`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`____________
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`OXFORD NANOPORE TECHNOLOGIES, INC.
`
`Petitioners
`
`v.
`
`PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
`
`Patent Owner
`
`____________
`
`Case No. Unassigned
`
`Patent 9,738,929
`
`____________
`
`DECLARATION OF DR. PATRICK HRDLICKA IN SUPPORT OF
`
`PETITION FOR INTER PARTES REVIEW OF U.S. PATENT NO. 9,738,929
`
`
`
`
`Oxford, Exh. 1002, p. 1
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`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`TABLE OF CONTENTS
`
`Page
`BACKGROUND AND QUALIFICATIONS .............................................. 1
`
`LEGAL UNDERSTANDING ....................................................................... 3
`
`
`
`I.
`
`II.
`
`A. Anticipation .......................................................................................... 4
`B. Obviousness .......................................................................................... 4
`C. Claim Construction ............................................................................. 7
`III. THE PRIOR ART........................................................................................ 10
`
`Prior Art Considered ........................................................................ 10
`A.
`IV. LEVEL OF ORDINARY SKILL IN THE ART ...................................... 11
`
`V.
`
`BACKGROUND OF SEQUENCING NUCLEIC ACIDS USING
`NANOPORES AND MOLECULAR MOTORS ...................................... 12
`
`A. Nanopore Sequencing Using Enzyme Chaperones ........................ 12
`B.
`Sequencing of Complementary Strands to Improve Accuracy .... 15
`VI. OVERVIEW OF THE ’929 PATENT ....................................................... 16
`
`A. Overview of the Subject Matter of the ’929 Patent ........................ 16
`B. Overview of the Prosecution History ............................................... 19
`VII. SUMMARY OF PRIOR ART .................................................................... 23
`
`A. Nanopore Sequencing using Enzyme Chaperones was Known in
`the Art Prior to the Earliest Priority Date Claimed by the ’929
`Patent .................................................................................................. 23
`1.
`U.S. Patent Publication No. 2006/0063171 (“Akeson”) ....... 23
`2.
`U.S. Patent No. 6,936,433 (“Akeson ’433”) ........................... 26
`
`
`
`i
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`Oxford, Exh. 1002, p. 2
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`

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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`
`B.
`
`Sequencing of Both Strands of a Polynucleotide was Known in the
`Art Prior to the Earliest Priority Date Claimed by the ’929 Patent
` ............................................................................................................. 27
`1.
`Sanger ....................................................................................... 27
`2.
`U.S. Patent No. 6,087,099 (“Gupte”) ..................................... 28
`3.
`U.S. Patent Publication No. 2005/0142559 (“Makrigiorgos”)
` ................................................................................................... 31
`C. Various Linkers for Connecting Complementary Strands of DNA
`were Known in the Art Prior to the Earliest Priority Date
`Claimed by the ’929 Patent .............................................................. 34
`1. Miner ........................................................................................ 34
`2.
`O’Dea ........................................................................................ 35
`VIII. SUMMARY OF COMBINATIONS .......................................................... 36
`
`IX. THERE IS A REASONABLE LIKELIHOOD THAT THE
`CHALLENGED CLAIMS ARE UNPATENTABLE .............................. 37
`
`A. Ground 1: Claims 1-8, 10-11 and 16 are obvious over Akeson and
`Gupte .................................................................................................. 37
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson and Gupte ............................. 37
`Claim 1 ..................................................................................... 38
`Claim 2 ..................................................................................... 50
`Claim 3 ..................................................................................... 50
`Claim 4 ..................................................................................... 51
`Claim 5 ..................................................................................... 51
`Claim 6 ..................................................................................... 52
`Claim 7 ..................................................................................... 55
`
`2.
`3.
`4.
`5.
`6.
`7.
`8.
`
`
`
`ii
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`Oxford, Exh. 1002, p. 3
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`

