PTO/SB/57 (02-09)
`PTO/SB/57 (02-09)
`Approved for use through 08/31/2010. OMB 0651-0033
`Approved for use through 08/31/2010. OMB 0651-0033
`U.S. Patent and Trademark Office: U.S. DEPARTMENT OF COMMERCE
`U.S. Patent and Trademark Office: U.S. DEPARTMENT OF COMMERCE
`Under the,Paperwolk Reduction Act of 1995, no persons are required to respond to a collection of informistion unless it displays a valid OMB control number.
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`(Also referred to as FORM PTO-1465)
`(Also referred to as FORM PTO-1465)
`REQUEST FOR EX PARTE REEXAMINATION TRANSMITTAL FORM
`REQUEST FOR EX PARTE REEXAMINATION TRANSMITTAL FORM
`
`Address to:
`Address to:
`Mail Stop Ex Parte Reexam
`Mail Stop Ex Parte Reexam
`Commissioner for Patents (cid:9)
`Commissioner for Patents (cid:9)
`P.O. Box 1450
`P.O. Box 1450
`
`Alexandria, VA 22313-1450
`Alexandria, VA 22313-1450 (cid:9)
`1. ID This is a request for (cid:9) ex parte reexamination pursuant to 37 CFR 1.510 of patent number (cid:9)
`1. 0 This is a request for (cid:9) ex parte reexamination pursuant to 37 CFR 1.510 of patent number (cid:9)
`issued 8/15/1998 (cid:9). The request is made by:
`issued 5/15/1995 (cid:9). The request is made by:
`n third party requester.
`ri patent owner. (cid:9)
`El patent owner. (cid:9)
`0 third party requester.
`2. ri The name and address of the person requesting reexamination is:
`
`2. 0 The name and address of the person requesting reexamination is:
`
`Attorney Docket No.: BLG-RE-00002
`Attorney Docket No.: BLG-RE-00002
`Date: 6/25/10 (cid:9)
`Date: 6/25/10
`
`5,808,045
`5,808,045
`
`.S PTO
`S. PTO
`
`1111141111111111111
`
`111111111111111111
`11111111111111111111111111
`06/25
`06/25
`1";"(i
`
`3. (cid:9) El (cid:9)
`3. 0 (cid:9)
`111 (cid:9)
`0 (cid:9)
`
`a. A check in the amount of $ 2520.00
`a. A check in the amount of $ 2520.00
`
`(cid:9) is enclosed to cover the reexamination fee, 37 CFR 1.20(c)(1);
`(cid:9) is enclosed to cover the reexamination fee, 37 CFR 1.20(c)(1);
`
`b. The Director is hereby authorized to charge the fee as set forth in 37 CFR 1.20(c)(1)
`b. The Director is hereby authorized to charge the fee as set forth in 37 CFR 1.20(c)(1)
`• or
`to Deposit Account No. (cid:9)
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`to Deposit Account No. (cid:9)
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`0 (cid:9)
`[11 (cid:9)
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`c. Payment by credit card. Form PTO-2038 is attached.
`c. Payment by credit card. Form PTO-2038 is attached.
`
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`37 CFR 1.26(c). If payment is made by credit card, refund must be to credit card account.
`37 CFR 1.26(c). If payment is made by credit card, refund must be to credit card account.
`
`
`
`
`5. (cid:9)
`
`0 A copy of the patent to be reexamined having a double column format on one side of a separate paper is
`enclosed. 37 CFR 1.510(b)(4)
`enclosed. 37 CFR 1.510(b)(4)
`
`4. (cid:9) n Any refund should be made by 0 check or 0 credit to Deposit Account No. (cid:9)
`4. n Any refund should be made by E check or ri credit to Deposit Account No. (cid:9)
`5, (cid:9) ri A copy of the patent to be reexamined having a double column format on one side of a separate paper is
`6. (cid:9) ri CD-ROM or CD-R in duplicate, Computer Program (Appendix) or large table
`[7 CD-ROM or CD-R in duplicate, Computer Program (Appendix) or large table
`111 Landscape Table on CD
`[7 Landscape Table on CD
`0 Nucleotide and/or Amino Acid Sequence Submission
`0 Nucleotide and/or Amino Acid Sequence Submission
`If applicable, items a. — c. are required.
`If applicable, items a. — c. are required.
`
`6. (cid:9)
`
`7. (cid:9)
`7. (cid:9)
`
`a. 0 Computer Readable Form (CRF)
`a. 0 Computer Readable Form (CRF) •
`b. Specification Sequence Listing on:
`b. Specification Sequence Listing on:
`i. q CD-ROM (2 copies) or CD-R (2 copies); or
`i. q CD-ROM (2 copies) or CD-R (2 copies); or
`ii. ri paper
`ii. 11 paper
`c. 0 Statements verifying identity of above copies
`q Statements verifying identity of above copies
`c.
`[7 A copy of any disclaimer, certificate of correction or reexamination certificate issued in the patent is included.
`0 A copy of any disclaimer, certificate of correction or reexamination certificate issued in the patent is included.
`9. (cid:9) n Reexamination of claim(s) 1 -7
`9. (cid:9) n Reexamination of claim(s) 1-7
`(cid:9)is requested.
`(cid:9)is requested.
`10. EI A copy of every patent or printed publication relied upon is submitted herewith including a listing thereof on
`10. 0 A copy of every patent or printed publication relied upon is submitted herewith including a listing thereof on
`Form PTO/SB/08, P10-1449, or equivalent.
`Form PTO/SB/08, PTO-1449, or equivalent.
`
`8. (cid:9)
`8. (cid:9)
`
`11. Ei An English language translation of all necessary and pertinent non-English language patents and/or printed
`11. 0 An English language translation of all necessary and pertinent non-English language patents and/or printed
`publications is included.
`publications is included. (cid:9)
`.
`
`[Page 1 of 2J
`[Page 1 of 2]
`This collection of information is required by 37 CFR 1.510. The information is required to obtain or retain a benefit by the public which is to file (and by the USPTO to
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`Page 1 of 94
`
`Columbia Exhibit 2009
`Illumina, Inc. v. The Trustees of Columbia
`University in the City of New York
`IPR2018-00291
`
`WWW.DIGITALEVIDENCEGROUP.COM
`
`.
`
`Romesberg
`Exhibit 2054
`(3-15-21)
`
`Columbia Ex. 2054
`Illumina, Inc. v. The Trustees of
`Columbia University in the City of
`New York
`IPR2020-00988, -01065, -01177,
`-01125, -01323
`
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`

