U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`DECLARATION OF DR. NORMAN NELSON
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
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`___________________________________________
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`HOLOGIC, INC.,
`Petitioner
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`v.
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`ENZO LIFE SCIENCES, INC.
`Patent Owner
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`____________
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`U.S. Patent No. 7,064,197
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`SYSTEM, ARRAY AND NON-POROUS SOLID SUPPORT
`COMPRISING FIXED OR IMMOBILIZED NUCLEIC ACIDS
`____________
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`Page 1 of 66
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`HOLOGIC EXHIBIT 1002
`Hologic v. Enzo
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`Declaration of Dr. Norman Nelson
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`DECLARATION OF DR. NORMAN NELSON
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`
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
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`___________________________________________
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`HOLOGIC, INC.,
`Petitioner
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`v.
`
`ENZO LIFE SCIENCES, INC.
`Patent Owner
`
`____________
`
`U.S. Patent No. 7,064,197
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`SYSTEM, ARRAY AND NON-POROUS SOLID SUPPORT
`COMPRISING FIXED OR IMMOBILIZED NUCLEIC ACIDS
`____________
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`Page 1 of 66
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`HOLOGIC EXHIBIT 1002
`Hologic v. Enzo
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`Table of Contents
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`QUALIFICATION AND EXPERIENCE ....................................................... 1
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`RELEVANT LEGAL STANDARDS ............................................................. 3
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`I.
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`II.
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`III. LEVEL OF ORDINARY SKILL IN THE ART ............................................. 6
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`IV. SUMMARY OF MY OPINIONS ................................................................... 7
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`V.
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`THE ’197 PATENT ......................................................................................... 9
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`VI. CLAIMS 17, 19, 25, 105, 106, 114, 116, 119, 128, 129, 150, 152, 178,
`180, 186, AND 187 ARE ANTICIPATED BY FISH. ..................................11
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`A.
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`B.
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`Fish (Ex. 1006) ....................................................................................11
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`Fish discloses surface treatment of plastic microtitration trays
`with poly-L-lysine to bind nucleic acids in hybridizable form to
`the surface of the microtitration wells. ................................................12
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`VII. CLAIMS 130, 131, 151, AND 154 WOULD HAVE BEEN
`OBVIOUS IN VIEW OF FISH .....................................................................27
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`VIII. CLAIMS 120 AND 189 WOULD HAVE BEEN OBVIOUS BASED
`ON FISH IN VIEW OF METZGAR AND SATO .......................................29
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`IX. CLAIMS 113, AND 185 WOULD HAVE BEEN OBVIOUS BASED
`ON FISH IN VIEW OF GILHAM ................................................................31
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`X.
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`CLAIMS 17, 19, 25, 105, 106, 114, 119, 120, 128, 129, 131, 150, 151,
`152, 178, 180, 186, AND 189 WOULD HAVE BEEN OBVIOUS
`BASED ON VPK IN VIEW OF METZGAR. ..............................................33
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`A. Van Prooijen-Knegt (Ex. 1008, “VPK”) .............................................33
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`B. VPK discloses surface treatment of glass slides with
`alkylaminosilane to bind nucleic acids in hybridizable form to
`the surface of the glass slides ..............................................................34
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`XI. CLAIMS 113, 116, 130, 154, 185, AND 187 WOULD HAVE BEEN
`OBVIOUS BASED ON NOYES IN VIEW OF VPK AND
`FURTHER IN VIEW OF METZGAR AND RAMACHANDRAN. ...........40
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`XII. CONCLUSION ............................................................................................44
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`LIST OF MATERIALS CONSIDERED ............................................................... i
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`ii
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`I, Norman Nelson, do hereby declare:
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`1. I am making this declaration at the request of Hologic, Inc. (“Hologic”) in the
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`matter of the Inter Partes Review of U.S. Patent No. 7,064,197 to Rabbani et al.
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`(“the ’197 patent”).
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`2. My qualifications are established by my resume, which I understand is provided
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`as Exhibit A to this Declaration.
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`3. I am being compensated for my work on this matter, but my opinions are based
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`on my own views of the patented technology and the prior art. My
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`compensation in no way depends on the outcome of this proceeding or the
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`content of my testimony.
