`US007713 698B2
`
`c12) United States Patent
`Ju et al.
`
`(IO) Patent No.:
`(45) Date of Patent:
`
`US 7,713,698 B2
`May 11, 2010
`
`(54) MASSIVE PARALLEL METHOD FOR
`DECODING DNA AND RNA
`
`(75)
`
`Inventors: Jingyue Ju, Englewood Cliffs, NJ (US);
`Zengmin Li, New York, NY (US); John
`Robert Edwards, New York, NY (US);
`Yasuhiro Itagaki, New York, NY (US)
`
`(73) Assignee: The Trustees of Columbia University
`in the City of New York, New York, NY
`(US)
`
`( *) Notice:
`
`Subject to any disclaimer, the term ofthis
`patent is extended or adjusted under 35
`U.S.C. 154(b) by O days.
`
`(21) Appl. No.: 11/894,690
`
`(22) Filed:
`
`Aug. 20, 2007
`
`(65)
`
`Prior Publication Data
`
`US 2008/0131895 Al
`
`Jun. 5,2008
`
`Related U.S. Application Data
`
`(60) Continuation of application No. 10/702,203, filed on
`Nov. 4, 2003, now Pat. No. 7,345,159, which is a
`division of application No. 09/972,364, filed on Oct. 5,
`2001, now Pat. No. 6,664,079, and a continuation-in(cid:173)
`part of application No. 09/684,670, filed on Oct. 6,
`2000, now abandoned.
`
`(60) Provisional application No. 60/300,894, filed on Jun.
`26, 2001.
`
`(51)
`
`Int. Cl.
`C12Q 1168
`C12P 19134
`C07H 21102
`C07H 21104
`C07H 19104
`C07G3/00
`C07H 21/00
`
`(2006.01)
`(2006.01)
`(2006.01)
`(2006.01)
`(2006.01)
`(2006.01)
`(2006.01)
`
`(52) U.S. Cl. ......................... 435/6; 435/91.1; 435/91.2;
`536/4.1; 536/23.1; 536/24.3; 536/24.33; 536/25.3;
`536/26.6
`(58) Field of Classification Search ..................... 435/6,
`435/91.1, 91.2; 536/23.1, 24.3, 24.33, 25.3,
`536/4.1, 26.6
`See application file for complete search history.
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`4,711,955 A
`
`12/1987 Ward et al.
`
`(Continued)
`
`FOREIGN PATENT DOCUMENTS
`
`EP
`
`0992511 A
`
`4/2000
`
`(Continued)
`
`OTHER PUBLICATIONS
`
`Arbo et al. (1993) "Solid Phase Synthesis of Protected Peptides
`Using New Cobalt (III) Amine Linkers," Int. J Peptide Protein Res.
`42:138-154.
`
`(Continued)
`
`Primary Examiner-Jezia Riley
`(74) Attorney, Agent, or Firm-John P. White; Cooper &
`DunhamLLP
`
`(57)
`
`ABSTRACT
`
`This invention provides methods for attaching a nucleic acid
`to a solid surface and for sequencing nucleic acid by detecting
`the identity of each nucleotide analogue after the nucleotide
`analogue is incorporated into a growing strand of DNA in a
`polymerase reaction. The invention also provides nucleotide
`analogues which comprise unique labels attached to the
`nucleotide analogue through a cleavable linker, and a cleav(cid:173)
`able chemical group to cap the -OH group at the 3'-position
`of the deoxyribose.
`
`17 Claims, 28 Drawing Sheets
`
`'~~:~Ith
`
`DNAlomplales
`(,10,000)
`
`dA(1,R) dA<i::-I ~:~to~~3':~roup)
`d0(3,R) d0(~=~·3
`
`<C(2,R) dc(~=~·
`
`2
`
`dT(4,R)dT~~-
`
`4
`
`Fluon,ocenoe
`•mlHIOn(nm)
`
`5255555!!0610
`A C G T
`
`(2)
`(a)WIOohU.c....,
`
`r,t.-.l,r--,!,-,i,,
`
`~ '
`
`AddpolymeraN (cid:127) nd
`dA{l,RJ.<Cj2,R),
`dl3(3.R),dT(4,R)
`
`{b)lmagelhedv,,
`cnMcllopct!c
`
`rnd1hesequence ~-~=
`
`~
`MU...lighl(350nm)IO
`~lh•dva
`(b)Chlmlcal~<:leeveR
`
`Page 1
`
`Illumina Ex. 1014
`IPR Petition - USP 10,435,742
`
`
`
`US 7,713,698 B2
`Page 2
`
`U.S. PATENT DOCUMENTS
`
`9/1988 Herman
`4,772,691 A
`4/1989 Dattagupta
`4,824,775 A
`4,863,849 A
`9/1989 Melamede
`5,043,272 A
`8/1991 Hartley
`6/1992 Urdea
`5,118,605 A
`5,174,962 A
`12/1992 Brennan
`12/1992 Stavrianopoulos
`5,175,269 A
`4/1994 Cheeseman
`5,302,509 A
`5,308,990 A
`5/1994 Takahashi et al.
`5,328,824 A
`7/1994 Ward et al.
`5,332,666 A
`7/1994 Prober et al.
`7/1995 Hyman
`5,436,143 A
`5,437,975 A
`8/1995 McClelland et al.
`5,449,767 A
`9/1995 Ward et al.
`5,476,928 A
`12/1995 Ward et al.
`5,516,664 A
`5/1996 Hyman
`5,534,424 A
`7/1996 Uhlen et al.
`5,547,839 A
`8/1996 Dower et al.