`

`PTO/SS/57 (02-09)
`PTO/SB/57 (02-09)
`Approved for use through 08/31/2010. OMB 0651-0033
`Approved for use through 08/31/2010. OMB 0651-0033
`U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE
`U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE
`Under the Paperwork Reduction Act of 1995, no persons are required to respond to a collection of information unless it displays a valid OMB control number.
`Under the Paperwork Reduction Act of 1995, no persons are required to respond to a collection of information unless it displays a valid OMB control number.
`
`12.
`12.
`
`X
`X
`
`The attached detailed request includes at least the following items:
`The attached detailed request includes at least the following items:
`
`a. A statement identifying each substantial new question of patentability based on prior patents and printed
`a. A statement identifying each substantial new question of patentability based on prior patents and printed
`publications. 37 CFR 1.510(b)(1)
`publications. 37 CFR 1.510(b)(1)
`b. An identification of every claim for which reexamination is requested, and a detailed explanation of the pertinency
`b. An identification of every claim for which reexamination is requested, and a detailed explanation of the pertinency
`and manner of applying the cited art to every claim for which reexamination is requested. 37 CFR 1.510(b)(2).
`and manner of applying the cited art to every claim for which reexamination is requested. 37 CFR 1.510(b)(2).
`
`13.
`13.
`
`q
`
`A proposed amendment is included (only where the patent owner is the requester). 37 CFR 1.510(e)
`A proposed amendment is included (only where the patent owner is the requester). 37 CFR 1.510(e)
`
`14.
`14.
`
`X
`X
`
`a. It is certified that a copy of this request (if filed by other than the patent owner) has been served in its entirety on
`a. It is certified that a copy of this request (if filed by other than the patent owner) has been served in its entirety on
`the patent owner as provided in 37 CFR 1.33(c).
`the patent owner as provided in 37 CFR 1.33(c).
`The name and address of the party served and the date of service are:
`The name and address of the party served and the date of service are:
`LERNER DAVID LITTENBERG KRUMHOLZ & MENTLIK
`LERNER DAVID LITTENBERG KRUMHOLZ & MENTLIK
`
`600 SOUTH AVENUE WEST
`600 SOUTH AVENUE WEST
`WESTFIELD NJ 07090-1497
`WESTFIELD NJ 07090-1497
`
`Date of Service: (cid:9)
`Date of Service: (cid:9)
`
`. or
`• or
`b. A duplicate copy is enclosed because service on patent owner was not possible. An explanation of the efforts
`b.. A duplicate copy is enclosed because service on patent owner was not possible. An explanation of the efforts
`made to serve patent owner is attached. (cid:9) See MPEP 2220.
`made to serve patent owner is attached. (cid:9) See MPEP 2220.
`15. (cid:9) Correspondence Address: Direct all communications about the reexamination to:
`15. (cid:9) Correspondence Address: Direct all communications about the reexamination to:
`
`6/25/10 (cid:9)
`6/25/10 (cid:9)
`
`X
`X
`
`OR
`OR
`
`Address
`Address
`
`City
`City
`
`Country
`Country
`
`Telephone
`Telephone
`
`The address associated with Customer Number:
`The address associated with Customer Number:
`
`35938
`35938
`
`Firm or
`Firm or
`Individual Name (cid:9)
`Individual Name
`
`
`
`State
`State
`
`Email
`Email
`
`Zip
`Zip
`
`16. q (cid:9) The patent is currently the subject of the following concurrent proceeding(s):
`The patent is currently the subject of the following concurrent proceeding(s):
`16. (cid:9)
`a. Copending reissue Application No.
`a. Copending reissue Application No.
`q b. Copending reexamination Control No.
`b. Copending reexamination Control No.
`c. Copending Interference No.
`c. Copending Interference No.
`q d. Copending litigation styled:
`d. Copending litigation styled:
`
`WARNING: Information on this form may become public. Credit card information should not be
`WARNING: Information on this form may become public. Credit card information should not be
`included (cid:9)
`this form. Provide credit card information and authorization on PTO-2038.
`included (cid:9)
`this form. Provide cre,clit card information and authorization on PTO-2038.
`6/25/10
`6/25/10
`Date
`Date
`46,230 (cid:9) q For Patent Owner Requester
`46,230 (cid:9) q For Patent Owner Requester
`Registration No. jig For Third Party Requester
`Registration No. j;4 For Third Party Requester
`
`Authorized Signature (cid:9)
`Authorized Signature (cid:9)
`Michael A. Whittaker (cid:9)
`Michael A. Whittaker (cid:9)
`Typed/Printed Name (cid:9)
`Typed/Printed Name (cid:9)
`
`• (cid:9)
`
`[Page 2 of 2]
`[Page 2 of 2]
`
`Page 2 of 94
`
`q
`q
`