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`4. In preparing this Declaration, I reviewed and considered the ’197 patent, the
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`prosecution history of the ’197 patent, and the documents listed at the end of
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`this declaration. Importantly, I have reviewed the related Petition, which I
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`understand Hologic will file at the United States Patent and Trademark Office
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`(USPTO) at the same time as this Declaration is filed at the USPTO.
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`QUALIFICATION AND EXPERIENCE
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`I.
`5. I obtained a Ph.D. in Chemistry, with a focus in Biochemistry, in 1982 from
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`University of California, San Diego. I also received a Bachelor of Science in
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`Chemistry from California Institute of Technology in 1976.
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`6. I have nearly 31 years of experience in molecular diagnostics and nucleic acid
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`chemistry, particularly nucleic acids analysis. I am and was very knowledgeable
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`about conventional techniques for attaching nucleic acids to other moieties like
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`solid supports or labels. I worked for Gen-Probe Incorporated (now acquired by
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`Hologic, Inc.)—a pioneer and leader in molecular diagnostics—for 27 years
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`(June 1985-August 2012). While at Gen-Probe, I co-invented, reduced to
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`practice, and played a key role in commercialization of multiple core
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`technologies involving nucleic acids analysis, which are currently in FDA-
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`approved products.
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`7. I started my career at Gen-Probe as a scientist (1985-2005), where I developed
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`and implemented key nucleic acids-based technologies and assays, including
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`nucleic acids capture/immobilization and labeling techniques, hybridization,
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`amplification and detection of nucleic acids. As the Director of Biochemistry at
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`Gen-Probe (2005-2009), I led a multidisciplinary team in the development of
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`multiplexed nucleic acids-based assays. And as the Senior Director of
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`Discovery Research at Gen-Probe (2009-2012), I focused on the development
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`and commercialization of various nucleic acids-based diagnostic products.
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`8. I have been working as a consultant in the field of nucleic acids-based
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`diagnostics, DNA sequencing and Genomics since 2012.
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`9. My research work has led to 37 issued U.S. patents and over 100 issued or
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`U.S. Patent No. 7,064,197
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`pending patent applications worldwide.
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`10. I have co-authored over 20 peer-reviewed journal articles and over 35 technical
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`poster presentations in field of nucleic acids-based diagnostics. I have also
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`delivered numerous technical presentations at conferences. And I have also
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`chaired or served in the program committee of many conferences and symposia
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`related to my field of work.
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`11. I have extensive experience in the field of nucleic acid immobilization,
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`hybridization, and detection—the technical field of the ’197 patent. Upon
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`joining Gen-Probe, I extensively researched and studied the existing field of
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`nucleic acids analysis going back to the mid-1970s. Study and knowledge of the
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`prevailing technologies was a requirement for my success as a scientist in
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`developing novel or improved technologies. After Hologic retained me for
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`preparing this Declaration, I have re-familiarized myself with the pre-1983
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`scientific literature and patent publications in the field of nucleic acid
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`immobilization, hybridization, and detection (the earliest priority date listed on
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`the face of the ’197 patent).
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`II. RELEVANT LEGAL STANDARDS
`12. The opinions I express in this declaration involve the application of my
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`technical knowledge and experience to the evaluation of certain prior art with
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`respect to the ’197 patent. In addition, I understand that the following legal
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`principles apply, as explained to me by Hologic’s legal counsel.
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`13. I understand that, in proceedings like this one before the USPTO, a claim in an
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`unexpired patent shall be given its broadest reasonable interpretation in light of
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`the specification of the patent in which it appears. I also understand that district
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`courts may apply a different claim construction standard, and that claims there
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`should be given their ordinary meaning to a person having ordinary skill in the
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`art at the relevant timeframe in light of the claim language, patent specification,
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`and prosecution history. I have read Section VIII of the Petition which sets out
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`the interpretation of certain claim terms in the Petition. I agree with the
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`statements made in that section. I have been informed of certain terms that have
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`already been interpreted by a court. My opinions in this declaration remain the
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`same under either claim construction standard discussed in the Petition or the
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`claims construction standard from the court.
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`14. I understand that a patent claim can be unpatentable if it is anticipated in view
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`of the prior art. I understand that anticipation of a claim requires that every
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`element of a claim be disclosed expressly or inherently in a single prior art
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`reference, arranged as in the claim.