`5,547,859 A
`8/1996 Goodman et al.
`5,556,748 A
`9/1996 Douglas
`5,599,675 A
`2/1997 Brenner
`5,602,000 A
`2/1997 Hyman
`5,637,469 A
`6/1997 Wilding et al.
`8/1997 Mathies
`5,654,419 A
`5,658,736 A
`8/1997 Wong
`5,709,999 A
`1/1998 Shattuck et al.
`5,728,528 A
`3/1998 Mathies
`5,763,594 A
`6/1998 Hiatt et al.
`5,770,365 A
`6/1998 Lane et al.
`5,770,367 A
`6/1998 Southern
`5,789,167 A
`8/1998 Konrad
`5,798,210 A
`8/1998 Canard et al.
`5,804,386 A
`9/1998 Ju
`9/1998 Hiatt et al.
`5,808,045 A
`9/1998 Ju
`5,814,454 A
`10/1998 Khan et al.
`5,821,356 A
`11/1998 Katzir
`5,834,203 A
`12/1998 Reeve et al.
`5,849,542 A
`12/1998 Glazer
`5,853,992 A
`1/1999 Chee et al.
`5,856,104 A
`2/1999 Mathies
`5,869,255 A
`2/1999 Hiatt et al.
`5,872,244 A
`3/1999 Ju
`5,876,936 A
`3/1999 Haff et al.
`5,885,775 A
`6/1999 Kumar et al.
`5,908,755 A
`8/1999 Kwok
`5,945,283 A
`9/1999 Ju
`5,952,180 A
`10/1999 Brenner
`5,962,228 A
`12/1999 Canard et al.
`6,001,566 A
`12/1999 Gordon
`6,001,611 A
`12/1999 Benson et al.
`6,008,379 A
`2/2000 Mathies
`6,028,190 A
`4/2000 Ju
`6,046,005 A
`6/2000 Koster
`6,074,823 A
`6,087,095 A * 7/2000 Rosenthal et al. .............. 435/6
`6,136,543 A
`10/2000 Anazawa et al.
`6,175,107 Bl
`1/2001 Juvinall
`6,197,557 Bl
`3/2001 Makarov et al.
`6,210,891 Bl
`4/2001 Nyren
`6,214,987 Bl
`4/2001 Hiatt et al.
`6,218,118 Bl
`4/2001 Sampson
`6,218,530 Bl
`4/2001 Rothschild et al.
`6,221,592 Bl
`4/2001 Schwartz et al.
`6,232,465 Bl
`5/2001 Hiatt et al.
`6,242,193 Bl
`6/2001 Anazawa
`6,245,507 Bl
`6/2001 Bogdanov
`6,255,475 Bl
`7/2001 Kwiatkowski
`6,274,320 Bl
`8/2001 Rothberg et al.
`6,277,607 Bl
`8/2001 Tyagi
`6,287,821 Bl
`9/2001 Shi et al.
`6,294,324 Bl
`9/2001 Bensimon et al.
`
`6,309,836 Bl
`6,312,893 Bl
`6,316,230 Bl
`6,361,940 Bl
`6,380,378 Bl
`6,524,829 Bl
`6,555,349 Bl
`6,613,508 Bl
`6,613,513 Bl
`6,627,748 Bl
`6,632,655 Bl
`6,639,088 B2
`6,664,079 B2
`6,664,399 Bl
`6,713,255 Bl
`6,780,591 B2
`6,787,308 B2
`6,818,395 Bl
`6,833,246 B2
`6,864,052 Bl
`6,911,345 B2
`6,934,636 Bl
`6,982,146 Bl
`7,037,687 B2
`7,056,661 B2
`7,056,666 B2
`7,057,026 B2
`7,057,031 B2
`7,074,597 B2
`7,078,499 B2
`7,105,300 B2
`7,329,496 B2
`7,414,116 B2
`7,427,673 B2
`7,459,275 B2
`2002/0012966 Al
`2002/0168642 Al
`2003/0008285 Al
`2003/0022225 Al
`2003/0027140 Al
`2003/0044871 Al
`2003/0054360 Al
`2003/0099972 Al
`2003/0166282 Al
`2003/0186256 Al
`2003/0190680 Al
`2003/0198982 Al
`2004/0014096 Al
`2004/0096825 Al
`2004/0185466 Al
`2005/0032081 Al
`2005/0239134 Al
`2006/0003352 Al
`2006/0057565 Al
`2006/0105461 Al
`2006/0240439 Al
`2006/0252938 Al
`2007/0166705 Al
`2007/0275387 Al
`
`10/2001 Kwiatkowski
`11/2001 Van Ness et al.
`11/2001 Egholm
`3/2002 Van Ness et al.
`4/2002 Kitamura et al.
`2/2003 Seeger
`4/2003 O'Donnell
`9/2003 Ness et al.
`9/2003 Paree et al.
`9/2003 Ju et al.
`10/2003 Mehta et al.
`10/2003 Kwiatkowski
`12/2003 Ju et al.
`12/2003 Sabesan
`3/2004 Makino eta!.
`8/2004 Williams et al.
`9/2004 Balasubramanian
`11/2004 Quake et al.
`12/2004 Balasubramanian
`3/2005 Drmanac et al.
`6/2005 Quake et al.
`8/2005 Skierczynski et al.
`1/2006 Schneider et al.
`5/2006 Williams et al.
`6/2006 Korlach et al.
`6/2006 Dower et al.
`6/2006 Barnes
`6/2006 Olejnik et al.
`7/2006 Ju
`7/2006 Odedra et al.
