 2013 [cited by applicant]
US 20130316912A1 · Bjornson et al. · 2013 [cited by applicant]
US 20140094375A1 · Kamtekar et al. · 2014 [cited by applicant]
US 20150050659A1 · Sebo et al. · 2015 [cited by applicant]
US 20150293022A1 · Buckhout-White et al. · 2015 [cited by applicant]
US 20150330987A1 · Bjornson et al. · 2015 [cited by applicant]
US 20170136433A1 · Sun et al. · 2017 [cited by applicant]
US 20170362651A1 · Rothberg et al. · 2017 [cited by applicant]
US 20180211003A1 · Travers et al. · 2018 [cited by applicant]
US 20180299460A1 · Emili · 2018 [cited by applicant]
US 20180346507A1 · Sebo et al. · 2018 [cited by applicant]
US 20190010183A1 · Bjornson et al. · 2019 [cited by applicant]
US 20190024168A1 · Rothberg et al. · 2019 [cited by applicant]
US 20190249153A1 · Kamtekar et al. · 2019 [cited by applicant]
US 20190330688A1 · Rothberg et al. · 2019 [cited by applicant]
US 20200031861A1 · Rothberg et al. · 2020 [cited by applicant]
US 20200141944A1 · Emili et al. · 2020 [cited by applicant]
US 20200148727A1 · Tullman et al. · 2020 [cited by applicant]
US 20200232017A1 · Rothberg et al. · 2020 [cited by applicant]
CA 2373385A1 · 2000 [cited by applicant]
CA 2457513A1 · 2003 [cited by applicant]
CN 1373813A · 2002 [cited by applicant]
CN 1771336A · 2006 [cited by applicant]
CN 1938328A · 2007 [cited by applicant]
CN 101346472A · 2009 [cited by applicant]
CN 101434988A · 2009 [cited by applicant]
CN 101636406A · 2010 [cited by applicant]
CN 102124128A · 2011 [cited by applicant]
CN 102329884A · 2012 [cited by applicant]
CN 102782159A · 2012 [cited by applicant]
CN 103866010A · 2014 [cited by applicant]
CN 105001292A · 2015 [cited by applicant]
EP 1179085A1 · 2002 [cited by applicant]
EP 1681356A1 · 2006 [cited by applicant]
EP 1421213B1 · 2010 [cited by applicant]
EP 2226330A1 · 2010 [cited by applicant]
EP 2263087A1 · 2010 [cited by applicant]
EP 2814953A1 · 2014 [cited by applicant]
GB 2398383A · 2004 [cited by applicant]
JP H07502992A · 1995 [cited by applicant]
JP 2002543847A · 2002 [cited by applicant]
JP 2005507674A · 2005 [cited by applicant]
JP 2009518009A · 2009 [cited by applicant]
JP 2015073523A · 2015 [cited by applicant]
JP 2016011429A · 2016 [cited by applicant]
WO WO9309128A1 · 1993 [cited by applicant]
WO WO0070073A1 · 2000 [cited by applicant]
WO WO0109389A3 · 2001 [cited by applicant]
WO WO03089670A2 · 2003 [cited by applicant]
WO WO2003102239A2 · 2003 [cited by applicant]
WO WO2004096997A2 · 2004 [cited by applicant]
WO WO2005044836A2 · 2005 [cited by applicant]
WO WO2007041342A2 · 2007 [cited by applicant]
WO WO2007064905A2 · 2007 [cited by applicant]
WO WO2007070572A2 · 2007 [cited by applicant]
WO WO2007015168A3 · 2007 [cited by applicant]
WO WO2009114182A1 · 2009 [cited by applicant]
WO WO2010065322A1 · 2010 [cited by applicant]
WO WO2010115016A2 · 2010 [cited by applicant]
WO WO2010117420A2 · 2010 [cited by examiner]
WO WO2011150852A1 · 2011 [cited by applicant]
WO WO2012027625A2 · 2012 [cited by examiner]
WO WO2016187580A1 · 2016 [cited by applicant]
WO WO2016193231A1 · 2016 [cited by applicant]
WO WO2017201514A1 · 2017 [cited by applicant]
WO WO2019023257A1 · 2019 [cited by applicant]
WO WO2019040825A1 · 2019 [cited by applicant]
WO WO2020154546A1 · 2020 [cited by applicant]
Brown et al., Synthesis of a modified thymidine monomer for site-specific incorporation of reporter groups into oligonucleotides. Tetrahedron Letters. 2001;42:2587-2591. [cited by applicant]