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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`Claim 8 ..................................................................................... 57
`9.
`10. Claim 10 ................................................................................... 59
`11. Claim 11 ................................................................................... 60
`12. Claim 16 ................................................................................... 62
`B. Ground 2: Claim 12 is obvious over Akeson, Gupte and Miner .. 64
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson, Gupte and Miner. ............... 64
`Claim 12 ................................................................................... 65
`2.
`C. Ground 3: Claim 17 is obvious over Akeson, Gupte and Akeson
`’433. ..................................................................................................... 67
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson, Gupte and Akeson ’433. ..... 67
`Claim 17 ................................................................................... 68
`2.
`D. Ground 4: Claims 1-8, 10-11 and 13 are obvious over Akeson,
`Sanger and Makrigiorgos ................................................................. 69
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson, Sanger and Makrigiorgos .. 69
`Claim 1 ..................................................................................... 70
`Claim 2 ..................................................................................... 81
`Claim 3 ..................................................................................... 82
`Claim 4 ..................................................................................... 82
`Claim 5 ..................................................................................... 83
`Claim 6 ..................................................................................... 83
`Claim 7 ..................................................................................... 86
`Claim 8 ..................................................................................... 88
`
`2.
`3.
`4.
`5.
`6.
`7.
`8.
`9.
`
`iii
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`Oxford, Exh. 1002, p. 4
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`

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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`
`10. Claim 10 ................................................................................... 89
`11. Claim 11 ................................................................................... 90
`12. Claim 13 ................................................................................... 90
`E. Ground 5: Claim 9 is obvious over Akeson, Gupte and
`Makrigiorgos. ..................................................................................... 91
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson, Gupte and Makrigiorgos. .. 91
`Claim 9 ..................................................................................... 93
`2.
`F. Ground 6: Claim 12 is obvious over Akeson, Sanger,
`Makrigiorgos and Miner .................................................................. 96
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson, Sanger, Makrigiorgos and
`Miner. ....................................................................................... 96
`Claim 12 ................................................................................... 96
`2.
`G. Ground 7: Claims 14 and 15 are obvious over Akeson, Sanger,
`Makrigiorgos and O’Dea. ................................................................. 98
`1.
`A person of ordinary skill in the art would have been
`motivated to combine Akeson, Sanger, Makrigiorgos and
`O’Dea. ....................................................................................... 98
`Claim 14 ................................................................................... 99
`2.
`Claim 15 ................................................................................. 100
`3.
`X. CONCLUSION .......................................................................................... 101
`
`
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`
`iv
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`Oxford, Exh. 1002, p. 5
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`