`9/2006 Paree et al.
`2/2008 Dower et al.
`8/2008 Milton et al.
`9/2008 Balasubramanian et al.
`12/2008 Dower et al.
`1/2002 Shi et al.
`11/2002 Drukier
`1/2003 Fischer
`1/2003 Monforte
`2/2003 Ju et al.
`3/2003 Cutsforth et al.
`3/2003 Gold et al.
`5/2003 Olejnik et al.
`9/2003 Brown eta!.
`10/2003 Fischer
`10/2003 Rothschild et al.
`10/2003 Seela et al.
`1/2004 Anderson et al.
`5/2004 Chenna et al.
`9/2004 Ju et al.
`2/2005 Ju et al.
`10/2005 Goren stein et al.
`1/2006 Lipkin et al.
`3/2006 Ju et al.
`5/2006 Tom-Moy et al.
`10/2006 Smith et al.
`11/2006 Sava et al.
`7/2007 Milton et al.
`11/2007 Ju
`
`FOREIGN PATENT DOCUMENTS
`
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`WO
`WO
`WO
`WO
`
`0995804
`1182267
`1291354
`0808320
`1337541
`1218391
`1790736
`WO 90/13666
`WO 91/06678
`WO 92/10587
`WO 93/05183
`
`4/2000
`2/2002
`3/2003
`4/2003
`3/2007
`4/2007
`5/2007
`11/1990
`5/1991
`6/1992
`3/1993
`
`Page 2
`
`
`
`US 7,713,698 B2
`Page 3
`
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`
`WO 93/21340
`WO 94/14972
`WO 96/07669
`WO 96/23807
`WO 96/27025
`WO 97/08183
`WO 97/27317
`WO 97/35033
`WO 98/30720
`WO 98/44151
`WO 99/57321
`WO 00/02895
`WO 00/06770
`WO 00/09753
`WO 00/15844
`WO 00/18956
`WO 00/50172
`WO 00/50642
`WO 00/53805
`WO 00/53812
`WO 00/70073
`WO 01/16375
`WO 01/23610
`WO 01/25247
`WO 01/27625 A
`WO 01/32930
`WO 01/57248
`WO 01/57249
`WO 01/92284
`WO 02/02813
`WO 02/22883 Al
`WO 02/29003
`WO 02/072892
`WO 02/079519 Al
`WO 02/088381
`WO 02/088382
`WO 03/002767
`WO 03/020968
`WO 00/21974
`WO 03/048178
`WO 03/048387
`WO 99/05315
`WO 03/085135
`WO 2004/007773
`WO 2004/055160
`WO 2004/018493
`WO 2004/018497
`WO 2005/084367
`WO 2006/073436
`WO 2007 /002204
`WO 2007/053702
`WO 2007/053719
`WO 2007/062105
`WO 2008/069973 A2
`
`10/1993
`7 /1994
`3/1996
`8/1996
`9/1996
`3/1997
`7 /1997
`9/1997
`7 /1998
`10/1998
`11/1999
`1/2000
`2/2000
`2/2000
`3/2000
`4/2000
`8/2000
`8/2000
`9/2000
`9/2000
`11/2000
`3/2001
`4/2001
`4/2001
`4/2001
`5/2001
`8/2001
`8/2001
`12/2001
`1/2002
`3/2002
`4/2002
`9/2002
`10/2002
`11/2002
`11/2002
`1/2003
`3/2003
`4/2003
`6/2003
`6/2003
`9/2003
`10/2003
`1/2004
`1/2004
`3/2004
`3/2004
`9/2005
`7/2006
`1/2007
`5/2007
`5/2007
`5/2007
`6/2008
`
`OTHER PUBLICATIONS
`
`Axelrod, V.D. et al. (1978) "Specific termination of RNA polymerase
`synthesis as a method of RNA and DNA sequencing," Nucleic Acids
`Res. 5(10) :3549-3563.
`Badman, E. R. et al. (2000) "A Parallel Miniature Cylindrical Ion
`Trap Array," Anal. Chem (2000) 72:3291-3297.
`Badman, E. R. et al. (2000) "Cylindrical Ion Trap Array with Mass
`Selection by Variation in Trap Dimensions," Anal. Chem. 72: 5079-
`5086.
`Burgess, K. et al. (1997) "Photolytic Mass Laddering for Fast Char(cid:173)
`acterization of Oligomers on Single Resin Beads," J Org. Chem.
`62: 5662-5663.
`(1993)
`and Glazer, A.N.
`Benson, S.C., Mathies, R.A.,
`"Heterodimeric DNA-binding dyes designed for energy transfer:
`stability and applications of the DNA complexes," Nucleic Acids Res.
`21:5720-5726.
`
`Benson, S.C., Singh, P., and Glazer, A.N. (1993) "Heterodimeric
`DNA-binding dyes designed for energy transfer: synthesis and spec(cid:173)
`troscopic properties," Nucleic Acids Res. 21:5727-5735.
`Bergseid M., Baytan A.R., Wiley J.P., Ankener W.M., Stolowitz,
`Hughs K.A., and Chestnut J.D. (2000) "Small-molecule base chemi(cid:173)
`cal affinity system for the purification of proteins," Bio Techniques
`29:1126-1133.
`Buck, G.A. et al. (1999) "Design Strategies and Performance of
`Custom DNA Sequencing Primers," Bio Techniques 27 (3) :528-536.
`Buschmann et al. (1999) "The Complex Formation of a,m(cid:173)
`Dicarboxylic Acids and a,m-Diols with Cucurbituril and
`a-Cyclodextrin," Acta Chim. Slav. 46 (3):405-411.
