`Case 1:12—cv—OO274—LPS Document 74-3 Filed 05/06/13 Page 1 of 39 Page|D #: 865
`
`EXHIBIT C
`
`
`
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 2 of 39 PageID #: 866
`“'1llflllillllflilllflllfilllllliififlllilllfllmlllllflfllfillflllllflfifi
`
`US008097405B1
`
`(12) Ulllted States Patent
`Engelhardt et al.
`
`(10) Patent No.:
`(45) Date of Patent:
`
`US 8,097,405 B1
`Jan. 17, 2012
`
`1/1932 Cféa ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ 535/27
`4,310,552 A
`fihnargllllif 8‘ 31 ~~~~~~~~~~~~~ ~~ 424/180
`A
`4:358:35 A ,1, 11/1982 Falkow et 31.
`.................. N 435/5
`4,373,071 A
`2/1983 Itakura
`4,375,401 A
`3/1933 CatS1IT1P001aS
`2
`ij_’1:‘11]1I‘:e”‘1' """""""" " 536/29
`4:415:732 A
`11/1983 Camthers
`4,443,594 A
`4/1984 Buckmarm .................... ,, 536/27
`4,450,772 A
`7/ 1934 13eI10Vi0 61 31 ~~~~~~~~~~~~~ ~~ 514/311
`2522:1222:
`11;13::311::n
`2
`Sfitglhers
`4,534,647 A
`8/1985 Gross
`.............. .. 435/6
`4,581,333 A *
`4/1986 K01_1ri1s1<y et al.
`/
`455985049 A
`7;1986 Z"_hnkfi_
`1
`j,‘;22§f§§ Q
`@133? $331,; °”" """"""""" 536 27
`4,668,777 A
`5/1987 Caruthers
`4,707,440 A
`11/1987 Stavrianopoulos ............. .. 435/6
`
`.. 435/91
`4,708,935 A
`11/1987 Suhadolnik et al.
`.................... .. 536/29
`4,711,955 A * 12/1987 Ward et al.
`4,757,141 A
`7/1988 Fung
`4,828,979 A
`5/1989 K1
`1.
`..
`435/6
`
`4,333,251 A
`5/1939 Mjzgfttfl. ................ H 543/303
`4,347,240 A
`7/1939 Ryser
`(Continued)
`
`FOREIGN PATENT DOCUMENTS
`
`DE
`
`A1814134
`
`9/ 1970
`(Continued)
`
`OTHER PUBLICATIONS
`Hartman et a1., Biopolymers, vol. 20, No. 12, pp. 2635-2648, 1981 .*
`Biochemistry by Lehniger [Published by Worth Publishers, Inc., 70
`Fifth Avenue, New York, NY 10011] pp. 638-639, 1970.*
`Dunn et al., Cell vol. 12, pp. 23-26, 1977.*
`Becker et a1., “Irreversible Inhibition of Biotin Transport in Yeast by
`Biotinyl-p-nitrophenyl Ester,” Proc. Nat’l. Acad. Sci.
`(USA)
`5332504-2507 (1971)
`
`.
`(Continued)
`
`.
`.
`.
`Primary Examiner — John Brusca
`AUO}"I’l€y, Agent, 0}’ Firm —Natal1e Bogdanos,
`E11eGe“d1°fi3 E59
`
`ABSTRACT
`(57)
`A process for determining the sequence of nucleic acids of
`interest employs nucleotides or nucleotide analogs that have
`been made detectable by non-radioactive modifying or label-
`ing. Such nucleotides or nucleotide analogs are modified on
`the sugar moieties, the phosphate moieties or the base moi-
`eties, including base analogs. Modified nucleotide analogs
`can be attached to or coupled to or incorporated into DNA or
`RNA. The modified or labeled nucleotides or nucleotide ana-
`
`logs are also useful in processes for detecting the presence of
`nucleic acids of interest and for characterizing chromosomal
`sequences. Detection processes using the modified or labeled
`nucleotides or nucleotide analogs extend to the use ofa gel for
`separating or resolving hybrids formed between non-radio-
`actively labeled oligonucleotides orpolynucleotides and such
`nucleic acids of interest.
`
`198 Claims, 4 Drawing Sheets
`
`(54) NUCLEIC ACID SEQUENCING PROCESSES
`USING NON-RADIOACTIVE DETECTABLE
`MODIFIED OR LABELED NUCLEOTIDES OR
`NUCLEOTIDE ANALOGS, AND OTHER
`PROCESSES FOR NUCLEIC ACID
`DETECTION AND CHROMOSOMAL
`CHARACTERIZATION USING SUCH
`NON-RADIOACTIVE DETECTABLE
`MODIFIED OR LABELED NUCLEOTIDES OR
`
`(75)
`
`Inventors: Dean Engelhardt, New York, NY (US);
`Elazar Rabbani, New York, NY (US);
`Stanley Kline, Brooklyn, NY (US);
`Jannis G. Stavrianopoulos, New York,
`NY (Us); Dollie Kirtikar, Elmhurst, NY
`(US)
`
`(73) Assignee: Enzo Biochem, Inc., Farrningdale, NY
`(US)
`.
`.
`.
`.
`Sublect. 10 any dlsclalmers. the term Ofthls
`patent 1s extended or adjusted under 35
`U.S.C. 154(b) by 0 days.
`
`.
`( * ) N01199:
`
`(21) APP1 N0‘ 08/489069
`
`(22)
`
`Filed:
`
`Jun. 7, 1995
`
`Related U.S. Application Data
`
`(60) Continuation of application No. 07/954,772, filed on
`S613, 30, 1992, now abandoned, which is a continuation
`Of aPP11Ca110I1 N0, 07/548,348, 1'11€d
`011 -1111, 2, 1990,
`now abandoned, which is a division of application No.
