DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant's submission filed on 14 July 2026 has been entered.
Claims 45-50, 56-58, 63-69, 73-75 and 77-81 are currently pending and are considered here with respect to the elected species of a constant rate of moving the polynucleotide strand, moving the polynucleotide strand continuously, selectively modifying the strand by controlling the number of nucleotides that are modified, a transmembrane protein pore as the nanopore, and electromagnetic radiation as the reaction condition.
Any rejection not reiterated herein has been withdrawn.
Response to Arguments
Applicant’s arguments in the Response of 14 July 2026 have been considered but are not persuasive.
Applicant argues that nanoclusters formed in the cited combination do not comprise “selectively chemically modifying” the polynucleotide. This has been addressed in the new grounds of rejection below.
Applicant further argues that the nanocluster-based Write Mechanism 4 of Mansuripur does not teach use of a transmembrane protein pore, and that the transmembrane protein pore limitation is only met by combining distinct embodiments of Mansuripur using hindsight reasoning. This is not persuasive because Mansuripur teaches using a transmembrane ion channel in Write Mechanism 4 and further teaches use of an “α-hemolysin ion-channel-forming protein” nanopore for a related read function, and it would have been obvious to use such an α-hemolysin pore as the transmembrane ion channel in forming the silver nanoclusters (see modified 103 rejection below for more detailed analysis).
Applicant further teaches that Mansuripur teaches that Write Mechanism 4 uses a walled chamber rather than a membrane, and use of a membrane would change the principal of operation. This is not persuasive because Mansuripur teaches that Write Mechanism 4 uses a transmembrane ion channel (see 103 rejection, below), and as such it would have been obvious to use a membrane for at least part of the barrier separating the cis and trans sides of the chamber in Write Mechanism 4. Moreover, Mansuripur further describes a chamber in which a “partitioning wall has another small hole in which a [α-hemolysin] nano-pore 162 embedded in lipid membrane 155 has been inserted” ([0068]). Thus, the teaching of a “wall” in Write Mechanism 4 does not preclude use of a transmembrane protein pore.
Applicant further argues that the teaching in Croquette that the rate of voltage-driven translocation is too fast and uncontrolled is limited to read operations, and that Croquette does not mention write operations such as that of Mansuripur. Applicant also argues that Mansuripur teaches voltage-driven translocation without providing any indication that such would be insufficient for write operations. This is not persuasive because Croquette teaches that the voltage driven translocation method suffer from “uncontrolled DNA strand electrophoresis through nanopores” ([0005]). While Croquette does not mention write operations, Mansuripur teaches that the nanocluster write mechanism relies on timing irradiation pulses with the translocation ([0090] - “Upon detection of a change in ion current signifying the initiation of translocation, the trans side of the channel will be irradiated with a short laser pulse (<1 μs duration) corresponding approximately to the residence time of a nucleotide in the channel.”) The “uncontrolled” translocation noted by Croquette would thus be problematic for the write mechanism of Mansuripur, and one of ordinary skill in the art would have reasonably sought a more controlled translocation using the means taught by Croquette.
Claim Rejections - 35 USC § 112 (new matter)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 45-50, 56-58, 63-69, 73-75 and 77-81 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 45 has been amended to recite “selectively chemically modifying nucleotides … wherein the selective chemical modifications comprise modifications to the backbone, the sugar, and/or the bases of the nucleotides”. To the extent Applicant might argue that the term “chemically modifying” requires a covalent structural modification of the polynucleotide, the instant specification does not describe such a modification coextensive in scope with the claims. The specification does not use the term “chemical modification” or its equivalent with respect to the polynucleotide of the instant method. The term “chemical modification” is used repeatedly with respect to other elements of the invention such as the constituents of the membrane (Published Spec. US20220042967, [0314], [0326]), but broader terminology (such as modification by “chemical means”; [0038]) is used with respect to the polynucleotide. The specification describes particular types of modifications, including chain scission, side chain modification and addition of chemical groups ([0247]), but the the claims are not limited to such modifications. As such, the claims comprise new matter.
For the purpose of applying prior art, the claims are construed below to give the term “chemically modifying” its broadest reasonable interpretation consistent with the specification, such that the modification is not limited to a covalent structural modification of the polynucleotide.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 45-50, 55-58, 63-69 and 72-81 are rejected under 35 U.S.C. 103 as obvious over the combination of US20040001371 to Mansuripur et al. (cited in IDS of 27 May 2022) in view of US20160319344 to Croquette et al., as evidenced by New et al., Nanoscale 8.41 (2016): 17729-17746.
