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(12) Patent Application Publication (10) Pub. No.: US 2015/0368710 A1 Fuller Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2015/0368710 A1 Fuller Et Al US 2015036871 OA1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0368710 A1 Fuller et al. (43) Pub. Date: Dec. 24, 2015 (54) CHEMICAL METHODS FOR PRODUCING (22) Filed: Mar. 23, 2015 TAGGED NUCLEOTDES Related U.S. Application Data (71) Applicants: Carl W. Fuller, Berkeley Heights, NJ (US); Shiv Kumar, Belle Mead, NJ (60) Provisional application No. 61/969,628, filed on Mar. (US); Jingyue Ju, Englewood Cliffs, NJ 24, 2014. (US); Randall Davis, Pleasanton, CA (US); Roger Chen, Saratoga, CA (US) Publication Classification (51) Int. C. (72) Inventors: Carl W. Fuller, Berkeley Heights, NJ (US); Shiv Kumar, Belle Mead, NJ CI2O I/68 (2006.01) (US); Jingyue Ju, Englewood Cliffs, NJ C07H 17/02 (2006.01) (52) U.S. C. (US); Randall Davis, Pleasanton, CA CPC .............. CI2O I/6874 (2013.01); C07H 17/02 (US); Roger Chen, Saratoga, CA (US) (2013.01); C12O 1/6806 (2013.01) (73) Assignees: The Trustees of Columbia University in the City of New York, New York, NY (57) ABSTRACT (US); Genia Technologies, Inc., This disclosure provides systems and methods for attaching Mountain View, CA (US) nanopore-detectable tags to nucleotides. The disclosure also provides methods for sequencing nucleic acids using the dis (21) Appl. No.: 14/666,124 closed tagged nucleotides. Patent Application Publication Dec. 24, 2015 Sheet 1 of 40 US 2015/036871.0 A1 FIG. I. Patent Application Publication Dec. 24, 2015 Sheet 2 of 40 US 2015/036871.0 A1 Patent Application Publication Dec. 24, 2015 Sheet 3 of 40 US 2015/036871.0 A1 f C YN-so o=-c-A-d-- Follo 8. {C} C. : 3. Ra R (dCp)-(PO)-dC N N HO-N & NH, gKY o=-o NYN N- E) 3. YoC . KN-- N w o to C N ---x . {}r-i-le-for-creas C {- C- C- fi :- s '...'s & 32 (dGp)-(PO)-tiG FIG. 3 Patent Application Publication Dec. 24, 2015 Sheet 4 of 40 US 2015/036871.0 A1 (dTp)-(PO)-dT FIG. 4 Patent Application Publication Dec. 24, 2015 Sheet 5 of 40 US 2015/036871.0 A1 : Patent Application Publication Dec. 24, 2015 Sheet 6 of 40 US 2015/036871.0 A1 s Patent Application Publication Dec. 24, 2015 Sheet 7 of 40 US 2015/036871.0 A1 Ce: {{}rrent Reactigs 388to: Ca 8: 3. 3 S “as protatiity of Current isites FIG. 7 Patent Application Publication Dec. 24, 2015 Sheet 8 of 40 US 2015/036871.0 A1 Nucleic Sample Nucleic Acid Preparation Acid Extraction Sequencing FIG. 8 Patent Application Publication Dec. 24, 2015 Sheet 9 of 40 US 2015/036871.0 A1 FIG. 9A Patent Application Publication Dec. 24, 2015 Sheet 10 of 40 US 2015/036871.0 A1 Patent Application Publication Dec. 24, 2015 Sheet 11 of 40 US 2015/036871.0 A1 S. S ?y n OO OY O. O. O. O. O. O. On OY Patent Application Publication Dec. 24, 2015 Sheet 12 of 40 US 2015/036871.0 A1 FIG. I.0 Patent Application Publication Dec. 24, 2015 Sheet 13 of 40 US 2015/036871.0 A1 S0IIS0IIS0IIS0IIS0II II(9IAI Patent Application