`07/140,980, filed on Jan. 5, 1988, now abandoned,
`which is a Continuation ofapplication No. 06/674,352,
`filed on Nov, 21, 1984, now abandoned, which is a
`continuation of application No. 06/391,440, filed on
`Jun. 23, 1982, now abandoned.
`
`(51)
`
`Int. Cl.
`C12Q 1/68
`
`(2006.01)
`
`......................................... .. 435/6; 536/243
`(52) U.S. Cl.
`(58) Field of Classification Search ................ .. 435/5, 6,
`435/7.1, 91.1, 91.2, 810; 436/501, 63; 536/22.1,
`536/231, 24.1, 243—2433, 25.3; 735/77,
`735/78
`See application file for complete search history.
`
`(56)
`
`References Clted
`U.S. PATENT DOCUMENTS
`
`9/1975 Carpino
`1/1976 Harnden ....................... .. 424/85
`
`6/1976 Secrist, III et al.
`260/211.5
`................. .. 536/27
`7/1977 Robins et al.
`10/1978 Chirikjian
`11/1978 Lampson et a1.
`4/1979 Kaplan
`....... .. 260/112.5 R
`7/1980 Carrico et al.
`10/1980 Boguslaskiet a1.
`............ .. 435/7
`3/1981 Carrico et al.
`536/27
`
`4/1981 Scherberg
`536/25
`10/1981 Weber ......................... .. 436/536
`
`
`
`............. .. 424/85
`
`3,906,031 A
`3,931,397 A
`3,960,840 A
`4,038,480 A
`4,119,521 A
`4,124,702 A
`4,151,065 A
`4,213,893 A
`4,230,797 A
`4,255,566 A
`4,260,737 A
`4,293,310 A
`
`
`
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 3 of 39 PageID #: 867
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 3 of 39 Page|D #: 867
`
`US 8,097,405 B1
`Page 2
`
`U.S. PATENT DOCUMENTS
`
`........... .. 536/27
`
`........ .. 536/23.1
`
`7/1989 Smith
`4,849,513 A
`8/1989 Fung
`4,855,225 A
`...................... .. 536/27
`11/1989 Rapaport
`4,880,918 A
`8/1990 Ruth ............................. .. 536/27
`4,948,882 A *
`5/1991 Smith
`5,015,733 A
`6/1992 Smith
`5,118,800 A
`6/1992 Smith
`5,118,802 A
`11/1992 Kostichka
`5,162,654 A
`12/1992 Smith
`5,171,534 A
`5/1993 Schwartz
`5,212,059 A
`5/1993 Fung
`5,212,304 A
`8/1993 Engelhardt et al.
`5,241,060 A *
`9/1993 Pagano
`5,242,906 A
`11/1993 Fung et al.
`5,258,538 A
`5,260,433 A * 11/1993 Engelhardt et al.
`5,366,860 A
`11/1994 Bergot
`5,541,311 A
`7/1996 Dahlberg
`5,591,600 A
`1/1997 Ecker
`5,591,720 A
`1/1997 Anderson
`5,614,617 A
`3/1997 Cook
`5,643,730 A
`7/1997 Banker
`5,643,780 A
`7/1997 Baker
`5,652,094 A
`7/1997 Usman
`5,665,710 A
`9/1997 Rahman
`5,736,294 A
`4/1998 Ecker
`5,807,677 A
`9/1998 Eigen
`5,811,232 A
`9/1998 Crooke
`5,874,564 A
`2/1999 Ecker
`5,891,468 A
`4/1999 Martin
`5,914,230 A
`6/1999 Liu
`A
`5,998,383
`12/1999 Wright
`FOREIGN PATENT DOCUMENTS
`A1617886
`1/1971
`A2507901
`9/1976
`0027631 B1
`4/1981
`0061760 A1
`10/1982
`0061761 A1
`10/1982
`0061762 A2
`10/1982
`0063879 B1
`11/1982
`0068875
`1/1983
`0070687
`1/1983
`0090789
`10/1983
`0097341
`1/1984
`0169787 A1
`1/1986
`0225807 A2
`6/1987
`0261283
`3/1988
`2019408
`* 10/1979
`2019408 A
`10/1979
`2036029 A
`6/1980
`2040943
`9/1980
`2153356
`8/1985
`S49126395
`12/1974
`53133283
`11/1978
`57011999
`1/1982
`S58502205
`12/1983
`S5944648
`3/1984
`S5993100
`5/1984
`S59126252
`7/1984
`6096610
`5/1985
`S60161559
`8/1985
`60169495
`9/1985
`S60242368
`12/1985
`57042632
`3/1986
`61103824
`5/1986
`A659573
`4/1979
`8302276
`7/1983
`8302277
`7/1983
`8303260
`9/1983
`8602929
`5/1986
`8606726
`11/1986
`8607361
`12/1986
`
`DE
`DE
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`GB
`GB
`GB
`GB
`GB
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`JP
`SU
`W0
`W0
`W0
`W0
`W0
`W0
`
`OTHER PUBLICATIONS
`Halloran et al., “The Preparation of Nucleotide-protein Conjugates:
`Carbodiimides as Coupling Agents,” J'.
`Immunol., 96:373-378
`(1966).
`
`Manning et al., “A New Method of in situ Hybridization,”
`Chromosoma, 53:107-117 (1975).
`Kropinski et al., “5-(4 -Aminobutylaminomethyl) uracil, an Unusual
`Pyrimidine from the Deoxyribonucleic Acid of Bacteriophage
`121W-14,” Biochemistry, 12: 15 1-157 (1973).