`

`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`Patent No.: 5,808,045
`Patent No.: 5,808,045
`Application No.: 08/486,897
`Application No.: 08/486,897
`Attorney Docket No.: 68205.000103
`Attorney Docket No.: 68205.000103
`
`Application Number
`Application Number (cid:9)
`Filed (cid:9)
`Filed
`Applicant
`Applicant (cid:9)
`Title
`Title (cid:9)
`
`TC/Art Unit
`TC/Art Unit
`Examiner: (cid:9)
`Examiner:
`
`7142
`7142
`
`Confirmation No.: (cid:9)
`Confirmation No.: (cid:9)
`
`: (cid:9)
`08/486,897
`08/486,897 (cid:9)
`: (cid:9)
`June 7, 1995
`June 7, 1995
`(cid:9) Andrew C. HIATT
`: Andrew C. HIATT
`•
`COMPOSITIONS FOR ENZYME CATALYZED TEMPLATE-INDEPENDENT
`COMPOSITIONS FOR ENZYME CATALYZED TEMPLATE-INDEPENDENT
`CREATION OF PHOSPHODIESTER BONDS USING PROTECTED
`CREATION OF PHOSPHODIESTER BONDS USING PROTECTED
`NUCLEOTIDES
`NUCLEOTIDES
`1623
`1623
`James 0. WILSON
`: James 0. WILSON
`
`Docket No.
`Docket No. (cid:9)
`Customer No. (cid:9)
`Customer No.
`
`: 68205.000103
`: 68205.000103
`: 21967
`: 21967
`
`Commissioner for Patents
`Commissioner for Patents
`P.O. Box 1450
`P.O. Box 1450
`Alexandria, VA 22313-1450
`Alexandria, VA 22313-1450
`
`REVOCATION OF POWER OF ATTORNEY WITH NEW POWER
`REVOCATION OF POWER OF ATTORNEY WITH NEW POWER
`OF ATTORNEY AND CHANGE OF CORRESPONDENCE ADDRESS
`OF ATTORNEY AND CHANGE OF CORRESPONDENCE ADDRESS
`
`Sir:
`Sir:
`
`Illumina, Inc., a corporation, having a place of business at Illumina, Inc., 9885 Towne
`Illumina, Inc., a corporation, having a place of business at Illumina, Inc., 9885 Towne
`
`Centre Drive, San Diego, CA 92121 is the assignee of total interest in the above-captioned patent
`Centre Drive, San Diego, CA 92121 is the assignee of total interest in the above-captioned patent
`
`application pursuant to an Assignment recorded August 24, 2010 at Reel 024864, Frame 0900.
`application pursuant to an Assignment recorded August 24, 2010 at Reel 024864, Frame 0900.
`
`Pursuant to 37 C.F.R. § 3.73(b), the undersigned, who is empowered to act on behalf of
`Pursuant to 37 C.F.R. § 3.73(b), the undersigned, who is empowered to act on behalf of
`
`the Assignee, hereby declares that he has reviewed the evidentiary documents of the chain of title
`the Assignee, hereby declares that he has reviewed the evidentiary documents of the chain of title
`
`and certifies that, to the best of Assignee's knowledge and belief, title to the above-captioned
`and certifies that, to the best of Assignee's knowledge and belief, title to the above-captioned
`
`patent application is with the Assignee.
`patent application is with the Assignee.
`
`Assignee hereby revokes any and all previous Powers of Attorney in the above-identified
`Assignee hereby revokes any and all previous Powers of Attorney in the above-identified
`
`application and hereby appoints, both jointly and severally, the practitioners associated with
`application and hereby appoints, both jointly and severally, the practitioners associated with
`
`Page 3 of 94
`
`(cid:9)
`(cid:9)
`