`

`
`
`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`DECLARATION OF PATRICK HRDLICKA
`
`
`I, Patrick Hrdlicka, declare as follows:
`
`
`1.
`
`I make this declaration based on my own personal knowledge and, if
`
`called upon to testify, would testify competently to the matters contained herein.
`
`2.
`
`I have been asked to provide technical assistance in the inter partes
`
`review of U.S. Patent No. 9,738,929 (“the ’929 Patent”).
`
`3.
`
`This declaration is a statement of my opinions on issues related to the
`
`unpatentability of claims 1-17 of the ’929 Patent in view of my knowledge,
`
`training, and experience in the relevant art in combination with the legal standards
`
`and the prior art identified in Sections II and III, below
`
`I.
`
`BACKGROUND AND QUALIFICATIONS
`4.
`In forming my opinions, I have relied upon my knowledge, training,
`
`and experience in the relevant art. While my qualifications are stated more fully in
`
`my curriculum vitae (Ex. 1003), here I provide a brief summary of my
`
`qualifications.
`
`5.
`
`I received a B.Sc., a M.Sc. and a Ph.D. in Chemistry from the
`
`University of Southern Denmark in 2000, 2004, and 2006 respectively.
`
`6.
`
`I am a Professor in the Department of Chemistry at the University
`
`of Idaho. My responsibilities include: maintaining a visible and nationally
`
`recognized research program
`
`in nucleic acid chemistry; contributing
`
`to
`
`
`
`1
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`
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`Oxford, Exh. 1002, p. 6
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`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`departmental teaching, which includes teaching courses in organic chemistry,
`
`medicinal chemistry and nucleic acid chemistry; recruitment, advising, and
`
`mentoring of undergraduate and graduate students, and providing service to the
`
`department, college, university, and scientific community.
`
`7. My research interests focus on the use of chemically modified
`
`oligonucleotides and nanomaterials as therapeutics, diagnostics and smart
`
`materials. More specifically, my research team strives to develop: i) novel
`
`methodologies
`
`for
`
`site-specific and sequence-unrestricted recognition of
`
`chromosomal DNA, ii) probes for detection of nucleic acids with
`
`single
`
`nucleotide
`
`polymorphisms
`
`(SNPs),
`
`iii)
`
`antisense oligonucleotides with
`
`improved hybridization and pharmacokinetic profiles and
`
`iv) sensors for
`
`detection of biological and chemical threat agents.
`
`8.
`
`I have published over 60 peer-reviewed articles in peer-reviewed
`
`international journals, which have been cited more than 1,350 times by other
`
`researchers. Over the years, I have helped secured in excess of $2M in
`
`external funding from NIH-EUREKA, DoD/ONR, the Idaho SBOE and other
`
`entities as a Principal Investigator (PI) or co-PI. I am a co-inventor on eight
`
`patents (five provisional patents and three PCT applications—two of which have
`
`issued). Our DNA- targeting Invader technology has been licensed to a US biotech
`
`company for use in diagnostic assays in animal reproduction technology.
`
`
`
`2
`
`
`
`Oxford, Exh. 1002, p. 7
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`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`9.
`
`I am an active reviewer of manuscripts and grant proposals submitted
`
`
`
`to international journals and agencies (150+ reviews) and serve on the Scientific
`
`Advisory Council of the Oligonucleotide Therapeutics Society. I have been a
`
`consultant for Isis Pharmaceuticals (now Ionis Pharmaceuticals), the leading
`
`company in the discovery and development of antisense oligonucleotide drugs, and
`
`Minitube of America (now MOFA Global), a major provider of advanced animal
`
`reproduction technologies.
`
`10. My accomplishments have been recognized in the form of three
`
`awards from the University of Idaho: the 2010 College of Science, Early Career
`
`Faculty Award; the 2012 President’s Mid-career Faculty Award; and the 2013
`
`Excellence in Research and Creative Activity Award.
`
`II. LEGAL UNDERSTANDING
`11. My opinions are also informed by my understanding of the relevant
`
`law. I understand that the patentability analysis is conducted on a claim-by-claim
`
`and element-by-element basis, and that there are several possible reasons that a
`
`patent claim may be found to be unpatentable.
`
`12.
`
`I understand that earlier publications and patents may act to render a
`
`patent unpatentable for one of two reasons: (1) anticipation and (2) obviousness.
`
`
`
`3
`
`
`
`Oxford, Exh. 1002, p. 8
`
`