`Torrence et al., “5-0-Alkylated Derivatives of 5-Hydroxy-2‘-
`deoxyuridine as Potential Antiviral Agents. Anti-Herpes Activity of
`5-Propynyloxy-2'-deoxyuridine,”
`.1. Med. Chem.,
`21 :228-231
`(1978).
`“Synthesis of Nucleotide Anhydrides by Anion
`Michelson,
`Exchange,” Biochem. Biophys. Acta., 9111-13 (1964).
`Cech et al. “A facile synthesis of 5-(perfluoroalkyl)-pyrimidines,”
`Nucl. Acids Res., 2:2183-2192 (1979).
`Schram et al., “Pyrrolopyrimidine Nucleosides VIII. Synthesis of
`Sangivamycin Derivatives Possessing Exocyclic Heterocycles at
`C5,” .1. Carbohydrate. Nucleosides. Nucleotides, 1:39-54 (1974).
`Bleackley et al., “The preparation of 5-cyanouracil and 5-cyano-2'-
`deoxyuridine from the corresponding 5-iodo derivative and cuprous
`cyanide,” Nucl. Acids Res., 2:683-690 (1975).
`Roberts et al., “Uridine and Cytidine Derivatives,” .1. Am. Chem. Soc.
`74:668-669 (1952).
`Bauman et al., “Rapid and High Resolution Detection of in situ
`Hybridisation to Polytene Chromosomes Using Fluorochrome-la-
`beled RNA,” Chromosoma, 8421-18 (1982).
`Bauman et al., “A new method for fluorescene microscopical local-
`ization of specific DNA sequences by in situ hybridization of
`fluorochrome-labelled RNA,” Exp. Cell Res., 128:485-490 (1980).
`Gerhard et al., “Localization of a Unique Gene by Direct Hybridiza-
`tion in situ,” Proc. Natl. Acad. Sci. (USA), 78:3755-3759 (1981).
`Miller, J., “Experiment 52, Assay of the lac Repressor by Binding to
`Operator,” Experiments in Molecular Genetics, Cold Spring Harbor
`Laboratory, pp. 367-370 (1972).
`Ueda et al., “Conversion of Uridine Nucleotides to the 6-Cyano
`Derivatives: Synthesis of 0rotidylic Acid (Nucleosides
`and
`Nucleotides),” ./'. Carbohyd/1, Nucleosides, Nucleotides, 5:261-271
`(1978).
`Brunngraber et al., “Purification and Properties of a Nucleoside
`Phosphotransferase from Carrot,” J Biol. Chem., 242:4834-4840
`(1967).
`the Carboxyl Groups of
`“Modification of
`al.,
`Wilchek et
`Ribonuclease by Attachment ofGlycine or Alanylglycine,” Biochem-
`istry, 6:247-252 (1967).
`Vogt, “Purification and Properties of S1 Nuclease from Aspergillus,”
`Methods in Enzymology, 65:248-255 (1980).
`Monod et al., “0n the Nature of Allosteric Transitions: A Plausible
`Model,” .1. Mol. Biol., 12:88-118 (1965).
`Pastan et al., “Cyclic Adenosine Monophosphate in Bacteria,” Sci-
`ence, 1691339-344(1969).
`Gilbert et al., “The Nucleotide Sequence of the lac Operator,” Proc.
`Natl. Acad. Sci. (USA), 70:3581-3584 (1973)
`Pardee, “Membrane Transport Proteins,” Science, 162:632-637
`(1968).
`Hazelbaur et al., “Role of the Galactose Binding Protein in
`Chemotaxis ofEscherichia coli toward Galactose,”Nature NewBio.,
`230:101-104 (1971).
`biotin-labeled
`of
`synthesis
`“Enzymatic
`Langer
`et
`al.,
`polynucleotides: Novel nucleic acid affinity probes,” Proc. Natl.
`Acad Sci. (USA), 7816633-6637(1981).
`Nishimura et al., “Synthetic Nucleosides and Nucleotides. XV. 1)
`5-Dimethylamino-2-oxidoisoquinolin-1-yl Diazomethane: A Novel
`Water-Soluble Fluorescent Labelling Agent for Nucleotides,” Chem.
`Pharm Bull., 28: 1695-1703 (1980).
`Kwah et al., “Myocardinal Infarct Imaging of Antibodies to Canine
`Cardiac Myosin with Indium-111-Diethylenetriamine Pentaacetic
`Acid,” Science 209:295-297 (1980).
`Torrence, et al., “Interferon Inducers: General Survey and Classifi-
`cation,” Methods in Enzymology, vol. 78, Interferons, Part A, pp.
`291-299 (Pestka, Edu.), Academic Press, New York, 1981.
`Siebenlist et
`al., “Contacts between Escherichia coli RNA
`polymerase and an early promoter of phage T7,” Proc. Natl. Acad.
`Sci. (USA), 771122-126, Jan. 1980.
`Maxam et al., “A New Method for Sequencing DNA,” Proc. Natl.
`Acad Sci. (USA), 74:560-564, 1977.
`
`
`
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 4 of 39 PageID #: 868
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 4 of 39 Page|D #: 868
`
`US 8,097,405 B1
`Page 3
`
`Heggeness et al., “Avidin Binds to Condensed Chromatin,” Stain
`Technol. 52:165-169 (1977).
`Heggeness et ai., “Use of the Avidin-Biotin Complex for the Local-
`ization of Actin and Myosin with Fluorescence Microscopy,” .1. Cell
`Biol. 73:783-788 (1977).
`Bayer et ai. “The Use of the Avidin-Biotin Complex as a Tool in
`Molecular Biology,” Methods ofBiochem Analysis 26: 1-45 (1980).
`Hoffman et ai ., “Iminobiotin Affinity Columns and Their Application
`to Retrieval of Streptavidin,” Proc. Natl. Acad. Sci. 77:4666-4668
`(1980).
