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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 6 Jan. 2026 has been entered.
Claims 45-50, 55-58, 63-69 and 72-81 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Any rejection not reiterated herein has been withdrawn.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 6 Jan. 2026 have been considered but are not persuasive.
Applicant argues that it was known in the art (as evidenced by Wang) that silver binds to an inhibits motor proteins such as those taught by Croquette, and that one of ordinary skill would thus not expect a reasonable expectation of success in combining the silver ion-based method of Mansuripur with motor protein translocation as taught by Croquette. This is not persuasive because the method of Mansuripur comprises binding a polynucleotide strand with ionic silver (Ag+) on a cis side of a membrane/nanopore (Mansuripur, left side of membrane in Fig. 7d), and irradiating the strand so as to cause formation of silver nanoclusters on the strand within the trans chamber as the strand is being translocated through the nanopore (Mansuripur, [0089]; Fig. 7D). Croquette teaches a similar method of translocating a polynucleotide through a nanopore wherein a motor protein on the cis side of the membrane aids in the translocation (Croquette, Figs. 1-4; [0093]). Thus, the motor protein in the method of the cited combination would be exposed to a polynucleotide complexed with ionic silver on the cis side of the membrane/nanopore. The Wang reference cited by Applicant shows that silver nanoparticles bind to and inhibit RNA polymerase (e.g., Wang, p. 4172, 1st ¶). Wang specifically distinguishes such nanoparticle effects from those of ionic silver, which was shown not to inhibit RNA polymerase transcription activity (Wang, p. 4175, 1st full ¶; p. 4177, 1st full ¶). Consistent with this, Funai evidences that DNA polymerase has catalytic activity/processivity in the presence of silver ions (Funai, p. 6624, right col.). Thus, Applicant has not provided any evidence indicating that one of ordinary skill would expect the ionic silver present on the cis side of the membrane in contact with the motor protein to interfere with the motor protein activity in the method of the cited combination (see MPEP 2145 - If a prima facie case of obviousness is established, the burden shifts to the applicant to rebut the prima facie case; arguments presented by applicant cannot take the place of factually supported objective evidence).
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.
Regarding claims 45-47, 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 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 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 the nanoreactor is an ion channel in a lipid membrane 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]). 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 claim 55, 72-74 and 76-78, Mansuripur teaches that the writing step is carried out using a nanoreactor comprising a membrane ion channel/nano-pore ([0086]). Mansuripur further 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 it would have been obvious to use such channel to carry out the writing process via deposition of metal nanoclusters. α-hemolysin is a β-barrel protein pore (see US20160319344 (cited below), [0068]).
Regarding claims 56, 57 and 75, 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.
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
No claim is allowed.
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/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657