`

`
`
`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`A. Anticipation
`13. First, I understand that a single prior art reference, article, patent or
`
`publication “anticipates” a claim if each and every element of the claim is
`
`disclosed in that prior art reference, arranged as in the claim. I further understand
`
`that, where a claim element is not explicitly disclosed in a prior art reference, the
`
`reference may nonetheless anticipate a claim if the missing claim element is
`
`necessarily present in the apparatus or a natural result of the method disclosed, i.e.,
`
`the missing element is “inherent.”
`
`B. Obviousness
`14. Second, I understand that the prior art may render a patent claim
`
`“obvious.” I understand that two or more prior art references (e.g., prior art
`
`articles, patents or publications) that each disclose fewer than all elements of a
`
`patent claim may nevertheless be combined to render a patent claim obvious if the
`
`combination of the prior art collectively discloses all elements of the claim and one
`
`of ordinary skill in the art at the time would have been motivated to combine the
`
`prior art in such a way. I understand that this motivation to combine need not be
`
`explicit in any of the prior art, but may be inferred from the knowledge of one of
`
`ordinary skill in the art at the time the patent was filed. I also understand that one
`
`of ordinary skill in the art is not an automaton, but is a person having ordinary
`
`creativity. I further understand that one or more prior art references, articles,
`
`
`
`4
`
`
`
`Oxford, Exh. 1002, p. 9
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`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`patents or publications that disclose fewer than all of the elements of a patent claim
`
`may render a patent claim obvious if including the missing element would have
`
`been obvious to one of skill in the art (e.g., the missing element represents only an
`
`insubstantial difference over the prior art or a reconfiguration of a known system).
`
`15. Under the doctrine of obviousness, I understand that a claim may be
`
`invalid if the differences between the invention and the prior art are such that the
`
`subject matter as a whole would have been obvious at the time the invention was
`
`made to a person of ordinary skill in the art to which the subject matter pertains.
`
`16.
`
`I understand that obviousness is based on the scope and content of the
`
`prior art, the differences between the prior art and the claim, the level of ordinary
`
`skill in the art, and secondary indicia of obviousness and non-obviousness to the
`
`extent they exist.
`
`17.
`
`I understand that any evidence of secondary indicia of non-
`
`obviousness should be considered when evaluating whether a claimed invention
`
`would have been obvious to one of ordinary skill at the time of invention. These
`
`secondary indicia of non-obviousness may include, for example:
`
` a long felt but unmet need in the prior art that was satisfied by the
`
`claimed invention;
`
` commercial success of processes claimed by the patent;
`
` unexpected results achieved by the invention;
`
`
`
`5
`
`
`
`Oxford, Exh. 1002, p. 10
`
`

`

`
`
`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
` praise of the invention by others skilled in the art;
`
` the taking of licenses under the patent by others; and
`
` deliberate copying of the invention.
`
`18.
`
`I understand that there must be a relationship between any such
`
`secondary indicia and the claimed invention.
`
`19.
`
`It is also my understanding that there are additional considerations
`
`that may be used as further guidance as to when the above factors will result in a
`
`finding that a claim is obvious, including the following:
`
` the claimed invention is simply a combination of prior art elements
`
`according to known methods to yield predictable results;
`
` the claimed invention is a simple substitution of one known element
`
`for another to obtain predictable results;
`
` the claimed invention uses known techniques to improve similar
`
`devices or methods in the same way;
`
` the claimed invention applies a known technique to a known device or
`
`method that is ready for improvement to yield predictable results;
`
` the claimed invention would have been “obvious to try” choosing
`
`from a finite number of identified, predictable solutions, with a
`
`reasonable expectation of success;
`
`
`
`6
`
`
`
`Oxford, Exh. 1002, p. 11
`
`