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`15. I understand that a patent claim can be unpatentable for obviousness only if the
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`invention described in the claim would have been obvious to a person of
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`ordinary skill in the art at the time the invention was made, taking into account
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`(1) the scope and content of the prior art, (2) the differences between the prior
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`art and the claimed invention, and (3) the level of ordinary skill in the art, and
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`(4) any secondary considerations of non-obviousness, including commercial
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`success of products or processes using the invention, long felt need for the
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`invention, failure of others to make the invention, industry acceptance of the
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`invention, and copying of the invention by others.
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`16. I further understand that multiple references can be combined with one another,
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`or pursuant to the knowledge of a person of ordinary skill in the art, to render a
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`claim obvious. I also understand that there must be a reason that would have
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`prompted a person of ordinary skill in the relevant field to combine the features
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`of the prior art in the way the claimed invention does.
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`17. I also understand that a person skilled in the art must reasonably expect that the
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`combination will work.
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`18. In determining whether a piece of prior art could have been combined with
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`other prior art or with other information within the knowledge of a person
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`having ordinary skill in the art, I understand that it is proper to conclude that a
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`claim is obvious if it is no more than a predictable use of prior art elements
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`according to their established functions and the person of ordinary skill in the
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`art would have reasonably expected success.
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`III. LEVEL OF ORDINARY SKILL IN THE ART
`19. It is my understanding that when considering the claims of the ’197 patent and
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`the prior art, I must do so based on the perspective of one of ordinary skill in
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`the art at the relevant effective filing date. Even though I am an expert, I
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`consider myself totally qualified as to the level of ordinary skill at the relevant
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`time(s). My understanding is that the purported effective filing date of the ’197
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`patent is January 27, 1983, but that the ’197 patent may in fact be entitled to a
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`priority date no earlier than May 9, 1985. All of my analyses below are based
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`on the level of skill in the art at least as early as of January 27, 1983. I
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`offer no opinion here regarding the effective filing date of the ’197 patent, as I
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`understand that is a legal determination, and I am not a lawyer.
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`20. I understand that several factors are to be considered in determining who would
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`be a person of ordinary skill in the art. These factors include: (1) the types of
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`problems encountered in the art; (2) the prior art solutions to those problems;
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`(3) the rapidity with which innovations are made; (4) the sophistication of the
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`technology; and (5) the educational level of active workers in the field.
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`21. Based on these factors as well as my experience and expertise, a person of
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`ordinary skill in the field of nucleic acid detection, immobilization, and
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`hybridization as of both the 1983 and the 1985 filing dates would have (i)
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`possessed or would have been actively pursuing an advanced degree in organic
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`chemistry and/or biochemistry, (ii) attained at least two years of experience in a
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`chemistry or biochemistry laboratory and would have been familiar with
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`nucleic acid chemistry, and (iii) have been knowledgeable of conventional
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`techniques for attaching nucleic acids to other moieties like solid supports or
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`labels. This level of skill applies to all my obviousness analyses below.
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`IV. SUMMARY OF MY OPINIONS
`22. I have been asked to consider the ’197 patent and certain prior art references
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`and to offer my opinions on the relation of that prior art to the claims of the
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`’197 patent.
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`23. The ’197 patent in general describes methods for fixing or immobilizing nucleic
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`acids to solid supports, which can be subsequently hybridized to polynucleotide
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`probes capable of generating a soluble signal. Ex. 1001, 1:23-32; 5:40-46; 5:61-
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`6:32. Broadly, the ’197 patent claims relate to non-porous solid supports with
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`fixed or immobilized nucleic acids, and systems and arrays comprising such
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`non-porous solid supports.
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`24. Two strands of nucleic acids hybridize to one another through hydrogen
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`bonding between complementary nucleotides (bases) that naturally pair with
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`one another. Under the Watson-Crick base pairing model, the nucleotide “A”
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`pairs with the nucleotide “T” on the opposite strand, and the nucleotide “C”
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`pairs with the nucleotide “G” on the opposite strand. In RNA molecules, “T” is
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`replaced by “U” to form an “A-U” base pair. To be considered “hybridizable,” a
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`nucleic acid strand does not have to hybridize along its entire length to another
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`strand—there only has to be some degree of possible hybridization between
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`complementary nucleotides of two strands of nucleic acids.
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`25. Fixation or immobilization of nucleic acid sequences in hybridizable form to
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`different types of solid supports, including non-porous solid supports, was
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`known more than a year before the January 27, 1983, filing date of the first
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`application. I discuss several such publications in detail below, such as Ex.