Regarding claims 45-47 and 74, Mansuripur teaches a method of encoding data on a polynucleotide (e.g., DNA) strand, comprising: (A) moving the polynucleotide strand with respect to a nanoreactor; and (B) selectively chemically modifying portions of the polynucleotide strand as they move through the nanoreactor; wherein the pattern of selective modifications on the polynucleotide strand encodes data on the strand (entire doc, including [0012]-[0016]; [0033]-[0044]; [0084]-[0091]; Fig. 7d). The method comprises using the polynucleotide strand as a medium/support structure onto which data is written by selective deposition of metal nanoclusters (e.g., Ag+) onto sequential portions of the strand, such that the overall length and base composition of the strand is not altered ([0084]-[0091]; Fig. 7d). The strand can be a single-stranded polynucleotide ([0086]).
Regarding the recitation in claim 45 that the polynucleotide is moved through a transmembrane protein nanopore, Mansuripur teaches that the nanoreactor is an ion channel which separates a reaction chamber between a cis side from which the unmodified strand is fed to a trans side in which the strand is modified with the metal nanoclusters via application of reaction conditions that cause deposition of the nanoclusters ([0084]-[0091]; [0107]-[0109]; Fig. 7d). The strand is translocated through the channel via a flow of current through the channel ([0090]). The portion of Mansuripur dedicated to the metal nanocluster-based writing mechanism (“Write Mechanism 4”) refers to use of an “ion channel” which is also referred to as a ”transmembrane channel” for both writing and reading the nanocluster-encoded data ([0089], [0091]). Other portions of Mansuripur describe use of an “α-hemolysin ion-channel-forming protein” nanopore for writing and reading functions ([0068]; [0075]; [0107]-[0109]), and it would have been obvious to use the same type of α-hemolysin ion-channel nanopore for the transmembrane ion channel in Write Mechanism 4. One of ordinary skill would have had a reasonable expectation of success in doing so because Mansuripur teaches use of such a hemolysin transmembrane protein nanopore for applications involving translocation of the polynucleotide from a cis to a trans side of a membrane/barrier using an ion current through the channel in the same manner as in Write Mechanism 4 (e.g., Read Mechanism 1 at [0105]-[0114]; see also, [0086] stating that the nanoclusters can be read via a mechanism as described in Read Mechanism 1).
Regarding the recitation in claim 45 of “selectively chemically modifying nucleotides … wherein the selective chemical modifications comprise modifications to the backbone, the sugar, and/or the bases of the nucleotides”. New evidences that Ag+ ions bind strongly to specific sites (N7 or purines, N3 of pyrimidines) of polynucleotide bases (New, p. 17732, 1st full ¶; also, under 4.1.1.), and thus the method of Mansuripur would result in modification of the bases of the nucleotides. The term “chemically modifying” is not expressly defined in the specification and is given its broadest reasonable interpretation consistent with the specification (see MPEP 2111). While the specification does not use the term “chemical modification” or its equivalent with respect to the polynucleotide of the instant method, the specification describes modifying the polynucleotide “by chemical means” (Published Spec. US20220042967, [0038]) including the use of metal ions as a means for modification (Spec., [0256]). Thus, “chemically modifying” is construed herein to include any modification involving chemical means such as metal ions. Mansuripur teaches modifying the polynucleotide via nanocluster formation via chemical means wherein Ag+ ions are reduced to form the nanoclusters ([0090]), and such modification is “selectively chemically modifying” the polynucleotide.
Regarding claim 48, the method of Mansuripur would result in the modification of at least one nucleotide and one of ordinary skill would have recognized that the method could be carried out for any desired number of modifications depending on the data content being encoded.
Regarding claims 49-50, Mansuripur teaches that a polynucleotide strand can be translocated through an ion channel by applying an electric potential across the membrane such that a current flows through the channel which translocates the charged polynucleotide strand ([0056]; [0090]; [0105]-[0110]; Fig. 8a-8b), and it would have been obvious to utilize such method for translocating the strand during the writing of metal nanoclusters onto the strand. Applying a constant electric potential across the membrane would lead to a continuous current flow and a continuous/constant translocation of the strand through the channel.
Regarding claims 56, 57, 75 and 78, Mansuripur teaches that the metal deposition reaction can be carried out in the internal volume of the nano-pore and the volume surrounding the nanopore ([0089]-[0091]; Fig. 7d). Regarding claim 75, Mansuripur teaches deposition of silver nanoclusters of about 10 nm size and describes polynucleotide strands having a length of over 10 µm ([0086]-[0087]), and it would have been obvious to use a trans chamber surrounding the nanopore having sufficient size/volume (e.g., at least tens of microns, providing for a nanovolume extending at least 30 nm from the nanopore) to accommodate a polynucleotide of such size. It is noted that claim 75 only requires that the nanopore has a space extending at least 30 nm from the nanopore, and does not require any specific step or structure within such range.
Regarding claim 58, Mansuripur teaches that the deposition of metal nanoclusters is selectively controlled by application of short laser light (electromagnetic radiation) pulses that correspond to the residence time of a nucleotide in the channel during translocation, wherein the pulses cause reduction of Ag+ ions via thermal reaction to form the nanoclusters ([0084]-[0091]; Fig. 7d). The timing of the light pulses allows for the controlled deposition of nanoclusters (controlling the number of nucleotides being modified) corresponding to the information that is being encoded ([0091]).