`Canard, B. et al. (1995) "Catalytic editing properties of DNA
`polymerases," Proc. Natl. Acad. Sci. USA 92:10859-10863.
`Caruthers, M.H. (1985) "Gene synthesis machines: DNA chemistry
`and its uses," Science 230:281-285.
`Chee, M. et al. (1996) "Accessing genetic information with high
`density DNA arrays," Science 274:610-614.
`Chen, X. and Kwok, P.-Y. ( 1997) "Template-directed dye-terminator
`incorporation (TDI) assay: a homogeneous DNA diagnostic method
`based on fluorescence resonance energy transfer," Nucleic Acids Res.
`25:347-353.
`Chiu, N.H., Tang, K., Yip, P., Braun, A., Koster, H., and Cantor, C.R.
`(2000) "Mass spectrometry of single-stranded restriction fragments
`captured by an undigested complementary sequence," Nucleic Acids
`Res. 28:E3 l.
`Edwards, J. et al. (2001) "DNA sequencing using biotinylated
`dideoxynucleotides and mass spectrometry," Nucleic Acids Res.
`29(21) 1041-1046.
`Elango, N. et al. (1983) "Amino Acid Sequence of Human Respira(cid:173)
`tory Syncytial Virus Nucleocapsid Protein," Nucleic Acids Research
`11( 17) : 5941-5951.
`Fallahpour, R.A. (2000) "Photochemical and Thermal reactions of
`Azido-Oligopyridines: Diazepinones, a New Class of Metal-Com(cid:173)
`plex Ligands," Helvetica ChimicaActa. 83:384-393.
`Fei, Z. et al. (1998) "MALDI-TOF mass spectrometric typing of
`single nucleotide polymorphisms with mass-tagged ddNTPs,"
`Nucleic Acids Research 26( 11) :2827-2828.
`Fu, D.J., Tang, K., Braun,A., Reuter, D., Darnhofer-Demar, B., Little,
`D.P., O'Donnell, M.J., Cantor, C.R., and Koster, H. (1998) "Sequenc(cid:173)
`ing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry,"
`Nat. Biotechnol. 16:381-384.
`Griffin, T.J. et al. ( 1999) "Direct Genetic Analysis by Matrix-Assisted
`Laser Desorption/Ionization Mass Spectrometry," Proc. Nat. Acad.
`Sci. USA 96:6301-6306.
`Hacia J.G., Edgemon K., Sun B., Stern D., Fodor S.A., and Collins
`F.S. (1998) "Two Color Hybridization Analysis Using High Density
`Oligonucleotide Arrays and Energy Transfer Dyes," Nucleic Acids
`Res. 26:3865-6.
`Haff L.A., et al. ( 1997) "Multiplex Geno typing of PCR Products with
`Mass Tag-Labeled Primers," Nucleic Acids Res. 25(18):3749-3750.
`Hafliger, D. et al. (1997) "Seminested RT-PCR Systems for Small
`Round Structured Viruses and Detection of Enteric Viruses in Sea(cid:173)
`food," International Journal of Food Microbiology 37 :27-36.
`Renner, W.D. et al. (1983) "Enzyme Action at 3' Termini oflonizing
`Radiation-Induced DNA Strand Breaks," J Biol. Chem.
`258(24): 15198-15205.
`Hultman et al. (1989) "Direct Solid Phase Sequencing of Genomic
`and Plasmid DNA Using Magnetic Beads as Solid Support," Nucleic
`Acids Research 17(3):4937-4946.
`Hyman, E.D., (1988) "A new method of sequencing DNA," Analyti(cid:173)
`cal Biochemistry 174:423-436.
`Ireland, R.E. and Varney, M.D. ( 1986) "Approach to the total synthe(cid:173)
`sis of chlorotluicolide synthesis of (±)-19.20-dihydro-24-O(cid:173)
`methylchlorothricolide, methyl ester, ethyl carbonate," J Org. Chem.
`51 :635-648.
`Kamal, A., Laxman, E., and Rao, N.V. (1999) "A mild and rapid
`regeneration of alcohols
`from
`their
`allylic
`ethers by
`chlorotrimethylsilane/sodium iodide," Tetrahedron Lett 40:371-372.
`Ikeda, K. et al. (1995) "AN on-Radioactive DNA Sequencing Method
`Using Biotinylated Dideoxynucleoside Triphosphates and Delta
`TTH DNA Polymerase," DNA Research 2(31 ):225-227.
`
`Page 3
`
`
`
`US 7,713,698 B2
`Page 4
`
`Jiang-Baucom, P. et al. (1997) "DNA Typing of Human Leukocyte
`Antigen Sequence Polymorphisms by Peptide Nucleic Acid Probes
`and MALDI-TOF Mass Spectrometry," Anal. Chem. 69:4894-4896.
`Ju, J. et al. ( 1996) "Cassette labeling for facile construction of energy
`transfer fluorescent primers," Nuc. Acids Res. 24(6): 1144-1148.
`Ju, J., Glazer, A.N., and Mathies, R.A. ( 1996) "Energy transfer prim(cid:173)
`ers: A new fluorescence labeling paradigm for DNA sequencing and
`analysis," Nature Medicine 2: 246-249.
`Ju, J., Ruan C., Fuller, C.W., Glazer, A.N., and Mathies, R.A. (1995)
`"Fluorescence energy transfer dye-labeled primers for DNA
`sequencing and analysis," Proc. Natl. A cad. Sci. USA 92: 4347-4351.