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`1006, Ex. 1007, Ex. 1008, and Ex. 1019. Hybridizable single-stranded nucleic
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`acids bound to solid supports were routinely used for identifying biological
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`materials in samples and separating biological materials from samples prior to
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`January 27, 1983. See, e.g., Ex. 1007, p. 301, right col., first paragraph
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`(discussing (1) analytical methods to detect nucleic acids and (2) affinity
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`chromatography and sample preparation (separating biological material)).
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`26. As explained in detail below, Fish (Ex. 1006) teaches every technical detail of
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`claims 17, 19, 25, 105, 106, 114, 116, 119, 128, 129, 150, 152, 178, 180, 186,
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`and 187 of the ’197 patent.
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`27. Also as explained in detail below, a person of ordinary skill in the art would
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`have understood that claims 130, 131, 151, and 154 would have been obvious in
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`view of Fish; claims 120 and 189 would have been obvious based on Fish in
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`view of Metgar, and further in view of Sato; and that claims 113 and 185 would
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`have been obvious based on Fish in view of Gilham.
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`28. I now summarize conclusions involving VPK.
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`29. Also as explained in detail below, claims 113, 116, 130, 154, 185, and 187
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`would have been obvious in view of Noyes, VPK, Metzgar, and Ramachandran
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`30. Also as explained in detail below, claims 17, 19, 25, 105, 106, 114, 119, 120,
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`128, 129, 131, 150, 151, 152, 178, 180, 186, and 189 would have been obvious
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`in view of VPK and Metzgar.
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`31. In my conclusions of obviousness of certain claims, I consider that the claimed
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`arrays are no more than a predictable use of prior art elements according to their
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`established functions and that one of ordinary skill in the art would have
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`reasonably expected success in making such arrays. They involve prior art
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`technologies used in suggested and predictable ways to achieve expected
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`results.
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`V. THE ’197 PATENT
`32. The ’197 patent describes non-porous solid supports with fixed or immobilized
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`nucleic acids, and systems and arrays comprising such non-porous solid
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`supports. Ex. 1001, Title and Abstract.
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`33. The ’197 patent identifies conventional microtiter well plates, glass plates
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`having “an array of depressions or wells,” and polystyrene plates having wells
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`as examples of non-porous solid supports to which nucleic acids may be fixed
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`or immobilized. Ex. 1001, 8:65-9:5; 11:56-58; 12:7-26; and 12:54-58.
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`34. The ’197 Patent also explains that polynucleotide analyte sequences fixed or
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`immobilized to the non-porous solid supports may be hybridized to
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`complementary polynucleotide or oligonucleotide probes. See e.g., id. at 1:23-
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`32; 5:61-6:32; 8:65-9:30. I understand from Hologic’s legal counsel, as well as
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`my own extensive experience with patents that although not required by any of
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`the challenged claims, the ’197 Patent discusses that the complementary probe
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`may be provided with a chemical label capable of generating a soluble signal.
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`The ’197 Patent also discusses that hybridized probe-analytes may be identified
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`by detecting or quantifying the soluble signal, which in turn may indicate the
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`presence of the specific analyte sequence in a sample of interest.
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`35. As described below, arrays comprising non-porous supports having fixed or
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`immobilized nucleic acids in hybridizable form were known. Below I discuss
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`the following publications: Fish (Ex. 1006), Noyes (Ex. 1007), VPK (Ex. 1008),
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`Gilham (Ex. 1019) and Metzgar (Ex. 1009) and Ramachandran (Ex. 1028).
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`36. I understand that the term “array” means an orderly grouping or arrangement.
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`VI. CLAIMS 17, 19, 25, 105, 106, 114, 116, 119, 128, 129, 150, 152, 178, 180,
`186, AND 187 ARE ANTICIPATED BY FISH.
`A.
`37. Independent claims 17, 19, and 25 recite an “array,” which means an orderly
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`Fish (Ex. 1006)
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`arrangement. Fish discloses microtitration trays having a plurality of wells
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`arranged in rows in which nucleic acids are immobilized. Ex. 1006, p. 536, left
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`col., first full ¶. Thus, the microtitration tray of Fish is an “array,” as recited in
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`claims 17, 19, and 25, because the wells in the microtitration trays provide an
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`orderly grouping or arrangement of nucleic acids immobilized to the surface of
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`the wells in the trays. In fact, the ’197 Patent uses the term “array” in the
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`context of “glass plates” having “an array of depressions or wells.” Ex. 1001,
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`8:65-9:2. Claims 17 and 19 recite that the array comprises “various single-
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`stranded nucleic acids.” Fish shows various (different) single-stranded nucleic
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`acids immobized in the wells, e.g., poly dA and polydC.