`Pardue eta1., “Nucleic Acid Hybridization to the DNA of Cytological
`Preparations,” Methods in Cell Biol. 10: 1-16 (1975).
`Bergstrom et al., “C-5 Substituted Pyrimidine Nucleosides. 2. Syn-
`thesis via Olefin Coupling to Organopalladium Intermediates
`Derived from Uridine and 2'-Deoxyuridine,” JACS 100:8106-8112
`(1978).
`Bigge et ai., “Palladium-Catalyzed Coupling Reactions of Uracil
`Necleosides and Nucleotides,” JACS 102:2033-2038 (1979).
`Rigby et al., “Labeling Deoxyribonucleic Acid to High Specific
`Activity in Vitro by Nick Translation with DNA Polymerase I,” .1.
`Mol. Biol. 113: 1237-251 (1977).
`Bourguignon et al., “DNA of Minute Virus of Mice:Self-Priming,
`Nonpermutated Single-Stranded Genome with, a 5‘-Terminal Hair-
`pin Duplex,” ./'. Wrol. 20:290-306 (1976).
`Miller et al., “A general method for permeabilizing mono-layer and
`suspension cultured animal cells,” Exp. Cell Res. 120:421-425
`(1979).
`Schulman et al., “Attachment of protein affinity-labeling reagents of
`variable length and amino acid specificity to E. coli tRNA/Me’,” Nuc.
`AcidRes., 9: 1203-1217 (1981).
`biotin-labeled
`of
`synthesis
`Langer,
`et
`ai.,
`“Enzymatic
`polynucleotides: Novel nucleic acid affinity probes,” Chemical
`Abstracts, vol. 96, No. 7, Feb. 15, 1982, p. 207, Abstract No. 47771z.
`Clechet, P. et al., “Trace analysis of barium in water by means of
`cation resin-loaded paper and x-ray fluorescence analysis,” Chemical
`Abstracts, vol. 94, No. 25, Jun. 22, 1981, p. 366, Abstract No.
`214298t.
`Duke et al., “Conformational change accompanying modification of
`myosin ATPase,” Chemical Abstracts, vol. 66, No. 9, Feb. 27, 1967,
`p. 3326, Abstract No. 35045h.
`Duke et al., “Conformational change accompanying modification of
`myosin ATPase,” Biochem. Bioahys. Acta, 126:600-603 (1966).
`Kathawaia et al., “Darstellung von Desoxy-oligonucleotiden Mit
`2‘ .3 ' - [2 .4-Dimethoxy-benzyliden] -uridin
`al s
`Pho sphat-
`Schutzgruppe,” Liebigs Ann. Chem., 712: 195-200 (1968).
`Trouet et ai., “Targeting of antitumor and antiprotozoal drugs by
`covalent linkage to protein carriers,” ChemicalA bstracts, vol. 98, No.
`9, Feb. 28, 1983, p. 334-335, Abstract No. 77997m.
`Trouet et ai., “Targeting of antitumor and antiprotozoal drugs by
`covalent linkage to protein carriers,” NATO Adv. Study Inst. of Tar-
`geting of Drugs, Series A, Life Sciences, 47:19-30, Plenum Press,
`NewYork (1981).
`Angerer at ai., “An Electron Microscope Study of the Relative Posi-
`tions of the 4S and Ribosomai RNA Genes in HeLa Cell
`Mitochondrial DNA,” Cell 9:81-90 (1976).
`Mackey at ai., “Preparation and Characterization of Highly Radio-
`active in Vitro Labeled Adenovirus DNA and DNA Restriction Frag-
`ments ”Biochemistry, 16:4478-4482 (1977).
`of
`Derivatives
`Zhenodarova
`et
`ai .,
`“Spin-labeled
`Oligoribonucleotides as Spin Probes for Studying the Mechanism of
`the Effect of Enzymes,” Chemical Abstracts, vol. 91, 1979, p. 303,
`Abstract No. 85951n.
`Saiam et ai., “Synthesis of Nucleoside 5‘-([3-D-Glucopyranosyl
`Monophosphates) by the Sugar Ortho Ester Route,” Carbohydrate
`Research, 102:139-146 (1982).
`Saiam et ai., “Synthesis ofAcetylated oi-and [3-L-Fucosyl Esters of
`Nucleoside
`5‘-Monophosphates
`by the Orthoester Route,”
`Nucleosides & Nucleotides, 1:155-161 (1982).
`Maxam, A.M. and Gilbert, W., “Sequencing End-Labeled DNA with
`Base-Specific Chemical Cleavages,” Methods
`in Enzymology
`65:499-559 (1980).
`Sanger, F. et al., “DNA sequencing with chain-terminating inhibi-
`tors,” Proc. Natl. Acad. Sci. (USA) 74(12):5463-5467 (1977).
`
`Akusjarvi G., and Pettersson, U., “Nucleotide sequence at the junc-
`tion between the coding region fo the adenovirus 2 hexon messenger
`RNA and its leader sequence,” Proc. Natl. Acad Sci.
`(USA)
`75(12):5822-5826 (1978).
`Kitamura N. and Wimmer E., “Sequence of 1060 3‘-terminal
`nucleotides ofpoliovirus RNA as determined by a modification ofthe
`dideoxynucleotide method,” Proc. Natl. Acad.
`Sci.
`(USA)
`77(6):3196-3200 (1980).
`Yo shioka eta1., “Method for determining a DNA nucleotide sequence
`I,” Cell Engineering 1(1):93-101 (1982).
`Lee, D.C. and Roeder, R.G., “Transcription of Adenovirus Type 2
`Genes in a Cell-Free System: Aparent Heterogeneity of Initiation at
`Some Promoters,” Molecular and Cellular Biology 1(7):635-651
`(198 1).