`

`
`
`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
` there is known work in one field of endeavor that may prompt
`
`variations of it for use in either the same field or a different one based
`
`on design incentives or other market forces if the variations would
`
`have been predictable to one of ordinary skill in the art;
`
` there existed at the time of invention a known problem for which there
`
`was an obvious solution encompassed by the patent’s claims; and
`
` there is some teaching, suggestion, or motivation in the prior art that
`
`would have led one of ordinary skill to modify the prior art reference
`
`or to combine prior art reference teachings to arrive at the claimed
`
`invention.
`
`20. Finally, I understand that a claim may be deemed invalid for
`
`obviousness in light of a single prior art reference, without the need to combine
`
`references, if the elements of the claim that are not found in the reference can be
`
`supplied by the knowledge or common sense of one of ordinary skill in the
`
`relevant art.
`
`C. Claim Construction
`21.
`I have been instructed by counsel on the law regarding claim
`
`construction and patent claims, and understand that a patent may include two types
`
`of claims, independent claims and dependent claims. An independent claim stands
`
`alone and includes only the limitations it recites. A dependent claim can depend
`
`
`
`7
`
`
`
`Oxford, Exh. 1002, p. 12
`
`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`from an independent claim or another dependent claim. I understand that a
`
`dependent claim includes all the limitations that it recites in addition to all of the
`
`limitations recited in the claim from which it depends.
`
`22.
`
`It is my understanding that the broadest reasonable interpretation of a
`
`claim term may be the same as or broader than the construction of a term under the
`
`Phillips standard, but it cannot be narrower.
`
`23.
`
`I understand that to determine how a person of ordinary skill would
`
`understand a claim term, one should look to those sources available that show what
`
`one of skill in the art would have understood disputed claim language to mean.
`
`Such sources include the words of the claims themselves, the remainder of the
`
`patent’s specification, the prosecution history of the patent (all considered
`
`“intrinsic” evidence), and “extrinsic” evidence concerning relevant scientific
`
`principles, the meaning of technical terms, and the state of the art.
`
`24.
`
`I understand that, in construing a claim term, one looks primarily to
`
`the intrinsic patent evidence, including the words of the claims themselves, the
`
`remainder of the patent specification, and the prosecution history.
`
`25.
`
`I understand that extrinsic evidence, which is evidence external to the
`
`patent and the prosecution history, may also be useful in interpreting patent claims
`
`when the intrinsic evidence itself is insufficient.
`
`
`
`8
`
`
`
`Oxford, Exh. 1002, p. 13
`
`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`26.
`
`I understand that words or terms should be given their ordinary and
`
`
`
`accepted meaning unless it appears that the inventors were using them to mean
`
`something else. In making this determination, the claims, the patent specification,
`
`and the prosecution history are of paramount importance. Additionally, the
`
`specification and prosecution history must be consulted to confirm whether the
`
`patentee has acted as its own lexicographer (i.e., provided its own special meaning
`
`to any disputed terms), or intentionally disclaimed, disavowed, or surrendered any
`
`claim scope.
`
`27.
`
`I understand that in general, a term or phrase found in the introductory
`
`words of the claim, the preamble of the claim, should be construed as a limitation
`
`if it recites essential structure or steps, or is necessary to give life, meaning, and
`
`vitality to the claim. Conversely, a preamble term or phrase is not limiting where a
`
`patentee defines a structurally complete invention in the claim body and uses the
`
`preamble only to state a purpose or intended use for the invention. In making this
`
`distinction, one should review the entire patent to gain an understanding of what
`
`the inventors claim they actually invented and intended to encompass by the
`
`claims.
`
`28.
`
`I understand that language in the preamble limits claim scope (i) if
`
`dependence on a preamble phrase for antecedent basis indicates a reliance on both
`
`the preamble and claim body to define the claimed invention; (ii) if reference to the
`
`
`
`9
`
`
`
`Oxford, Exh. 1002, p. 14
`
`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`preamble is necessary to understand limitations or terms in the claim body; or (iii)
`
`if the preamble recites additional structure or steps that the specification identifies
`
`as important.
`
`III. THE PRIOR ART
`A.
`Prior Art Considered
`29.
`In addition to the ’929 Patent, I have considered the following prior
`
`art patents, patent applications and printed publications. It is my understanding
`
`that all of these references pre-date the ’929 Patent.
`
`30.
`
`I have considered the following materials in forming my opinions:
`
`Title
`Exhibit
`1004 U.S. Patent Application Publication No. 2006/0063171 (“Akeson”)
`
`1005 U.S. Patent No. 6,087,099 (“Gupte”)
`
`1006 U.S. Patent Publication No. 2005/0142559 (“Makrigiorgos”)
`
`1007 Miner et al., Nucleic Acids Res., 32(17):e135 (2004) (“Miner”)
`
`1008 O’Dea and McLaughlin, Current Protocols in Nucleic Acid Chemistry
`
`5.3.1-5.3.8 (2000) (“O’Dea”)
`
`1009
`
`Sambrook, Fritsch and Maniatis, Molecular Cloning, A Laboratory
`
`Manual (1989, 2nd Ed.) (“Sambrook”)
`
`1010 U.S. Patent No. 5,795,782 to Church et al. (“Church”)
`
`
`
`10
`
`
`
`Oxford, Exh. 1002, p. 15
`
`