`

`Patent No.: 5,808,045
`Patent No.: 5,808,045
`Application No.: 08/486,897
`Application No.: 08/486,897
`Attorney Docket No.: 68205.000103
`Attorney Docket No.: 68205.000103
`
`CUSTOMER NUMBER 21967
`CUSTOMER NUMBER 21967
`
`as its attorneys and agents with full power of substitution and revocation, to prosecute said
`as its attorneys and agents with full power of substitution and revocation, to prosecute said
`
`patent, including any and all continuation, divisional, renewal, substitute, reexamination and
`patent, including any and all continuation, divisional, renewal, substitute, reexamination and
`
`reissue applications based in whole or in part on said patent application, before the U.S. Patent
`reissue applications based in whole or in part on said patent application, before the U.S. Patent
`
`and Trademark Office, to transact all business in the U.S. Patent and Trademark Office
`and Trademark Office, to transact all business in the U.S. Patent and Trademark Office
`
`connected therewith, including receiving any Letters Patent issuing thereon, and to take any and
`connected therewith, including receiving any Letters Patent issuing thereon, and to take any and
`
`all other legal action with regard to this patent application.
`all other legal action with regard to this patent application.
`
`All correspondence and telephone communications should be addressed to:
`All correspondence and telephone communications should be addressed to:
`
`CUSTOMER NUMBER 21967
`CUSTOMER NUMBER 21967
`
`which corresponds to the following:
`which corresponds to the following:
`
`Intellectual Property Department
`Intellectual Property Department
`Hunton & Williams LLP
`Hunton & Williams LLP
`1900 K Street, N.W.
`1900 K Street, N.W.
`Suite 1200
`Suite 1200
`Washington, DC 20006-1109
`Washington, DC 20006-1109
`(202) 955-1500 (telephone)
`(202) 955-1500 (telephone)
`(202) 778-2201 (facsimile)
`(202) 778-2201 (facsimile)
`
`Dated:
`Dated:
`
`By:
`By:
`
`Aok
`abou
`Name: Chris (cid:9)
`abou
`Name: Chris (cid:9)
`Title: Senior Vice President
`Title: Senior Vice President
`and General Counsel
`and General Counsel
`Illumina, Inc.
`Illumina, Inc.
`9885 Towne Centre Drive
`9885 Towne Centre Drive
`San Diego, CA 92121
`San Diego, CA 92121
`
`2
`2
`
`Page 4 of 94
`
`