Publication Dec. 24, 2015 Sheet 14 of 40 US 2015/036871.0 A1 ZI(5)IAI ***·········*** ??????HT?TLITIIVIILI Patent Application Publication Dec. 24, 2015 Sheet 15 of 40 US 2015/036871.0 A1 1301 O O O O O O O O O O O O O O FIG. I.3 Patent Application Publication Dec. 24, 2015 Sheet 16 of 40 US 2015/036871.0 A1 1400 1401 1420 1402 1425 1415 1410 Patent Application Publication Dec. 24, 2015 Sheet 17 of 40 US 2015/036871.0 A1 ?I“OICH Patent Application Publication Dec. 24, 2015 Sheet 18 of 40 US 2015/036871.0 A1 8% ah-arop| ***8. Patent Application Publication Dec. 24, 2015 Sheet 19 of 40 US 2015/036871.0 A1 S. 288 1463 SS3 8: 4. 20, 28 43 s ey: ** s : 3. 2 Ceasastria-FEG38-Nii Coataris-PEG36-Nis FIG. I. 7 Patent Application Publication Dec. 24, 2015 Sheet 20 of 40 US 2015/036871.0 A1 Cell Current Readings --SS: ·: 200 400 ility of current Patent Application Publication Dec. 24, 2015 Sheet 21 of 40 US 2015/036871.0 A1 (ºd)queuno FIG. I. 9 Patent Application Publication Dec. 24, 2015 Sheet 22 of 40 US 2015/036871.0 A1 acid-haide Arairie fortation of aide Fortation of Shif's laase aid methylamic by recitaction Patent Application Publication Dec. 24, 2015 Sheet 23 of 40 US 2015/036871.0 A1 Patent Application Publication Dec. 24, 2015 Sheet 24 of 40 US 2015/036871.0 A1 ZZ(OICH *****... Patent Application Publication Dec. 24, 2015 Sheet 25 of 40 US 2015/036871.0 A1 viosage: St: - 8836. 8.8 : 8::::: Dec. 24, 2015 Sheet 26 of 40 US 2015/036871.0 A1 4. Patent Application Publication Dec. 24, 2015 Sheet 27 of 40 US 2015/036871.0 A1 {}{3 €|£ auste-ovi Patent Application Publication Dec. 24, 2015 Sheet 28 of 40 US 2015/036871.0 A1 s Patent Application Publication Dec. 24, 2015 Sheet 29 of 40 US 2015/036871.0 A1 s Patent Application Publication Dec. 24, 2015 Sheet 30 of 40 US 2015/036871.0 A1 S. : Xixieckia; Weight 933:S x: -. w - Ext&six with 388xistory-a- 8 8. prod:E. ReleasedEag ag-&Bcieotide ;38& poly;8:3sc - feastec with SA8 citates triphospitates 8tc. &ass is: FIG. 28 Patent Application Publication Dec. 24, 2015 Sheet 31 of 40 US 2015/036871.0 A1 * w **.-: x- ww. : x ; : -8.8 : : : X, : s 3. Abasic (dS Abasic (C3 Abasic (C & E. & & pyroidise Spernik or Seraisie 8: i, 3 x 8:y Exercieas: resistant axxiety Cy r c if & &Nississiei Netsiarie Bezikiriciazcie Beze:8: : -icazavities 3-Saxsit:exi Y- Fiaorescein-ciT (FiciT 3. pyriticise Fictesce: FIG. 29 Patent Application Publication Dec. 24, 2015 Sheet 32 of 40 US 2015/036871.0 A1 0£PAOLAI Patent Application Publication Dec. 24, 2015 Sheet 33 of 40 US 2015/036871.0 A1 2 (A) Template as -- NPS ::::::::::::::::::::::::::::::::::::::::: tagged-NTPs DNA Extension Product:) DNA Template Y Released Tags & unused tagged-NTPs (B) :88-y3-is-tiŠga--& 88.3%. 33:38: tio 980s 80 8 : 60 8 40 4. 8 is 20 20 8. 8 O 2. 3. 1 3) 300T 11000 boo 3. fiass triz ass (niz} 88:88-83-883.8 - 3.3%. 33333; i000 Tesbo T 12too 84 12. 