`

`
`
`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`1011 U.S. Patent No. 6,404,907 (“Gilchrist”)
`
`1012
`
`Sanger, “Determination of Nucleotide Sequences in DNA,” Science
`
`214:1205-1210 (1981) (“Sanger”)
`
`1013
`
`Prosecution History for U.S. Patent No. 9,738,929
`
`1014 U.S. Patent No. 6,936,433 (“Akeson ’433”)
`
`1016
`
`Struhl, “Cloning cookbook for the laboratory,” Nature 316:222 (July
`
`18, 1985) (“Struhl”).
`
`IV. LEVEL OF ORDINARY SKILL IN THE ART
`31.
`I understand that the person having ordinary skill in the art is a
`
`hypothetical person who is presumed to know the relevant prior art. I understand
`
`that the actual inventor’s skill is not determinative of the level of ordinary skill. I
`
`further understand the factors that may be considered in determining the level of
`
`skill include: the types of problems encountered in the art, prior art solutions to
`
`those problems; rapidity with which innovations are made; sophistication of the
`
`technology; and educational level of active workers in the field. I understand that
`
`not all such factors may be present in every case, and one or more of them may
`
`predominate.
`
`32.
`
`It is my opinion that a person of ordinary skill in the art in the field
`
`relevant to the ’929 Patent possesses a Ph.D. or an equivalent amount of
`
`
`
`11
`
`
`
`Oxford, Exh. 1002, p. 16
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`