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`38. Fish discloses a microradioimmunoassay system for measurement of anti-
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`double-stranded DNA (dsDNA) antibodies (antibodies that bind to dsDNA).
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`Ex. 1006 [Fish], Abstract. Although the main focus was directed toward ds-
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`DNA-specific antibodies, Fish also disclose the measurement of antibodies that
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`bind ssDNA (ssDNA). It was necessary to measure this activity in serum
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`samples in order to optimize the specificity of dsDNA-binding antibodies and
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`design the best performing assay for ds-DNA activity. Furthermore, binding to
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`ssDNA was a necessary control in the S1 nuclease experiments (see below).
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`Specifically, Fish discloses immobilizing of double-stranded and ssDNA to
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`plastic microtitration wells, incubating patient sera in the DNA-coated wells,
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`and detecting antibodies in patient sera that bind to DNA; those antibodies are
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`detected using second, radiolabeled anti-Ig antibodies (the second antibodies
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`bind to antibodies). Id. at Abstract; Figure 1 (showing measurements of anti-
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`DNA antibodies bound to the DNA-coated wells).
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`B.
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`Fish discloses surface treatment of plastic microtitration trays
`with poly-L-lysine to bind nucleic acids in hybridizable form to
`the surface of the microtitration wells.
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`39. All of independent claims 17, 19, and 25 refer to arrays comprising “non-
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`porous solid support.” I understand that all of the rest of the claims listed in the
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`VI header above depend from one or more of claims 17, 19, and 19, and thus
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`also include the “non-porous solid support” limitation.
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`40. Fish discloses the binding of ssDNA to the wells of a microtitration tray (also
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`known as microtiter plate). It is well known that wells of microtitration trays are
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`non-porous. In particular, the microtitration trays used in Fish are made of non-
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`porous polyvinyl. The ’197 patent is consistent with that understanding, as it
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`states that “the polynucleotide analyte sequence can be fixed “directly to a non-
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`porous solid support, such as a conventional microtiter well . . . .” Ex.
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`1001:12:54-57.
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`41. Moreover, wells of a microtitration tray must hold liquid in order to
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`successfully carry out the processes conducted in the wells—incubation,
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`washing, detection, etc.—and therefore, the microtitration trays must be non-
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`porous. The Patent Owner agreed with that correct technical understanding
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`when it explained that supports or systems that contain solutions must be non-
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`porous. For example, the Patent Owner stated during prosecution of European
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`Patent No. 0107440 (Application No. 84100836.0-2106) that “[a] support or
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`system…to which DNA is bound, being a depression or a well and allowing the
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`determination of the DNA whereby washing steps and substrate reactions…are
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`performed in the support/system must be non-porous.” Ex. 1016 at pp. 6-7.
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`Thus, the Patent Owner itself correctly agrees that surface of wells or
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`depressions, including those of a microtitration tray, are in fact non-porous.
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`42. The polyvinyl microtitration well disclosed by Fish is a non-porous solid
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`support as set forth in all of claims 17, 19, 25, 105, 106, 114, 116, 119, 128,
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`129, 150, 152, 178, 180, 186, and 187.
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`43. None of challenged claims require the solid support to have at least one or more
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`amine(s), hydroxyl(s), or epoxide(s), and a single-stranded nucleic acid fixed or
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`immobilized in hybridizable form to the solid support via one of those groups.
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`The challenged claims do require that the single-stranded nucleic acid be in
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`hybridizable form. Fish describes coating the wells of a microtitration tray with
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`poly-L-lysine (PLL, also referred to as PPL) prior to binding of nucleic acid.
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`Ex. 1006, p. 536, left col., first two full ¶¶. As described in the section titled,
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`“DNA coated microtitration trays,” a 50 µg/mL solution of PLL was added to
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`each well of a microtitration tray, incubated for 45 minutes at room
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`temperature, and then washed three times with normal saline. Id. This process
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`resulted in a microtitration tray coated with PLL.