`

`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`REEXAMINATION CONTROL NO.: 90/009,769
`REEXAMINATION CONTROL NO.: 90/009,769
`ATTORNEY DOCKET NO: 68205.000103
`ATTORNEY DOCKET NO: 68205.000103
`
`Control Number (cid:9)
`Control Number (cid:9)
`Inventors (cid:9)
`Inventors (cid:9)
`Patent Number (cid:9)
`Patent Number (cid:9)
`Issue Date (cid:9)
`Issue Date (cid:9)
`Title (cid:9)
`Title (cid:9)
`
`TC/Art Unit (cid:9)
`TC/Art Unit (cid:9)
`Examiner: (cid:9)
`Examiner: (cid:9)
`Docket No. (cid:9)
`Docket No. (cid:9)
`Customer No. (cid:9)
`Customer No. (cid:9)
`
`5114
`5114
`
`Confirmation No.: (cid:9)
`Confirmation No.: (cid:9)
`
`: 90/009,769 (cid:9)
`: 90/009,769 (cid:9)
`: Andrew C. HIATT et al.
`: Andrew C. HIATT et al.
`: 5,808,045
`: 5,808,045
`: September 15, 1998
`: September 15, 1998
`: COMPOSITIONS FOR ENZYME CATALYZED TEMPLATE-
`: COMPOSITIONS FOR ENZYME CATALYZED TEMPLATE-
`INDEPENDENT CREATION OF PHOSPHODIESTER BONDS
`INDEPENDENT CREATION OF PHOSPHODIESTER BONDS
`USING PROTECTED NUCLEOTIDES
`USING PROTECTED NUCLEOTIDES
`: 3991
`: 3991
`: Gary L. KUNZ
`: Gary L. KUNZ
`: 68205.000103
`: 68205.000103
`: 21967
`: 21967
`
`MAIL STOP EX PARTE REEXAM
`MAIL STOP EX PARTE REEXAM
`Commissioner for Patents
`Commissioner for Patents
`P.O. Box 1450
`P.O. Box 1450
`Alexandria, VA 22313-1450
`Alexandria, VA 22313-1450
`
`AMENDMENT AND RESPONSE TO NON-FINAL OFFICE
`AMENDMENT AND RESPONSE TO NON-FINAL OFFICE
`ACTION IN EX PARTE REEXAMINATION
`ACTION IN EX PARTE REEXAMINATION
`
`Sir:
`Sir:
`
`This amendment and response is responsive to the non-final Office Action issued
`This amendment and response is responsive to the non-final Office Action issued
`December 21, 2010 in the above-captioned ex parte reexamination. A one-month extension of
`December 21, 2010 in the above-captioned ex parte reexamination. A one-month extension of
`
`time was granted on February 7, 2011, thereby extending the due date for responding up to and
`time was granted on February 7, 2011, thereby extending the due date for responding up to and
`
`including March 21, 2011.
`including March 21, 2011.
`
`Amendments to the Claims begin on page 2 of this Amendment.
`Amendments to the Claims begin on page 2 of this Amendment.
`
`Remarks begin on page 9 of this Amendment.
`Remarks begin on page 9 of this Amendment.
`
`1
`1
`
`Page 5 of 94
`
`

`

`REEXAMINATION CONTROL NO.: 90/009,769
`REEXAMINATION CONTROL NO.: 90/009,769
`ATTORNEY DOCKET NO: 68205.000103
`ATTORNEY DOCKET NO: 68205.000103
`
`In the Claims
`In the Claims
`
`AMENDMENTS
`AMENDMENTS
`
`1. (original) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting
`1. (original) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting
`
`the 3' position which is an ester and which has the following formula:
`the 3' position which is an ester and which has the following formula:
`
`5' (cid:9)
`5' (cid:9)
`R2 - CH2 - C (cid:9)
`R2 - CH2 - C (cid:9)
`
`0
`0
`
`C
`C
`
`B
`B
`
`C -C
`C-C
`
`0
`0
`
`C=0
`C=0
`
`R
`R
`
`wherein Rz is a triphosphate and R is selected from the group consisting of: formate,
`wherein R2 is a triphosphate and R is selected from the group consisting of: formate,
`
`benzoylformate, (cid:9)
`benzoylformate, (cid:9)
`
`chloroacetate, (cid:9)
`chloroacetate, (cid:9)
`
`dichloroacetate, (cid:9)
`dichloroacetate, (cid:9)
`
`trichloroacetate, (cid:9)
`trichloroacetate, (cid:9)
`
`trifluoroacetate,
`trifluoroacetate,
`
`methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 2,6-
`methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 2,6-
`
`dichl oro-4-methyl phenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-
`dichloro-4-methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-
`
`bi s ( 1 , 1 -dimethylpropyl)phenoxyacetate, (cid:9)
`b i s ( 1,1 -di methylpropyl)pheno x yacetate, (cid:9)
`
`chlorodiphenylacetate, (cid:9)
`chlorodiphenylacetate, (cid:9)
`
`p-P-phenyl acetate, (cid:9)
`p-P-phenyl acetate, (cid:9)
`
`3 -
`3-
`
`phenylpropionate, 3-benzoylpropionate, isobutyrate, 4-oxopentanoate, pivaloate, adamanioate,
`phenylpropionate, 3-benzoylpropionate, isobutyrate, 4-oxopentanoate, pivaloate, adamanioate,
`
`crotonate, 4-methoxycrotonate, (E)-2-methyl-2-butenoate, o-(dibromomethyl)benzoate, o-
`crotonate, 4-methoxycrotonate, (E)-2-methyl-2-butenoate, o-(dibromomethyl)benzoate, o-
`
`(methoxycarbonyl)benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate and a-naphthanoate.
`(methoxycarbonyl)benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate and a-naphthanoate.
`
`2. (original) A mononucleoside 5' triphosphate having a removable blocking moiety protecting
`2. (original) A mononucleoside 5' triphosphate having a removable blocking moiety protecting
`
`the 3' position which is an ester and which has the following formula:
`the 3' position which is an ester and which has the following formula:
`
`2
`2
`
`Page 6 of 94
`
`