`Nomiya et al., “Method for determining a DNA nucleotide sequence
`II,” Cell Engineering 1(2): 105-1 15 (1982).
`Draper, D.E. and Gold, L ., “A Method for Linking Fluorescent Labels
`to Polynucleotides: Application to Studies of Ribosome-Ribonucleic
`Acid Interactions,” Biochemistry 19(9): 1774-1781 (1980).
`Bouloy M. et ai., “Cap and Internal Nucleotides of Reovirus mRNA
`Primers are Incorporated into Influenza Viral Complementary RNA
`During Transcription in Vitro,” Journal of Wrology 32(3):895-904
`(1979).
`Plotch S.J. et al., “Transfer of 5'-terminal cap of globin mRNA to
`influenza viral complementary RNA during transcription in vitro,”
`Proc. Natl. Acad Sci. (USA) 76(4)1618-1622 (1979).
`Kagakukai ed., “Fluorescence tagging” Biochemistry Experiments
`Course 2, Nucleic Acid Chemistry III, pp. 299-317 (1977).
`Yang, C-H., and S011, D., “Studies ofTransfer RNA Tertiary Structure
`by Singlet-Singlet Energy Transfer,” Proc. Natl. Acad. Sci. (USA)
`71(7):2838-2842 (1974).
`Douglass et al., “Methods and instrumentation for fluorescence
`quantitation of proteins and DNA’s in electrophoresis gels at the I ng
`level,”Electrophoresis ’78 N. Catsimpoolas, ed., pp. 155-165 (1978).
`Gilbert W.,
`“DNA-sequenzierung
`and gon-struktur
`(Nobel-
`Vortrag,}” Angenwandte Chemie 93: 1037-1046 (1981).
`Gilbert W., “DNA Sequencing and Gene Structure,” Science
`214(18):1305-1312 (1981).
`Maxam, A.M. and Gilbert, W., “Sequencing End-Labeled DNA with
`Base-Specific Chemical Cleavages,” Methods
`in Enzymology
`65:499-504 (1980).
`Sanger et ai ., “DNA Sequencing With Chain Terminating Inhibitors,”
`Proc. Natl. Acad. Sci (USA) 74:5463-5467 (1977).
`Smith A.J.H., “DNA Sequence Analysis by Primed Synthesis,” Meth-
`ods in Enzymology 65:560-580 (1980).
`Barrio J.R. eta1., “Fluorescent Adenosine and Cytidine Derivatives,”
`Biochemical and Biophysical Research Communications 46(2):597-
`604 (1972).
`Eshaglpour, H. et al., “Specific chemical labeling of DNA frag-
`ments,” Nucl. Acids Res. 7(6): 1485-1495 (1979).
`Guo et al., “New rapid methods for DNA sequencing based on
`exonuclease III digestion followed by repair synthesis,” Chem. Abst.
`97: 162 (abstract No. 1521k) (1982).
`Fiddes, J.C., “Isolation, cloning and sequence analysis of the cDNA
`for
`the oi-subunit of human chorionic gonadotropin,” Nature
`281(4):351-356 (1979).
`Husimi, Y. “DNA Sequences,” Oyo Buturi 51( 12) 1400 (1982).
`Secrist, J.A. et al., “Fluorescent modification of cyclic amp spectro-
`scopic properties and activity in enzyme systems,” Science 1 77:279-
`2 80 (1972).
`Stanley et al., “A difference approach to RNA sequencing,” Nature
`274:87-89 (1978).
`Tsuchiya M. et ai., “Developments of DNA fluorescent labeling and
`real-time fluorescent detection gel electrophoresis methods,” Bio-
`physics 22: 20-E-19 (1982).
`Ulanov et ai., “Electron microscopic determination of guanosine
`localization in DNA,” Chem. Abst. 67: 1692 (1967) (abstract No.
`17910c).
`Titus, J.A. et al., “Texas Red, a hydrophilic red-emitting fluorophore
`for use with fluorescein in dual parameter flow microfluorometric and
`fluorescence microscopic studies,” Journal ofImmunological Meth-
`ods 50: 193-204 (1982).
`
`
`
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 5 of 39 PageID #: 869
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 5 of 39 Page|D #: 869
`
`US 8,097,405 B1
`Page 4
`
`Langrnore J.P. and CreweA.V., “Progress Towards the Sequencing of
`DNA by Electron Microscopy,” Proceedings, Thirty-Second Annual
`Meeting, Electron Microscopy Society ofAmerica, Aug. 1315, 1974,
`St. Louis, Mo., Ed., Arceneaux, C., p. 376-377, (1974), Claitor’s
`Publishing Division: Baton Rouge, LA, USA (1974).
`Partial Translation in English of “Biochemistry Experiments Course
`2, Nucleic Acid Chemistry III—Methods of Higher Order Structure
`Study—”pp. 299-317 (1977), edited by Nihon Kagakukai, issued
`Feb. 25, 1977.
`Gilbert, W., “DNA Sequencing and Gene Structure,” Nobel lecture,
`Dec. 8, 1980, Harvard University, The Biological Laboratories, Cam-
`bridge, Mass. 02138 (USA).
`Gilbert, W., Science (14):1305-1312, (Dec. 18, 1981); and.
`Gilbert, W., Bioscience Reports 1:353-375 (1981).
`English translation of Fushing, Y. “DNA Sequences,” Oyo Buturi
`51(12):1400 (1982).
`English translation of Ulanov, B.P and Malysheva, L.F., “Potentials
`for Localization of Guanine in DNA by Electron Microscopy,” Bio-
`physics, vol. XII(2):325-326 (1967).