`

`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
`
`experience in molecular biology, genetics, biochemistry or a related field. It is my
`
`opinion that the person of ordinary skill in the art would have knowledge of DNA
`
`sequencing techniques including Maxam-Gilbert and Sanger sequencing, as well as
`
`other techniques available on or before the priority date of the ’929 Patent such as
`
`Applied Biosystems/Life Technologies, Solexa/Illumina, Helicos, and PacBio
`
`sequencing.
`
`V. BACKGROUND OF SEQUENCING NUCLEIC ACIDS USING
`NANOPORES AND MOLECULAR MOTORS
`A. Nanopore Sequencing Using Enzyme Chaperones
`33. The notion of using nanopores to sequence polynucleotides, such as
`
`DNA and RNA, has been around for decades. A typical nanopore sequencing
`
`system generally contains two chambers that are connected through a nanopore—a
`
`hole with a diameter on the order of one nanometer—embedded in a substrate.
`
`See, e.g., Ex. 1010, Figure 1; Ex. 1004, Figure 2D, Figure 10C.
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`12
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`Oxford, Exh. 1002, p. 17
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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
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`Ex. 1010, Figure 1.
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`During sequencing, a polynucleotide of interest, either double-stranded or single-
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`stranded,1 is added into one of the chambers, and an electric field is then applied
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`across the substrate, generating an electric force that pulls the negatively charged
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`polynucleotide through the nanopore. Id., 2:9-57. As individual nucleotides of the
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`polynucleotide pass through the nanopore, each nucleotide transiently blocks the
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`nanopore, causing a change of ionic current and producing an electric signal that
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`correlates to the size, shape and identity of the nucleotide. Id., 6:14-22; see also
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`1 Church discloses a method “to establish a voltage gradient across a membrane
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`containing a channel (e.g., α-hemolysin) through which a single stranded or double
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`stranded DNA is electrophoresed.” Ex. 1010, 7:31-34.
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`13
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`Oxford, Exh. 1002, p. 18
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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
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`id., Figure 3. Measuring such nucleotide-distinct signals allows one to determine
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`the nucleotides that make up the polynucleotide in a sequential manner, in other
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`words, the nucleotide sequence of the polynucleotide. Id.
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`34.
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` The use of enzyme chaperones, also referred to herein as “molecular
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`motors,” in nanopore sequencing was well recognized as of the priority date of the
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`’929 patent. Exemplary molecular motors that can be used with nanopore
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`sequencing include DNA polymerases, RNA polymerases, tRNA, ribosomes,
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`exonucleases and helicases. Id., 4:28-30; Ex. 1004, ¶¶[0013], [0047], claim 3.
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`Such molecular motors bind to the polynucleotide of interest and assists its
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`translocation through the nanopore, thus allowing the sequencing of the
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`polynucleotide. Ex. 1010, 4:11-30; see also id., Figure 2. Moreover, the
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`molecular motor has the advantage of controlling the rate of a polynucleotide
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`passing through a nanopore, resulting in “a higher degree of resolution with regard
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`to both the composition and spatial relationship between nucleotide units within a
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`polynucleotide.” Ex. 1004, ¶¶[0007], [0019], [0036]. For example, it was well
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`known that the rate of movement may be altered by changing reaction conditions,
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`e.g., “a change in voltage, pH, temperature, viscosity, or concentration of a
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`chemical species (e.g., ions, cofactors, energy sources, or inhibitors).” Id.,
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`¶[0009].
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`14
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`Oxford, Exh. 1002, p. 19
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`
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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
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`B.
`Sequencing of Complementary Strands to Improve Accuracy
`35. Before the priority date of the ’929 patent, it was well recognized that
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`an increased rate of accuracy in polynucleotide sequencing can be obtained by
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`determining the sequences of both complementary strands of a double-stranded
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`polynucleotide. See Ex. 1005, Ex. 1009, Ex. 1011 and Ex. 1012. As disclosed in
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`Sambrook, a widely-known manual on DNA sequencing and colloquially referred
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`to as “The Bible,”2 an increased rate of accuracy can be obtained by sequencing
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`both strands of the target DNA, comparing sequences of both strands and resolving
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`“all ambiguities and discrepancies.” Ex. 1009 (“Sambrook”), 13.20. Gilchrist,
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`which was published in 2002, discloses a method of improving sequencing
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`accuracy that includes obtaining forward and reverse data sets, which represent the
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`sequences of both complementary strands of a DNA molecule, and comparing
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`these sequences to determine the correct sequence of the DNA molecule. Ex.
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`1011, 2-61-3:7, claim 1; see also Ex. 1005 (“Gupte”), 1:13-15 (disclosing that “it is
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`common to sequence both strands of DNA to minimize any errors which may
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`occur in the sequencing”).
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`36. Even as early as 1980, sequencing of both strands of a double-
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`stranded nucleic acid was known to improve the accuracy of the sequencing. This
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`2 See, e.g., Struhl, Nature 316:222 (July 18, 1985) (Ex. 1016).
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`15
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`Oxford, Exh. 1002, p. 20
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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
`
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`is evidenced by the Nobel Laureate speech given Frederick Sanger in 1980, in
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`which he states “it [is] necessary to determine the sequence of each region on both
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`strands of the DNA” to minimize errors during DNA sequencing. Ex. 1012, 1207-
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`1208.
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`VI.
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` OVERVIEW OF THE ’929 PATENT
`A. Overview of the Subject Matter of the ’929 Patent
`37. The disclosure of the ’929 patent is primarily directed to methods for
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`performing intermittent detection during sequencing techniques that use optically
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`detectable labeling groups. Ex. 1001, 2:46-54, 5:19-40, 8:31-35, 20:15-36.
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`According to the ’929 patent, “one drawback to the use of optically detectable
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`labeling groups is that prolonged exposure of chemical and biochemical reactants
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`to [] light sources, alone, or when in the presence of other components, e.g., the
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`fluorescent groups, can damage such reactants.” Id., 1:55-59. The ’929 patent
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`states that the disclosed methods are useful “for mitigating photo-induced damage
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`in an illuminated reaction by subjecting the illuminated reaction to intermittent
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`illumination rather than constant illumination,” “particularly [for] reactions that
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`employ fluorescent or fluorogenic reactants.” Id., 5:19-22, 20:15-22.
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`38. The ’929 patent further describes nucleic acid templates that are
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`completely contiguous and include “a double-stranded portion comprised of two
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`complementary sequences and two single-stranded linking portions.” Id., 66:22-
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`16
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`Oxford, Exh. 1002, p. 21
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`Declaration of Dr. Patrick Hrdlicka in Support of
`Petition for IPR of U.S. Patent No. 9,738,929
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`27. The ’929 patent also includes a series of paragraphs and figures incorporated
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`into the specification via a preliminary amendment from Provisional