`

`REEXAMINATION CONTROL NO.: 90/009,769
`REEXAMINATION CONTROL NO.: 90/009,769
`ATTORNEY DOCKET NO: 68205.000103
`ATTORNEY DOCKET NO: 68205.000103
`
`5' (cid:9)
`5' (cid:9)
`R2—CH2 —C (cid:9)
`R2 - CH2 - C (cid:9)
`
`0
`0 (cid:9)
`
`B
`B
`/
`C
`C
`
`3' C—C\
`C—C
`
`0
`0
`
`C=0
`C=0
`
`R
`
`wherein R2 is triphosphate; and wherein R is selected from the group consisting of: H, CH3, CH3
`wherein R2 is triphosphate; and wherein R is selected from the group consisting of: H, CH3, CH3
`(CH2) where N is an integer from 1 to 12, (CH3)X+1 (CH), where x is an integer from 1 to 12,
`(CH,) where N is an integer from 1 to 12, (CH3)X+1 (CH)„ where x is an integer from 1 to 12,
`(CH3)„i (CH)„ (CH2),, where x and n are independent integers from 1 to 12, Cx (CH3)3x-(x)i)
`(CH3)x+i (CH)„ (CH2),, where x and n are independent integers from 1 to 12, Cx (CH3)3x-(x)i)
`(CH2)„ where x and n are independent integers from 1 to 12, and
`(CH2)n where x and n are independent integers from 1 to 12, and
`
`R4
`R4
`
`RI
`RI
`
`R5
`R5
`
`R6 R3
`
`where R1, R3, R4, R5 and R6 are selected from the group consisting of CH3, H or NO2.
`where RI, R3, R4, R5 and R6 are selected from the group consisting of CH3, H or NO2.
`
`3. (original) The mononucleoside 5'-triphosophate of claim 1 or 2 wherein R2 is a triphosphate
`3. (original) The mononucleoside 5'-triphosophate of claim 1 or 2 wherein R2 is a triphosphate
`
`and said mononucleoside 5'-triphosphate is a deoxynucleoside.
`and said mononucleoside 5'-triphosphate is a deoxynucleoside.
`
`4. (original) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting
`4. (original) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting
`
`the 3' position which has the following formula:
`the 3' position which has the following formula:
`
`5'
`5'
`R3 —CH z \
`R3—CH 2
`2N, (cid:9)
`\
`
`I
`I
`
`N
`
`3' /C—C
`3' /C—C
`
`
`
`R1 (cid:9)
`RI
`
`H
`
`wherein R2 is triphosphate; and wherein R1 is toluic, benzoic or acetic acid ester.
`wherein R2 is triphosphate; and wherein R1 is toluic, benzoic or acetic acid ester.
`
`3
`3
`
`Page 7 of 94
`
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`(cid:9)
`