`Jurinke, C., van de Boom, D., Collazo, V., Luchow, A., Jacob, A., and
`Koster H. (1997) "Recovery of nucleic acids from immobilized
`biotin-streptavidin complexes using anunonium hydroxide and
`application in MALDI-TOF mass spectrometry," Anal. Chem.
`69:904-910.
`Kim, S. et al. (2003) "Multiplex Genotyping of the Human
`132-adrenergic Receptor Gene Using Solid-phase Capturable
`Dideoxynucleotides and Mass Spectrometry," Analytical Biochem(cid:173)
`istry 316:251-258.
`Kim Sobin et al. (2002) "Solid Phase Capturable Dideoxynucleotides
`for Multiplex Genotyping Using Mass Spectrometry," Nucleic Acids
`Research 30(16):e85. l-e85.6.
`Kokoris, M. et al. (2002) High-throughput SNP Genotyping With the
`Masscode System, Molecular Diagnosis 5(4):329-340.
`Kolb et al. (2001) "Click Chemistry: Diverse Chemical Function
`From a Few Good Reactions," Angew. Chem. Int. Ed. 40:2004-2021.
`Kraevskii, A.A. et al. (1987) "Substrate Inhibitors of DNA
`Biosynthesis," Molecular Biology 21:25-29.
`Lee, L.G., et al. (1992) "DNA sequencing with dye labeled termina(cid:173)
`tors and T7 DNA polymerase effect of dyes and dNTPs on incorpo(cid:173)
`ration of dye terminators and probability analysis of termination
`fragments," Nucleic Acids Res. 20:2471-2483.
`Lee, L.G. et al, (1997) "New energy transfer dyes for DNA sequenc(cid:173)
`ing," Nucleic Acids Res. 25:2816-2822.
`Lewis et al. (2002) "Click Chemistry in Situ: Acetylcholinesterase as
`a Reaction Vessel for the Selective Assembly ofa Femtomolar Inhibi(cid:173)
`tor from an Array of Building Blocks," Angew. Chem. Int. Ed.
`41(6): 1053-1057.
`Leroy, E.M. et al. (2000) "Diagnosis of Ebola Haemorrhagic Fever by
`RT-PCR in an Epidemic Setting," Journal of Medical Virology
`60:463-467.
`Li, J. (1999) "Single Oligonucleotide Polymorphism Determination
`Using Primer Extension and Time-of-Flight Mass Spectrometry,"
`Electrophoresis 20: 1258-1265.
`Liu, H. et al. (2000) "Development of Multichannel Devices with an
`Array of Electrospray Tips for High-Throughput Mass Spectrom(cid:173)
`etry," Anal. Chem. 72:3303-3310.
`Lyamichev, A. et al. (1999) "Polymorphism Identification and Quan(cid:173)
`titative Detection of Genomic DNA by Invasive Cleavage of
`Oligonucleotide Probes," Nat. Biotech 17:292-296.
`Metzker, M.L. et al. ( 1994) "Termination of DNA synthesis by novel
`3' modified deoxyribonucleoside 5' triphosphates," Nucleic Acids
`Res. 22: 4259-4267.
`Monforte, J.A. and Becker, C.H. (1997) "High-throughput DNA
`analysis by time-of-flight mass spectrometry," Nat. Med. 3(3):360-
`362.
`Olejnik, J. et al. (1999) "Photocleavable peptide DNA conjugates:
`synthesis and applications to DNA analysis using MALDI MS,"
`Nucleic Acids Res. 27 :4626-4631.
`Olejnik, J. et al. ( 1995) "Photocleavable biotin derivatives: a versatile
`approach for the isolation of biomolecules," Proc. Natl. Acad. Sci.
`USA. 92:7590-7594.
`Pelletier, H. et al. (1994) "Structures of ternary complexes ofratDNA
`polymerase 13, a DNA template-primer, and ddCTP," Science
`264:1891-1903.
`Prober, J.M. et al. (1987) "A system for rapid DNA sequencing with
`fluorescent
`chain-terminating
`dideoxynucleotides,"
`Science
`238:336-341.
`Ronaghi, M., Uhlen, M., and Nyren, P. ( 1998) "A sequencing Method
`based on real-time pyrophosphate," Science 281:364-365.
`
`Rosenblum, B.B. et al. (1997) "New dye-labeled terminators for
`improved DNA sequencing patterns," Nucleic Acids Res. 25:4500-
`4504.
`Roskey, M.T., Juhasz, P., Smirnov, LP., Takach, E.J., Martin, S.A.,
`and Haff, L.A. (1996) "DNA sequencing by delayed extraction(cid:173)
`matrix-assisted laser desorption/ionization time of flight mass spec(cid:173)
`trometry," Proc. Natl. Acad. Sci. USA. 93:4724-4729.
`Ross, P. et al. (1998) High Level Multiplex Genotyping by MALDI(cid:173)
`TOF Mass Spectrometry. Nat. Biotech 16:1347-1351.
`Ross, P.L. et al. (1997) "Discrimination of Single-Nucleotide
`Polymorphisms in Human DNA Using Peptide Nucleic Acid Probes
`Detected by MALDI-TOF Mass Spectrometry," Anal. Chem.
`69:4197-4202.
`Saxon, E. and Bertozzi, C.R. (2000) "Cell surface engineering by a
`modified Staudinger reaction," Science 287:2007-2010.
`Schena, M., Shalon, D. and David, R. Brown P.O. (1995) "Quantita(cid:173)
`tive monitoring of gene expression patterns with a cDNA microar(cid:173)
`ray," Science 270: 467-470.
