I 1111111111111111 11111 111111111111111 11111 111111111111111 IIIIII IIII IIII IIII
`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
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`(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
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`

`

`US 7,713,698 B2
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