`

`5. (original) The mononucleoside 5'-triphosphate of claim 1, 2 or 4 wherein said removable
`5. (original) The mononucleoside 5'-triphosphate of claim 1, 2 or 4 wherein said removable
`
`blocking moiety is removable by an enzyme.
`blocking moiety is removable by an enzyme.
`
`REEXAMINATION CONTROL NO.: 90/009,769
`REEXAMINATION CONTROL NO.: 90/009,769
`ATTORNEY DOCKET NO: 68205.000103
`ATTORNEY DOCKET NO: 68205.000103
`
`6. (original) The mononucleoside 5'-triphosphate of claim 1, 2 or 4 wherein said removable
`6. (original) The mononucleoside 5'-triphosphate of claim 1, 2 or 4 wherein said removable
`
`blocking moiety is removable by a reaction which occurs within 2 to 10 minutes.
`blocking moiety is removable by a reaction which occurs within 2 to 10 minutes.
`
`7. (not reexamined) The mononucleoside 5'-triphosphate of claim 1, 2 or 4 wherein said
`7. (not reexamined) The mononucleoside 5'-triphosphate of claim 1, 2 or 4 wherein said
`
`removable blocking moiety is linked to a solid support.
`removable blocking moiety is linked to a solid support.
`
`8. (new) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting the
`8. (new) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting the
`
`3' position which is an ester and which has the following formula:
`3' position which is an ester and which has the following formula:
`
`B
`B
`5' (cid:9)
`5' (cid:9)
`/
`R2 —CH2—C (cid:9)
`C
`R2-CH2-C (cid:9)
`C
`\ /
`3/' C-C
`3' /C—C\
`
`0
`0 (cid:9)
`
`0 (cid:9)
`0
`
`H
`
`C=0
`C=0
`
`R
`
`wherein R2 is a triphosphate and R is selected from the group consisting of: benzoylformate,
`wherein R2 is a triphosphate and R is selected from the group consisting of: benzoylformate,
`
`methoxyacetate, (cid:9)
`methoxyacetate, (cid:9)
`
`triphenylmethoxyacetate, (cid:9)
`triphenylmethoxyacet ate, (cid:9)
`
`p-chlorophenoxyacetate, (cid:9)
`p-chlorophenoxyacetate, (cid:9)
`
`2,6-dichloro-4-
`2,6-dichloro-4-
`
`methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis( 1, 1 -
`methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis( 1, 1 -
`
`dimethylpropyl)phenoxyacetate, chlorodiphenylaeetate, p-P-phenylacetate, 3-phenylpropionate,
`dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, p-P-phenylacetate, 3-phenylpropionate,
`
`3-benzoylpropionate, isobutyrate, 4-oxopentanoate, pivaloate, adamanioate, crotonate, 4-
`3-benzoylpropionate, isobutyrate, 4-oxopentanoate, pivaloate, adamanioate, crotonate, 4-
`
`methoxycrotonate, (cid:9)
`methoxycrotonate, (cid:9)
`
`(E)-2-methyl-2-butenoate, (cid:9)
`(E)-2-methyl-2-butenoate, (cid:9)
`
`o-(dibromomethyl)benzoate, (cid:9)
`o-(dibromomethyl)benzoate, (cid:9)
`
`o-
`o-
`
`(methoxycarbonyl)benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate and oc-naphthanoate.
`(methoxycarbonyl)benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate and oc-naphthanoate.
`
`9. (new) A mononucleoside 5' triphosphate having a removable blocking moiety protecting the
`9. (new) A mononucleoside 5' triphosphate having a removable blocking moiety protecting the
`
`3' position which is an ester and which has the following formula:
`3' position which is an ester and which has the following formula:
`
`4
`4
`
`Page 8 of 94
`
`(cid:9)
`(cid:9)
`

`

`REEXAMINATION CONTROL NO.: 90/009,769
`REEXAMINATION CONTROL NO.: 90/009,769
`ATTORNEY DOCKET NO: 68205.000103
`ATTORNEY DOCKET NO: 68205.000103
`
`B
`B
`5' (cid:9)
`/
`0 (cid:9)
`5' (cid:9)
`0
`R2 -CH2 -C •C
`R2 -CH2 - C (cid:9)
`C
`
`3' C-C
`3' C-C
`
`0
`0
`
`C=0
`C=0
`
`R
`R
`
`wherein R2 is triphosphate; and wherein R is selected from the group consisting of: H, CH3
`wherein R1 is triphosphate; and wherein R is selected from the group consisting of: H, CH3
`(CH2) where N is an integer from 1 to 12, (CH31,3 (cid:9)
`(CH7) where N is an integer from 1 to 12, (CH3)„iKla, where x is an integer from 1 to 12,
`where x is an integer from 1 to 12,
`(CH31,±3 KUI (CH2 where x and n are inde pendent integers from 1 to 12 C_ (CH313x-(x)11
`
`
`13(CH31,(+1(CM (CH21, where x and n are independent iraeel•sfrilt0 12, C CH/ x-(x)i)
`(CH21, where x and n are independent integers from 1 to 12, and
`(CH21, where x and n are independent integers from 1 to 12, and
`
`R4
`R4 RI
`RI
`
`R5
`R5
`
`R6
`
`R3
`
`where R1, R3, R4, R5 and R6 are selected from the group consisting of CH3 or NO2.
`where R1, R3, R4, R5 and R6 are selected from the group consisting of CH3 or NO2.
`
`10. (new) The mononucleoside 5'-triphosophate of claims 8 or 9 wherein R2 is a triphosphate
`10. (new) The mononucleoside 5'-triphosophate of claims 8 or 9 wherein R7 is a triphosphate
`
`and said mononucleoside 5'-triphosphate is a deoxynucleoside.
`and said mononucleoside 5'-triphosphate is a deoxynucleoside.
`
`11. (new) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting
`11. (new) A mononucleoside 5'-triphosphate having a removable blocking moiety protecting
`
`the 3' position which has the following formula:
`the 3' position which has the following formula:
`
`5'
`5'
`R3 -CH2 (cid:9)
`R3 -CH (cid:9)
`
`2N,
`
`0 I
`I
`0
`
`3' /C-C
`3' /C-C
`
`
`
`R1 (cid:9)
`R1 (cid:9)
`
`H
`H
`
`wherein R2 is triphosphate; and wherein R1 is toluic or benzoic acid ester.
`wherein R, is triphosphate; and wherein R1 is toluic or benzoic acid ester.
`
`5
`5
`
`Page 9 of 94
`
`(cid:9)
`(cid:9)
`(cid:9)
`