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`44. The PLL treatment provides amine groups on the surface of the wells of the
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`microtitration tray. See, e.g., claims 42, 182, and 215 of the ’197 Patent
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`(reciting that surface treatment with polylysine provides amine groups) (Ex.
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`1001, 17 (claim 42), col. 23 (claim 182), col. 25 (claim 215)); see also Ex. 1017
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`[Taylor] at p. 2 (stating that “PLL …present amine functional groups ….”)
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`45. The creation of amine groups on the surface of a solid support is useful for the
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`immobilization of nucleic acids and other molecules to the support (including
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`non-porous solid support). Ex. 1017 [Taylor] at p. 2. The cationic nature of PLL
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`makes it an attractive molecular coating for the adhesion of negatively charged
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`biomolecules, such as DNA, as described in detail in ¶53 below. See, e.g., Ex.
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`1006 [Fish] at p. 535, left. col., first full ¶ (stating that PLL is “a positively
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`charged polymer”); see also Ex. 1018 [Aotsuka] at p. 160 (discussing that it is
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`reasonable to apply PLL for coupling with strongly charged antigens such as
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`dsDNA and that bonding of dsDNA and PLL is ionic).
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`Page 17 of 66
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`46. Fish discloses successful immobilization of ssDNA (a mixture of poly-dA and
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`poly-dC as well as denatured calf thymus DNA) to the PLL-coated
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`microtitration trays. Ex. 1006 [Fish], Abstract; p. 536, left col., first two full ¶¶;
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`Figure 1 (Description).
`
`47. Fish’s data in Fig. 1 confirm that the ssDNA (the poly dA + poly dC, and the
`
`denatured calf thymus DNA) was bound to the PLL coated wells. Fig. 1 at p.
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`539 of Ex. 1006 shows the results obtained after nuclease S1 treatment of the
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`three different types of immobilized DNA listed for two different patients (see
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`the second col. of Fig. 1 under the heading “Nucleic Acid.”. S1 digests ssDNA
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`but not double-stranded DNA. Ex. 1006, p. 538, right col., ¶1. The empty and
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`black bars in the last col. of Fig. 1 show the amount of antibody bound to the
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`DNA in the wells without S1 treatment (-) and with S1 treatment (+),
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`respectively. Ex. 1006, p. 539 Fig. 1. The longer the bar, the higher the level of
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`bound antibody. After addition of serum to the wells and the anti-DNA
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`antibodies in the serum are allowed to bind to the immobilized DNA, the wells
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`are washed to remove antibodies that are not bound to the immobilized DNA
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`and those that remain bound to the DNA are detected with a second, labeled
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`anti-Ig antibody that bind to remaining antibodies. Ex. 1006, p. 536, left col.,
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`third full ¶ and ¶ bridging the cols.; p. 538, right col., first ¶.
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`15
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`Page 18 of 66
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`48. The data in the last col. of Fig. 1 show that in the wells having bound double-
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`stranded poly dA-T for both patients (O.N. and B.E.) (see the top two bars in
`
`the first row (poly dA-dT), there was virtually no difference in binding with or
`
`without S1 treatment. Id. (The first row for each patient shows approximately
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`equal length empty and black bars (equal antibody binding) extending to about
`
`200). That was the expected result, since S1 does not digest double-stranded
`
`DNA and all of the immobilized DNA would still be available for binding after
`
`S1 treatment.
`
`49. In the wells with immobilized single-stranded nucleic acid, for both patients,
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`there was significantly less antibody binding to the immobilized single-stranded
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`nucleic acid with S1 treatment than without S1 treatment. This is shown by the
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`data in the second and third row (“poly dA + dC” and “denatured DNA”) for
`
`each patient, which show shorter black bars (S1 treated) than empty bars (no S1
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`treatment). That is the expected result for ssDNA, since S1 digests ssDNA.
`
`After S1 treatment which digests single-strands, less immobilized ssDNA
`
`would be available for antibody binding.
`
`50. Those results prove that ssDNA must have been immobilized to the PLL-coated
`
`wells. Because the wells are washed after the antibody is allowed to bind to
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`immobilized DNA, the antibody would have been washed away during the
`
`experiment if there was no DNA available for binding. Furthermore, there
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`16
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`Page 19 of 66
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`would have been no difference in antibody binding with or without S1
`
`treatment if immobilized ssDNA was not present.