`Seo et al. (2003) "Click Chemistry to Construct Fluorescent
`Qligonucleotides for DNA Sequencing," J. Org. Chem. 68:609.
`Speicher, M.R., Ballard, S.G., and Ward, D.C. (1996) "Karyotyping
`human chromosomes by combinatorial multi-fluor FISH," Nature
`Genetics 12: 368-375.
`Stoerker, J. et al. (2000) "Rapid Genotyping by MALDI-monitored
`nuclease selection from probe Libraries," Nat. Biotech 18:1213-
`1216.
`Tang, K., Fu, D.J., Julien, D., Braun, A., Cantor, C.R., and Koster, H.
`(1999) "Chip-based genotyping by mass spectrometry," Proc. Natl.
`Acad. Sci. USA. 96:10016-10020.
`Tong, X. and Smith, L.M. (1992) "Solid-Phase Method for the Puri(cid:173)
`fication of DNA Sequencing Reactions," Anal. Chem. 64:2672-2677.
`Wendy, Jen. et al. (2000) "New Strategies for Organic Catalysis: The
`First Enantioselective Orgacnocatalytic 1,3-Dipolar Cycloaddition,"
`J Am. Chem. Soc. 122:9874-9875.
`Welch MB, Burgess K, (1999) "Synthesis of fluorescent, photolabile
`3' -O-protected nucleoside triphosphates for the base addition
`sequencing scheme," Nucleosides and Nucleotides 18: 197-201.
`Woolley, A. T. et al. (1997) "High-Speed DNA Genotyping Using
`Microfabricated Capillary Array Electrophoresis Chips," Anal.
`Chem. 69:2181-2186.
`Office Action issued Oct. 25, 2002 in connection with U.S. Appl. No.
`09/972,364.
`Office Action issued Mar. 14, 2003 in connection with U.S. Appl. No.
`09/972,364.
`International Preliminary Examination Report issued on Mar. 18,
`2005 in connection with PCT/US03/21818.
`International Preliminary Examination Report issued on Jun. 13,
`2003 in connection with PCT/US0l/31243.
`International Preliminary Examination Report issued on Feb. 25,
`2003 in connection with PCT/US0l/28967.
`International Preliminary Examination Report issued on Mar. 17,
`2003 in connection with PCT/US02/09752.
`International Preliminary Report on Patentability issued on Sep. 5,
`2006 in connection with PCT/US05/006960.
`International Search Report issued May 13, 2002 in connection with
`PCT/US0l/31243.
`International Search Report issued Jan. 23, 2002 in connection with
`PCT/US0l/28967.
`International Search Report issued Sep. 18, 2002 in connection with
`PCT/US02/09752.
`International Search Report issued Sep. 26, 2003 in connection with
`PCT/US03/21818.
`International Search Report issued Jun. 8, 2004 in connection with
`PCT/US03/39354.
`International Search Report issued Nov. 4, 2005 in connection with
`PCT/US05/06960.
`International Search Report issued Dec. 15, 2006 in connection with
`PCT/US05/13883.
`Partial European Search Report issued Apr. 26, 2007 in connection
`with European Patent Application No. 07004522.4.
`Supplementary European Search Report issued Feb. 16, 2004 in
`connection with European Patent Application No. 01 97 7 533.
`
`Page 4
`
`
`
`US 7,713,698 B2
`Page 5
`
`Supplementary European Search Report issued Feb. 9, 2007 in con(cid:173)
`nection with European Patent Application No. 03 76 4568.6.
`Supplementary European Search Report issued May 25, 2005 in
`connection with European Patent Application No. 02 72 8606.1.
`Supplementary European Search Report issued Jun. 7, 2005 in con(cid:173)
`nection with European Patent Application No.01 96 8905.
`Written Opinion of the International Searching Authority issued Oct.
`27, 2005 in connection with PCT/US05/06960.
`Written Opinion of the International Searching Authority issued Dec.
`15, 2006 in connection with PCT/US05/13883.
`U.S. Appl. No. 09/658,077, filed Sep. 11, 2000, Ju et al.
`U.S. Appl. No. 09/684,670, filed Oct. 6, 2000, Ju et al.
`U.S. Appl. No. 09/972,364, filed Oct. 5, 2001, Ju et al.
`U.S. Appl. No. 09/823,181, filed Mar. 30, 2001, Ju et al.
`U.S. Appl. No. 10/194,882, filed Jul. 12, 2002, Ju et al.
`U.S. Appl. No. 10/380,256, filed Mar. 30, 2001, Ju et al.
`U.S. Appl. No. 10/591,520, filed Sep. 1, 2006, Ju et al.
`Li et al. (2003) "A photocleavable Fluorescent Nucleotide for DNA
`Sequencing and Analysis," PNAS 100(2):414-419.
`Meng et al. (2006) "Design and Synthesis of a Photocleavable Fluo(cid:173)
`rescent Nucleotide 3'-O-Allyl-dGTP-PC-Biodipy-FL-510 as a
`Reversible Terminator for DNA Sequencing by Synthesis," J Org.
`Chem 71:3248-3252.
`Ruparel et al. (2005) "Design and Synthesois of a 3'-O-Allyl
`Photocleavable Fluorescent Nucleotide as a Reversible Terminator
`for DNA Sequencing by Synthesis," PNAS 102(17):5932-5937.
`Seo et al. (2004) "Photocleavable Fluorescent Nucleotides for DNA
`Sequencing on a Chip Constructed by Site-Specific Coupling Chem(cid:173)
`istry," PNAS 101(15):5488-5493.