`English translation of Ulanov, B.P. et al., “On the Problem of Deter-
`mination of Base Sequence in Nucleic Acids,” Biophysics, vol. XII
`(2)1326-330(1967).
`Rose, S.D., “Mercuration of Modified Nucleotides: Chemical Meth-
`ods Toward Nucleic Acid Sequencing by electron Microscopy,”
`Biochimica et Biaphysica Acta 361 :23 1 -235 (1974).
`Salser, W.A., “DNA Sequencing Techniques,” Annual Review of
`Biochemistry 43:923:965 (1974).
`Whiting, R.F. and F.P. Ottenseyer, “Platinum DMSO: An Adenine-
`Specific Stain for DNA Sequencing by Electron Microscopy,”
`Abstract W-PM-J 14 Presented at Biophysical Society Program and
`Abstracts, Nineteenth Annual Meeting, Feb. 18-21, 1975, Philadel-
`phia, PA, published in Biophysical Journal 15:98a (1975).
`Frizell, J., “A Possible Electron Dense Label for the Use in the
`Sequencing ofDNA by Electron Microscopy,” Journal ofTheoretical
`Biology 59:241-242 (1976).
`Organic Chemistry ofNucleicAcids, PartB, Chapter 9, “Reactions of
`the Carbohydrate Residues ofNucleic Acids,” pp. 449-476, Edited by
`Kochetkov, N.K. and Budovskii, F.I., Plenum Press. London and New
`York (1972).
`Armstrong, V.W. and Eckstein, F., “Interaction of Substrate Ana-
`logues with Escherichia coli DNA-Dependent RNA Polymerase,”
`Eur .1. Biochem 70: 33-38 (1976).
`Rozovskaya, T.A. et al., “Introduction of a Fluorescent Label at the 3
`OH End of DNA and the 3 OH End of the Growing RNA Chain,”
`Mole/cub/amaya Biologiya 11(3): 598-610 (1977).
`“Spin-labeled
`Petrov
`A.I.
`and
`Sukhorukov
`B.I.,
`polyribonucleotides,” Nucleic Acids Research 8(18): 4221-4234
`(1980).
`Hiratsuka, T. and Uchida, K., “Preparation and Properties of 2 (or
`3)-O-(2,4,6-Trinitrophenyl) Adenosine 5‘-Triphosphate, an Analog
`of Adenosine Triphosphate,” Biochimica et Biophysica Acta 320
`635-647 (1973).
`“Cytochemical Hybridization with
`al.,
`et
`Bauman
`J.G.J.
`Fluorochrome-labeled RNA,” .1 Histochem. Cytochem. 29: 227-237
`(1981).
`Broker T.R. et al., “Electron microscopic visualization of tRNA
`genes with ferritin-avidin: biotin labels,” Nucleic Acids Research
`5(2): 363-384 (1978).
`Sodja A. and Davidson N., “Gene n1apping and gene enrichment by
`the avidin-biotin interaction: use of cytochrome-c as a polyamine
`bridge.” Nucleic Acids Research 5(2): 385-401 (1978).
`Daniel F.B. and Behrman E.J., “Osmium (VI) Complexes of the
`3‘,5'-Dinucleoside Monophosphates. ApU and UpA,” Biochemistry
`15: 565-568 (1976).
`Eberhard W. eta1., “Galactopyranosyl-[3(1 3')-ribonucleosides-struc-
`tural evidence and synthesis,” Nucleic Acids Research Symposium
`Series No.9: 15-19 (1981).
`Saffhill, R. and Hall, J., “A Convenient Preparation of Isomerically
`Pure Nucleoside
`5' Monophosphates
`From Unprotected
`Nucleosides,” .1. Carbohydrates Nucleosides Nucleotides 8(6): 573-
`553 (1981).
`
`Erlanger, B.F. et al., “Antibodies Specific for Ribonucleosides and
`Ribonucleotides and Their Reaction with DNA,” Proc. Natl. Acad.
`Sci. 52: 6R-74 (1964).
`Suzuki S., et al., “The Binding Sites ofNucleosides or Nucleotides to
`Diethylenetriaminecobalt (III),” Bioinorganic Chemistry 3: 281-293
`(1974).
`Petrov, A.I., “Complex formation between spin-labeled polyuridylic
`acid and pyrimidine nucleosides,” Nucleic Acids Research 8(23):
`5913-5929 (1980).
`Lippard, S.J., “Platinum Complexes, Probes ofPolynucleotide Struc-
`ture and Antitumor Drugs,” Accounts of Chemical Research 11
`(1978), 211-217.
`Hampton, A., “Studies of the Action of Adenylosuccinase with
`6-Thio Analogues of Adenylosuccinic Acid,” .1. Biol. Chem. 237
`(1962), 529-535.
`Beer, M. et al., “Biological Structure Determination Through Atomic
`Microscopy,” Chcmica Scnpta 14 (1979), 263-266.
`Chang, C-H. et al ., “Osmium-Labeled Polynucleotides. The Reaction
`of Osmium Tetroxide with Deoxyribonucleic Acid and Synthetic
`Polynucleotides in the Presence of Tertiary Nitrogen Donor
`Ligands,” Biochemistry 16 (1977), 33-38.
`Brossmer et al., “Synthese von 5-(oL-1)-Glucopyranosyloxyrnethl)-
`3-([3-D-ribofi1ranosyl)uracil and 3-(2- Desoxy- [3-D-ribofuranosyl)-
`5-( oi-D-glucopyranosy1oxymethyl)uracil als Analoga eines DNA-
`Bausteins,” Leibings Ann. Chem 975-981 (1974).
`of N6-suc-
`Chheda,G.B.,
`“Isolation
`and
`characterization
`cinyladenosine from human urine,” NucleicAcidResearch 4739-746
`(1977).