`

`12. (new) The mononucleoside 5'-triphosphate of claims 8, 9, or 11 wherein said removable
`12. (new) The mononucleoside 5'-triphosphate of claims 8, 9, or 11 wherein said removable
`blocking moiety is removable by an enzyme.
`blocking moiety is removable by an enzyme.
`
`REEXAMINATION CONTROL NO.: 90/009,769
`REEXAMINATION CONTROL NO.: 90/009,769
`ATTORNEY DOCKET NO: 68205.000103
`ATTORNEY DOCKET NO: 68205.000103
`
`13. (new) The mononucleoside 5'-triphosphate of claims 8, 9, or 11 wherein said removable
`13. (new) The mononucleoside 5'-triphosphate of claims 8, 9, or 11 wherein said removable
`
`blocking moiety is removable by a reaction which occurs within 2 to 10 minutes.
`blocking moiety is removable by a reaction which occurs within 2 to 10 minutes.
`
`14. (new) A composition comprising a mononucleoside 5'-triphosphate having a removable
`14. (new) A composition comprising a mononucleoside 5'-triphosphate having a removable
`
`blocking moiety protecting the 3' position which is an ester and which has the following formula:
`blocking moiety protecting the 3' position which is an ester and which has the following formula:
`
`B
`B
`5'
`0
`0 /
`,,
`R2 -CH2 n
`C
`
`R2-CH2-C
`\
` /
`3' C-C
`3' C—C
`
`0 (cid:9)
`0
`
`H
`
`C=0
`C=0
`
`R
`
`wherein R, is a triphosphate and R is selected from the group consisting of: formate,
`wherein R, is a triphosphate and R is selected from the group consisting of: formate,
`
`benzoylformate, (cid:9)
`benzoylformate, (cid:9)
`
`chloroacetate, (cid:9)
`chloroacetate, (cid:9)
`
`dichloroacetate, (cid:9)
`dichloroacetate, (cid:9)
`
`trichloroacetate, (cid:9)
`trichloroacetate, (cid:9)
`
`trifluoroacetate,
`trifluoroacetate,
`
`methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 2,6-
`methoxyacet ate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 2,6-
`
`dichloro-4-methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-
`di chl oro-4-methylphenoxyacetate , 2 ,6-d ichloro-4-(1,1,3 ,3-tetramethylbutyl)phenoxyac etate, 2,4 -
`
`bis(1,1-dimethylpropyl)phenoxyacetate, (cid:9)
`bi s(1,1-dimethylpropyl )phenoxyacetate , (cid:9)
`
`chlorodiphenylacetate, (cid:9)
`chlorodi phenyl acetate, (cid:9)
`
`p-P-phenylacetate, (cid:9)
`p-P-phenylacetate, (cid:9)
`
`3-
`3-
`
`phenvlpropionate, 3-benzoylpropionate, isobutyrate, 4-oxopentanoate, pivaloate, adamanioate,
`phenylpropionate, 3-benzoylpropionate, isobutyrate, 4-oxopentanoate, pivaloate, adamanioate,
`
`crotonate, 4-methoxycrotonate, (E)-2-methyl-2-butenoate, o-(dibromomethyl)benzoate, o-
`crotonate, 4-methoxycrotonate, (E)-2-methyl-2-butenoate, o-(dibromomethyl)benzoate, o-
`
`(methoxycarbonyl)benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate and a-naphthanoate,
`(methoxycarbonyl)benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate and oc-naphthanoate,
`
`wherein said composition further comprises a template independent polynucleotide polymerase.
`wherein