`Seo et al. (2004) "Four-Color DNA Sequencing by Synthesis on a
`Chip Using Photocleavable Fluorescent Nucleotides," PNAS
`102( 17): 5926-5931.
`Tuncel et al. ( 1999) "Catalytically Self-Threading Polyrotaxanes,"
`Chem. Comm. 1509-1510.
`Office Action issued Aug. 10, 2007 in connection with U.S. Appl. No.
`11/119,231.
`Office Action issued Sep. 21, 2007 in connection with U.S. Appl. No.
`10/380,256.
`Office Action issued Nov. 14, 2007 in connection with U.S. Appl. No.
`10/735,081.
`Restriction Requirement issued Oct. 1, 2007 in connection with U.S.
`Appl. No. 10/521,206.
`Official Action issued May 21, 2007 in connection with European
`Patent Application No. 01968905.8.
`Official Action issued Mar. 31, 2006 in connection with European
`Patent Application No. 01968905.8.
`U.S. Appl. No. 11/894,808, filed Aug. 20, 2007.
`Extended European Search Report issued Jul. 18, 2007 in connection
`with European Patent Application No. 07004522.4.
`International Search Report issued Oct. 29, 2007 in connection with
`PCT International Application No. PCT/US07/13559.
`Notice of Allowance issued Sep. 6, 2007 in connection with U.S.
`Appl. No. 10/702,203.
`Notification of Transmittal oflnternational Search Report and Writ(cid:173)
`ten Opinion, issued Nov. 23, 2007.
`U.S. Appl. No. 11/810,509, filed Jun. 5, 2007.
`Official Action issued Mar. 14, 2008 in connection with European
`Patent Application No. 07004522.4.
`Office Action issued Jul. 8, 2008 in connection with U.S. Appl. No.
`10/591,520.
`Notification of Transmittal oflnternational Search Report and Writ(cid:173)
`ten Opinion, issued Feb. 6, 2008 in connection with International
`Application No. PCT/US06/42739.
`Notification Concerning Transmittal of International Preliminary
`Report on Patentability (Including Written Opinion of the Interna(cid:173)
`tional Searching Authority) issued May 15, 2008 in connection with
`PCT/US2006/042698.
`Notification of Transmittal the International Search Report and Writ(cid:173)
`ten Opinion, issued May 22, 2008 in connection with International
`Application No. PCT/US06/45180.
`Notification of Transmittal the International Search Report and Writ(cid:173)
`ten Opinion, issued Aug. 16, 2008 in connection with International
`Application No. PCT/US07 /24646.
`
`Bai et al. (2003) "Photocleavage of a 2-nitrobenzyl linker bridging a
`fluorophore to the 5' end of DNA," PNAS, vol. 100, No. 2, pp.
`409-413.
`Nielsen et al. (2004) "Multiplexed sandwich assays in microarray
`format," Journal of Immunological Methods, vol. 290, pp. 107-120.
`Zhang et al. (2002) "Synthesis of Releasable Electrophore Tags for
`Applications in Mass Spectrometry," Bioconjugate Chem, vol. 13,
`pp. 1002-1012.
`Sep. 3, 2008 Office Action issued in connection with U.S. Appl. No.
`11/894,808.
`Nickel W, et al. ( 1992) "Interactions of azidothymidine triphosphate
`with the cellular DNA polymerases alpha, delta, and epsilon and with
`DNA primase". Journal of Biological Chemistry. 267(2):848-854.
`Notification of Transmittal of the International Search Report and the
`Written Opinion of the International Searching Authority, or the
`Declaration issued Sep. 9, 2008 in connection with International
`Application No. PCT/US06/24157.
`Hanshaw et al. (2004) "An Indicator displacement system for fluo(cid:173)
`rescent detection of phosphate oxyanions under physiological con(cid:173)
`ditions" Tetrahedron Letters, vol. 45, pp. 8721-8724.
`U.S. Appl. No. 11/922,385, filed Dec. 14, 2007, Ju et al.
`U.S. Appl. No. 12/084,338, filed Apr. 28, 2008, Ju et al.
`U.S. Appl. No. 12/085,343, filed May 19, 2008, Ju et al.
`Notice of Allowance issued Mar. 23, 2009 in connection with U.S.
`Appl. No. 11/894,808.
`Katherine J. Gibson and Stephen J. Benkovic (1987) "Synthesis and
`application of derivatizable oligonucleotides," Nucleic Acids
`Research, vol. 15, No. 16, pp. 6455-6467.
`Tatyana S. Godovikova et al. (1999) "5-[3- (E) - (4 -Azido- 2,3,5,6
`-tetrafluorobenzamido )propenyl-l ]-2' deoxyuridine-5 ' -
`the
`in
`triphosphate Substitutes for Thymidine-5'triphosphate
`Polymerase Chain Reaction," Bioconjugate Chem., vol. 10, pp. 529-
`537.
`Amy L. Kimzey and William S. Dynan (1998) "Specifid Regions of
`Contact between Human T-cell Leukemia Virus Type I Tax Protein
`and DNA Identified by Photocross-linking," The Journal of Biologi(cid:173)
`cal Chemistry, vol. 273, No. 22, pp. 13768-13775.
`U.S. Appl. No. 90/008,149, filed Aug. 4, 2006, Girten.
`U.S. Appl. No. 90/008,152, filed Aug. 3, 2006, Girten.
`Kraevskii et al., Substrate Inhibitors of DNA Biosynthesis, Molecu(cid:173)
`lar Biology, 21:25-29 (1987).