40 9000 10 i3000 ass (niz) FIG. 31 Patent Application Publication Dec. 24, 2015 Sheet 35 of 40 US 2015/036871.0 A1 (A) OH R B-D-nucleoside ot. -D-nucleoside (B) 3',5'-linked oligonucleotide 2',5'-linked oligonucleotide FIG, 3.3 Patent Application Publication Dec. 24, 2015 Sheet 36 of 40 US 2015/036871.0 A1 Patent Application Publication Dec. 24, 2015 Sheet 37 of 40 US 2015/036871.0 A1 GD29 FIG. 35 Patent Application Publication Dec. 24, 2015 Sheet 38 of 40 US 2015/036871.0 A1 (A) Single oiecuie Electronic SBS Data sing 4 Distinct Nanoag Nicieotides tit-x88, cic. is: 8: iii. 8: (B) o 6. ii.338 (see FIG. 36 Patent Application Publication Dec. 24, 2015 Sheet 39 of 40 US 2015/036871.0 A1 e e & cirg-ka-R-G-c-e-as-G-G-c-gressexxx-x-2-e-c-3-3-3-3-3-3-3-arc-a-a-a-a-a-ik-kas-K 888 . ; ; ; ; ; : . 888 . 8. Circussessessesses. 33:88-8-8-8-8 3-3 recencessessesseec. 98 f i: v. : S-3- s s f s s 6 f 5. 3XXXX-Xsy. - a 8 . ...: 3.xxi-xxx www.www.vxw8XXX8. ife FIG, 37 Patent Application Publication Dec. 24, 2015 Sheet 40 of 40 US 2015/0368710 A1 Circuiar Polymerase Template 8 s 8. Prirrer ethered t x· to pore Protein * x agged-Nucleotide FIG 38 US 2015/036871.0 A1 Dec. 24, 2015 CHEMICAL METHODS FOR PRODUCING of these four PEG-coumarin tagged dG nucleotides by DNA TAGGED NUCLEOTDES polymerase. See also, U.S. Patent Application Publication 0001. This application claims benefit under 35 U.S.C. Nos. US 2013/0244340A1 and US 2013/0264207 A1. S119(e) of U.S. Provisional Patent Application Ser. No. 0010 Recognized herein is the need for improved compo 61/969,628, filed Mar. 24, 2014, the contents of which are sitions and methods for nucleotide identification and nucleic hereby incorporated herein by reference. acid sequencing. 0002 This application incorporates-by-reference nucle otide and/or amino acid sequences which are present in the SUMMARY file named “150805 0575 85625 SequenceListing JAK. txt, which is 52 kilobytes in size, and which was created Aug. 0011 Provided herein are nucleotides with attached tags 5, 2015 in the IBM-PC machine format, having an operating and methods for attaching tags to nucleotides. The tags can be system compatibility with MS-Windows, which is contained attached by chemical reactions, such as "click chemistry. in the text file filed Aug. 5, 2015 as part of this application. 0012. In an aspect, the present disclosure provides a 0003. This invention was made with government support tagged nucleotide, comprising: (a) a poly-phosphate moiety under Grant number 5R01HG007415 awarded by the having a terminal phosphate; and (b) a tag covalently coupled National Institutes of Health. The government has certain to the terminal phosphate of the nucleotide by a triazole, a rights in the invention. 1.2-diazine, a disulfide, a secondary amine, a hydrazone, a thio-acetamide, or a maleimide-thioadduct. TECHNICAL FIELD 0013. In some embodiments of the tagged nucleotide, the 0004. This application relates to tagged nucleotide com tag is covalently coupled to the terminal phosphate by a positions, methods of preparing and using the disclosed triazole.
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