Regarding claims 63-65, and 79, Mansuripur teaches that the trans side of the nanoreactor is chemically modified with photosensitizer groups surrounding the nano-pore, such that excitation of the photosensitizer groups via irradiation causes the photosensitizer groups to transfer energy/radiation to the polynucleotide strand which reduces bound Ag+ atoms and forms the nanoclusters ([0089]-[0091]; Fig. 7d). Regarding claim 64, Mansuripur teaches use of photosensitizers such as rhodamine and cyanine dyes ([0089]) having excitation wavelengths in the visible range.
Regarding claims 66-68, 80 and 81, Mansuripur teaches that the method can further comprise a step of (C) determining the pattern of selective modifications on the polynucleotide strand by translocating the strand through a nanopore detector via a current (i.e. by applying a potential difference) running through the nanopore and monitoring the change (i.e. taking one or more measurements) in current as the strand passes through, wherein nanoclusters bound to the strand partially block the flow of current through the nanopore and result in a measurable change in the current indicative of the pattern/extent/presence of nanoclusters present on the strand ([0105]-[0110]; Fig. 8a-8b).
Regarding claim 69, Mansuripur teaches use of a transmembrane protein pore (α-hemolysin, a bacterial ion channel) for use in the write and read portions of the method ([0068]; [0107]-[0109]) and teaches that both the read and write processes involve translocating the strand through the nanopore via current flow through the nanopore resulting from an applied potential across the membrane ([0056]; [0090]; [0105]-[0110]; Fig. 8a-8b). It would have been obvious to one of ordinary skill to use the same nanopore for both the writing and reading steps, as doing so would allow for the entire process to be carried out using the same materials/apparatus. Using the same nanopore for both the writing and reading steps would have led to predictable results with a reasonable expectation of success because both the reading and writing steps use the same mechanism of translocating the strand via current flow generated using an electric potential, and as such the reading could be carried out by simply adding a current meter to the reaction chamber used for the writing process. Moreover, since the nanocluster deposition is controlled via irradiation, such deposition could be confined to the writing process and not interfere with the reading process.
Regarding claim 73 and 77, the α-hemolysin transmembrane protein pore taught by Mansuripur is a β-barrel protein pore (see US20160319344 (cited below), [0068]).
Claims 45-50, 55-58, 63-69 and 72-81 differ from Mansuripur in that: movement of the polynucleotide strand through the nanopore is controlled using a polynucleotide-handling enzyme.
Croquette teaches that methods such as that of Mansuripur in which a polynucleotide strand is translocated through an ion channel by application of an electric potential across a membrane comprising the nanopore are well known in the art and suffer from the limitation that the rate of strand translocation through the nanopore is too fast and uncontrolled (Croquette, [0001]-[0006]). Croquette teaches that the rate of translocation can be controlled by using a polynucleotide-handling enzyme, which can be a motor protein such as a polymerase, helicase, translocase or the like (i.e. the same type of motor proteins described in the instant specification; cf. published Spec. US20220042967, [0206]-[0234]) that limits the translocation rate according to the processivity rate of the enzyme (Croquette, [0011]-[0057]). The enzyme of Croquette is useful with the same type of transmembrane pore proteins as described in the instant specification (Croquette, [0058]-[0074]; cf. US20220042967, [0154]-[0175]).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to use the method of Mansuripur to encode data on a polynucleotide strand by translocating the strand through a nanopore and selectively depositing metal nanoclusters on the strand wherein the movement of the strand through the nanopore is controlled with a polynucleotide-handling motor enzyme as taught by Croquette because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to use a motor enzyme as taught by Croquette to control the translocation of the polynucleotide through the nanopore in the method of Mansuripur because Croquette teaches that methods such as Mansuripur that use an electric potential across a membrane to translocate polynucleotides through a nanopore suffer from the drawback of having a rate of translocation that is too fast and uncontrolled, and using a motor enzyme addresses this drawback by limiting the translocation rate according to the processivity rate of the enzyme. Using a motor enzyme as taught by Croquette to control the translocation of the polynucleotide through the nanopore in the method of Mansuripur would have led to predictable results with a reasonable expectation of success because Croquette teaches that the enzyme is useful for translocating polynucleotides across the same type of transmembrane protein nanopores as used in Mansuripur under substantially similar conditions of an applied electric potential. Moreover, Croquette teaches that the enzyme can be used to control translocation in sequencing methods similar to the read process of Mansuripur (cf. Croquette, [0075]-[0084] vs. Mansuripur, [0105]-[0114]).
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ROBERT J YAMASAKI whose telephone number is (571)270-5467. The examiner can normally be reached M-F 930-6 PST.
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/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657
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