Bunt et al., FRET from single to multiplexed signaling events. Biophys Rev. 2017;9:119-29. Epub Mar. 23, 2017. [cited by applicant]
Cheng-Yao, DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present. Frontiers in Microbiology. 2014. 10 pages. [cited by applicant]
Extended European Search Report dated May 6, 2021 for Application No. EP 18837972.1. [cited by applicant]
International Preliminary Report on Patentability for Application No. PCT/US2018/043526 dated Feb. 6, 2020. [cited by applicant]
International Preliminary Report on Patentability for Application No. PCT/US2019/041717 dated Jan. 28, 2021. [cited by applicant]
International Preliminary Report on Patentability for International Application No. PCT/US2017/033706 dated Nov. 29, 2018. [cited by applicant]
International Preliminary Report on Patentability for International Application No. PCT/US2020/014856 dated Aug. 5, 2021. [cited by applicant]
International Search Report and Written Opinion for Application No. PCT/US2019/041717 dated Nov. 13, 2019. [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/US2017/033706 dated Sep. 12, 2017. [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/US2018/043526 dated Oct. 3, 2018. [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/US2020/014856 dated Jun. 30, 2020. [cited by applicant]
Invitation to Pay Additional Fees for Application No. PCT/US2019/041717 dated Sep. 20, 2019. [cited by applicant]
Invitation to Pay Additional Fees for International Application No. PCT/US2020/014856 dated May 8, 2020. [cited by applicant]
Koushik et al., Cerulean, Venus, and VenusY67C FRET reference standards. Biophys J. Dec. 15, 2006;91(12):L99-L101. doi: 10.1529/biophysj.106.096206. Epub Oct. 13, 2006. PMID: 17040988; PMCID: PMC1779932. [cited by applicant]
Kretschy et al., Comparison of the sequence-dependent fluorescence of the cyanine dyes Cy3, Cy5, DyLight DY547 and DyLight DY647 on single-stranded DNA. PLoS One. Jan. 15, 2014;9(1):e85605. doi: 10.1371/journal.pone.008… [cited by applicant]
Kumar et al., Terminal phosphate labeled nucleotides: synthesis, applications, and linker effect on incorporation by DNA polymerases. Nucleosides Nucleotides Nucleic Acids. Nov. 2005;24(5-7):401-8. [cited by applicant]
Saito et al., Dual-labeled oligonucleotide probe for sensing adenosine via FRET: a novel alternative to SNPs genotyping. Chem Commun (Camb). Jun. 7, 2007;(21):2133-5. doi: 10.1039/b618465k. Epub Feb. 28, 2007. PMID: 175… [cited by applicant]
Sato et al., Polyproline-rod approach to isolating protein targets of bioactive small molecules: isolation of a new target of indomethacin. J Am Chem Soc. Jan. 31, 2007;129(4):873-80. doi: 10.1021/ja0655643. PMID: 17243… [cited by applicant]
Stryer et al., Energy transfer: a spectroscopic ruler. Proc Natl Acad Sci U S A. Aug. 1967;58(2):719-26. doi: 10.1073/pnas.58.2.719. PMID: 5233469; PMCID: PMC335693. [cited by applicant]
Takkellapati et al., Synthesis of aminomethyl-and bis-aminomethyl-fluorescein energy transfer terminators. Nucleosides Nucleotides Nucleic Acids. Dec. 2007;26(10-12):1467-70. [cited by applicant]
U.S. Appl. No. 61/069,247, filed Mar. 13, 2008, Korlach et al. [cited by applicant]
U.S. Appl. No. 61/979,724, filed Apr. 14, 2014. [cited by applicant]
Williams et al., An artificial processivity clamp made with streptavidin facilitates oriented attachment of polymerase-DNA complexes to surfaces. Nucleic Acids Res. Oct. 2008;36(18):e121. doi: 10.1093/nar/gkn531. Epub A… [cited by applicant]