`the modified nucleosides of RNA,”
`Limback et al., “Summary:
`Nucleic Acids Research 22 2183 -2196 (1994).
`Delaney, E.J. et al., “Synthesis of 5'Substituted EDTA-Like
`Nucleosides as Analogs of Nucleoside Phosphates,” .1. Carbohy-
`drates Nucleosides Nucleotides 8 445-459 (1981).
`Raggazzo and Behrman, “The Reactions of Oxo-Osmium Ligand
`Complexes with Isopentenyl Adenine
`and Its Nucleoside,”
`Bioinorganic Chem. 5 343-352 (1976).
`and
`Hoard, D.E.
`and Ott, D.G.,
`“Conversion of Mono-
`Oligodeoxyribonucleotides to 5‘-Triphosphates,” .1. Am. Chem. Soc.
`87 1785-1788 (1965).
`Martell and Calvin, Chemistry of the Metal Chelate Compounds,
`Prentice Hall, Englewood Cliffs NJ, USA 136.
`Dwyer, F.W. and Mellor, D.P, ChelatingAgents and Metal Chelates,
`3 (1974).
`Dunaway-Mariano, D. and Cleland, W.W., “Preparation and Proper-
`ties of Chromium(III) Adenosine 5’Triphosphate, Chromium(III)
`Adenosine 5'-Diphosphate,
`and Related Chromium(III)-Com-
`plexes.” Biochemistry 19 1496-1505 (1980).
`Liu, Y. and Wu, C., “Radiolabeling of Monoclonal Antibodies with
`Metal Chelates,” Pure andApplied Chem. 63 427-463(1991).
`Krejcarek, G.E. and Tucker, K.L., “Covalent Attachment of Chelat-
`ing Groups to Macromolecules,” Biochemical and Biophysical
`Research Communications 77, 581-583 (1977).
`Sundberg et al., “Selective Binding of Metal Ions to Macromolecules
`Using Bifunctional Analogs of EDTA.” .1. Medicinal Chemistry 17
`1304-1307 (1974).
`Dale, R.M.K. and Ward, D.C., “Direct Covalent Mercuration of
`Nucleotides and Polynucleotides,” Biochemistry 14 2458-2469
`(1975).
`Jeng et al., “The Use of Aryl Azido ATP Analogs as Photo Affinity
`Labels for Nyosin ATPase,” .1. Supramolecular Structure 3: 448-468
`(1975).
`Gottikh et al., “The General Synthetic Route to Amino Acid Esters of
`Nucleotides and Nucleosides-5‘-Triphosphates and Some Properties
`of These Compounds.” Tetrahedron 26: 4419-4433 (1970).
`Biochemistry, Third Edition, Stryer, L., Editor, pp. 96-97 W.H. Free-
`man and Co., NewYork (1988).
`Karlson, Kurzes Lchrbuch der Bioehemie (1972) (short textbook of
`biochemistry), George Thieme publishers, Stuttgart, in particular pp.
`169-170.
`Scheit, Karl H., NucleotideAnalogs.' Synthesis and Biological Func-
`tion, John Wiley & Sons, Inc., NewYork, 1980, 288 pages.
`Kornberg, A., DNA Synthesis, W. H. Freeman and Company, San
`Francisco, 1974, Chapter 7, pp. 227-228.
`
`
`
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 6 of 39 PageID #: 870
`Case 1:12-cv-00274-LPS Document 74-3 Filed 05/06/13 Page 6 of 39 Page|D #: 870
`
`US 8,097,405 B1
`Page 5
`
`Kornberg, A., DNA Replication, W. H. Freeman and Company, San
`Francisco, 1980, Chapter 12, “Inhibitors of Replication,” pp. 415-
`441.
`Adams, R. L. P. et al., Davidson ’s The Biochemistry ofthe Nucleic
`Acids, 8th Edition, Academic Press, New York, 1976, Chapter 11
`“Replication of DNA,” pp. 298-299.
`Langen, P., Antimetabolites ofNucleic Acid Metabolism.‘ The Bio-
`chemical Basis ofTheirAction, with Special Reference to theirAppli-
`cation in Cancer Therapy, Gordon and Breach, New York, English
`edition translated from the German by Dr. Thomas A. Scott, 1975, pp.
`143 -187.
`Darlix at al., Biochemistry 10: 1525-1531 (1971).
`Geider, K., European Journal ofBiochemistry 271554-563 (1972).
`Darlix and Fromageot, Biochimie 561703-710 (1974).
`Marcus, F., Cancer Research 3611847 (1976).
`Simoncsits and Tomasz, Tetrahedron Letters 44:3995-3998 (1976).
`Chladek et al., Biochemistry 16:4312-4319 (1977).
`Piperno and Alberts, Journal ofBiological Chemistry 253:5174-5179
`(1978).
`Reha-Krantz et al., Journal of Wrology 6 7: 60-66 (1993).
`Birch and Lee, Journal ofFood Science 41: 1403-1407 (1976).
`Lartey and Derechin, Preparative Biochemistry 9185-95 (1979).
`Roberts and Hayes, Scandinavian Journal of Dental Research
`881801-909 (1980).
`Kortnyk et al., Eur J Med Chem.—Chimica Therapeutica 15:77-84
`(1980).
`Keppler et al., Biochemical Journal 2061139-146 (1982).
`Yang and Metzler, Methods in Enzymology 621528-551 (1979).
`Stridh et al., Archives oflfirology 611245-250 (1979).
`Stoeckler et al., Biochemistry 191102-107 (1980).