`Kurata et al., Fluorescent quenching-based quantitative detection of
`specific DNA/RNA using BODIPY® FL-labeled probe of primer,
`Nucleic Acids Research, vol. 29, No. 6, p. e34 (2001).
`Welch et al., Synthesis of Nucleosides Designed for Combinatorial
`DNA Sequencing, Chemistry, European Journal, 5:951-960 (1999).
`Wada et al., 2- (Azidomethyl) benzoyl as a new protecting group in
`nucleosides, Tetrahedron Letters, :1069-1072 (2001).
`Sarfati et al., Synthesis of fluorescent derivatives of 3'- O-(6-
`aminohexanoyl) -pyrimidine nucleosides 5 '-triphosphates that act as
`DNA polymerase substrates reversibly tagged at C-3 ', JCS Perkin
`Trans, 1163-1171 (1995).
`(N-Methylanthranylamido) -4-0xo(cid:173)
`Rasolonjatovo et al., 6-N-
`Hexanoic Acid: A New Fluorescent Protecting Group Applicable to a
`New DNA Sequencing Method, Nucleosides & Nucleotides,
`17:2021-2025 (1998).
`Marquez et al., Selective Fluorescence Quenching of 2,3-
`Diazabicyclo [2.2.2]oct-2-ene by Nucleotides, Organic Letters,
`5:3911-3914 (2003).
`Nazarenko et al., Effect of primary and secondary structure of
`oligodeoxyribonucleotides on the fluorescent properties of conju(cid:173)
`gated dyes, Nucleic Acids Research, 30:2089-2095.
`Kvam et al., Characterization of singlet oxygen-induced guanine
`residue damage after photochemical treatment of free nucleosides
`and DNA, Biochemica et Biophysica Acta., 1217:9-15 (1994).
`Crespo-Hernandez et al., Part 1. Photochemical and Photophysical
`Studies of Guanine Derivatives: Intermediates Contributing to its
`Photodestruction Mechanism in Aqueous Solution and the Participa(cid:173)
`tion of the Electron Adduct, Photochemistry and Photo biology, 71 (5)
`:534-543 (2000) ..
`Buschmann et al., Spectroscopic Study and Evaluation of Red-Ab(cid:173)
`sorbing Fluorescent Dyes, Bioconjugate Chem., 14: 195-204 (2003).
`
`Page 5
`
`
`
`US 7,713,698 B2
`Page 6
`
`Torimura et al., Fluorescence-Quenching Phenomenon by
`Photoinduced Electron Transfer between a Fluorescent Dye and
`Nucleotide Base, Analytical Sciences, 17:155-160 (2001).
`Markiewicz et al., Anew method of synthesis of fluorescently labeled
`oligonucleotides and their application in DNA sequencing, Nucleic
`Acids Research, 25 :3672-3690 ( 1997).
`Maier et al., Synthesis and Properties of New Fluorescein-Labeled
`Oligonucleotides, Nucleosides and Nucleotides, 14:961-965 (1995).
`Bergmann et al., llyl As Internucleotide Protecting Group in DNA
`Synthesis to be Cleaved Off by Anunonia, Tetrahedron, 51:6971-
`6976 (1995).
`Guibe, Allylic Protecting Groups and Their Use in a Complex Envi(cid:173)
`ronment Part I: Allylic Protection of Alcohols, Tetrahedron,
`53: 13509-13556 (1997).
`Guibe, Allylic Protecting Groups and Their Use in a Complex Envi(cid:173)
`ronment Part II: Allylic Protecting Groups and their Removal through
`Catalytic Palladium n-Allyl Methodology, Tetrahedron,54:2967-
`3042 (1998).
`relative stability of ally! ether,
`Kloosterman et al., The
`allyloxycarbonyl ester and prop-2 enylidene acetal, protective groups
`toward Iridium, Rhodium and Palladium catalysts, Tetrahedron Let(cid:173)
`ters, 26:5045-5048 (1985).
`Kitamura et al., (P(C6H5)3) CpRu+Catalyzed Deprotection of Ally!
`Carboxylic Esters, J. Org. Chem., 67:4975-4977 (2002).
`Hayakawa et al., O-Allyl Protection of Guanine and Thymine Resi(cid:173)
`dues in Oligodeoxyribonucleotides, J. Org. Chem., 58:5551-5555
`(1993).
`Veeneman et al., An Efficient Approach to the Synthesis of
`Thymidine Driatives Containing Phosphate-Isoteric Methylene
`Acetyl Linkages, Tetrahedron, 47:1547-1562 (1991).
`Zavgorodny et al., 1-Alkylthioalkylation of Nucleoside Hydroxl
`Functions and Its Synthetic Application: A New Versatile Method in
`Nucleoside Chemistry, Tetrahedron Letters, 32:7593-7596 (1991).
`Seeger, Single Molecule Fluorescence: High-Performance Molecu(cid:173)
`lar Diagnosis and Screening, Bio forum, Git Verlag, Darmstadt, DE
`vol. 21, No. (1998) (German text).
`Rao et al., Four Color FRET Dye Nucleotide Terminators for DNA
`Sequencing, Nucleosides, Nucleotides & Nucleic Acids, 20:673-676
`(2001).
`
`J. Brunckova et al., Tetrahedron Letters, vol. 35, pp. 6619-6622
`(1994).
`S. Nishino et al., Heteroatom Chemistry, vol. 2, pp. 187-196 (1991).
`M. Krecmerova, Coll. Czech. Chem. Commun., vol. 55, pp. 2521-
`2536 ( 1990).