`
`51. The data in Figures 3 and 4 of Fish, which show binding of antibodies to
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`immobilized ssDNA, also proves the presence of immobilized ssDNA. Ex.
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`1006, p. 539, left col., first full paragraph; p. 540, right col.– Fig. 3 (data for the
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`single-stranded immobilized denatured calf thymus DNA); p. 541, left col.–Fig.
`
`4 (data for the immobilized single-stranded poly dA and poly dC). Fish
`
`describes measures that were taken to block non-specific antibody binding
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`directly to the surface of wells, and that allowed Fish to conclude that the data
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`in Figs. 3 and 4 show binding of antibodies to immobilized ssDNA. Ex. 1006,
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`p. 537, left col., fourth line under Table 2, through the paragraph bridging the
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`cols. on p. 537.
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`52. Specifically, Fish disclosed that a solution of 2% bovine gamma globulin
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`(BGG) and 1% bovine serum albumin (BSA) was added to the wells to block
`
`the antibodies from binding non-specifically to the wells Id. at p. 536, left col.,
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`third full ¶. Non-specific binding to the wells means antibody binds to the
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`surface of the wells rather than to DNA immobilized on the wells. Thus, Fish
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`accurately reported that the data in Figs. 3 and 4 was due to binding of the
`
`antibodies to immobilized ssDNA (specific binding). Those data provide further
`
`17
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`evidence that ssDNA in Fish bound effectively to the PLL-coated wells of the
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`microtitration trays.
`
`53. Figure 1 also demonstrates that the denatured calf thymus DNA remained in
`
`single-stranded form following immobilization. This means that the single
`
`complementary strands of the calf thymus DNA that was bound to the PLL did
`
`not anneal to each other. Thus, if complementary single-stranded nucleic acids
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`had been provided in a hybridizing solution, the bound calf thymus DNA would
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`have been accessible for hybridization. If the single strands of the denatured
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`calf thymus DNA had annealed to each other to form double strands, treatment
`
`with the nuclease would not have diminished the antibody binding results that
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`are clearly shown in Fig. 1 (third row for each patient which shows a long
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`empty bar (without S1 treatment) and a very short black bar (with S1
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`treatment)).
`
`54. With respect to binding of double-stranded DNA, Fish reports that poly dA-dT
`
`did not bind to polyvinyl surfaces without PLL treatment. Ex. 1006 [Fish] at p.
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`536, right col., second full ¶ (titled “The effect of PLL treatment on DNA
`
`surface binding.”). The binding of single-stranded DNA also would be
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`facilitated by the PLL coating because both single- and double-stranded DNA
`
`have negative charges that ionically interact with the positive charges of the
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`PLL.
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`18
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`Page 21 of 66
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`55. The DNA in Fish is immobilized to the microtitration tray wells via one or
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`more of the amines on the surface of the PLL coated trays. It is my
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`understanding that it is known that the amine groups of PLL form non-covalent
`
`bonds with nucleic acids via ionic interactions between the positive charges of
`
`the amine groups and the negative charges of the phosphate groups in the DNA
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`backb53one. Ex. 1001 [the ’197 Patent] at 8:57-60 (stating that alkylamine
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`treated surfaces are suitable for immobilizing negatively charged
`
`polyelectrolytes); see also Ex. 1020 [Diehl patent publication] at ¶ [0019] (“For
`
`the ionical binding, use is made of the fact that nucleic acids are generally
`
`negatively charged. By providing positive charges on the surface of the carrier,
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`binding between the negatively charged nucleic acids and the positively
`
`charged surface of the carrier can be achieved by an interaction of the charges.
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`For this purpose, glass surfaces coated with compounds providing positive
`
`charges, e.g. coated with poly-L-lysine and/or aminosilane, are used. Such
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`activated slides are well-known in the art.”).
`
`56. Fish does not explicitly discuss the immobilized single-stranded DNA is in
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`hybridizable form, because the Fish assay did not involve hybridization of such
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`ssDNA. . I understand that the term “hybridizable form” does not require a
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`showing of actual hybridization of two strands. Rather, it means that the single-
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`stranded nucleic acid is capable of binding through Watson Crick base pairing.
`
`19
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`57. Single-stranded DNA immobilized onto a solid support via the PLL method
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`U.S. Patent No. 7,064,197
`Declaration of Dr. Norman Nelson
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`used in Fish is necessarily in hybridizable form. This is clearly demonstrated in
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`subsequent research pape
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