`Montgomery, J. H. and H. Jeanette Thomas, “4-Amino-7-[3-D-
`Ribofuranosyl-7H-Imidazol[4,5-d]-v-Triazine(2-Aza-Adenosine)
`The Synthesis of 2-Azapurine Nucleosides from Purine Nucleosides
`Accomplished via Ring Opening Followed by Reclosure with
`Nitrous Acid,” in Nucleic Acid Chemistry.‘ Improved and New Syn-
`thetic Procedures, Methods and Techniques, Part Two, Dr. Leroy B.
`Townsend and Dr. R. Stuart Tipson, Editors, John Wiley & Sons, New
`York, 1978, No. 118, pp. 681-685.
`Shibaev, V. N. and S. M. Spiridonova, “1-Methyladenosine-5'-(oL- -
`Glucopyranosyl Pyrophosphate): Methylation of Adenosine Deriva-
`tives,” in Synthetic Procedures in Nucleic Acid Chemistry, vol. I,
`Werner Zorbach and R. Stuart Tipson, Editors, Interscience Publish-
`ers, NewYork, 1968, No. 14, pp. 481-462.
`Thomas, H. Jeanette and J. A. Montgomery, “3-Benzylpurines,” in
`Synthetic Procedures in Nucleic Acid Chemistry, vol.
`I, Werner
`Zorbach and R. Stuart Tipson, Editors, Interscience Publishers, New
`York, 1988, No. 10, pp. 28-30.
`Yamamoto at el., J Radiation Research 211239-247 (1980).
`Rhaese, H. J., Biochimica et Biophysics Acta 166131-326 (1968).
`Taylor, M. R., Acta Crystallogr B29:884-890 (1973).
`Walker et al., Australian Journal ofChemistry 2612391-2399 (1973).
`Srinivasan et al., J Chemical Society D241 1668-1669 (1970).
`Kaneko et al., “8,2-Anhydrides of Purine -8-Thiol Nucleosides (or of
`Purine 2‘-Thionucleosides): Synthesis of 8,2‘-Anhydronucleosides
`of Purine-8-thiol [or of 8,2‘-Anhydro-(2'-thionucleosides)] by use of
`Diphenyl Carbonate as the Cyclizing Agent,” in Nucleic Acid Chem-
`istry: Improved and New Synthetic Procedures, Methods and Tech-
`niques, Part Two, Dr. Leroy B. Townsend and Dr. R. Stuart Tipson,
`Editors, John Wiley & Sons, NewYork, 1978, No. 103, pp. 395-399.
`Robins, M. J. and G. L. Bason, “6-Chloro-9-(2-Deoxy-[3-D-Erythro-
`Pentofuranosyl)Purine from the Chlorination of 2'-Deoxyinosine:
`Direct Replacement of the 6-Oxo Group by a Chlorine Atom in a
`Purine 2'-Deoxynucleoside: Stabilization of the Glycosyl Bond
`Towards Cleavage by Acid,” in Nucleic Acid Chemistry.‘ Imoroved
`and New Synthetic Procedures, Methods and Techniques, Part Two,
`
`Dr. Leroy B. Townsend and Dr. R. Stuart Tipson, Editors, John
`Wiley & Sons, New York, 1978, No. 104, pp. 601-606.
`Zemlicka, J. and J. Owens, “6-Chloro-9-[3-D-Ribofuranosylpurine:
`AVersatile Intermediate in the Synthesis ofPurine Ribonucleo sides,”
`in NucleicAcid Chemistry.‘ Improved and New Synthetic Procedures,
`Methods and Techniques, Part Two, Dr. Leroy B. Townsend and Dr.
`R. Stuart Tipson, Editors, John Wiley & Sons, NewYork, 1978, No.
`106, pp. 611-614.
`Kochetkov et al., “3-Methyluridine 5‘-Phosphate: Methylation of
`Uridine Derivatives with Diazomethanez Phosphorylation of
`Nucleosides with Pyrophosphonyl Chloride,” in Synthetic Proce-
`dures in NucleicAcid Chemistry, vol. I, Werner Zorbach and R. Stuart
`Tipson, Editors, Interscience Publishers, New York, 1968, No. 152,
`pp. 497-499.
`[4-Methyl-2-[3-
`“3 -Methyl-6-Azauridine
`J.,
`Zemlicka,
`D-Riboluranosyl-AS-Triazin-3,5-(2H,4H)-Dione]: Alkylation of a
`Nucleoside Antimetabolite by Use of N,N-Dimethyl-formamide
`Dimethyl Acetal,” in Nucleic Acid Chemistry.‘ Improved and New
`Synthetic Procedures, Methods and Techniques, Part Two, Dr. Leroy
`B. Townsend and Dr. R. Stuart Tipson, Editors, John Wiley & Sons,
`NewYork, 1978, No. 78, pp. 451-453.
`“1-[3-
`Sorm,
`F.
`Pi skala,
`A.
`and
`D-Ribofuranosyl-6-Triazine-2,4-(1H,3H)-Dione
`(5-Azauridine):
`Direct Synthesis of a 5-Azauridine Ribonucleoside by the Fisher-
`Helferich Procedure,” in NucleicAcid Chemistry.‘ Improved andNew
`Synthetic Procedures, Methods and Techniques, Part Two, Dr. Leroy
`B. Townsend and Dr. R. Stuart Tipson, Editors, John Wiley & Sons,
`NewYork, 1978, No. 79, pp. 455-459.
`Poverenny et al., Molecular Immunology 161313-316 (1979).
`Visser, D. W. and P. Roy-Burman, “5-Hydroxyuridine 5-Phosphate
`Derivatives: Substitution Reactions at
`the Pyrimidine Ring of
`Nucleotides,” in Synthetic Procedures in Nucleic Acid Chemistry,
`vol. I, Werner Zorbach and R. Stuart Tipson, Editors, Interscience
`Publishers, NewYork, 1968, No. 1