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 .
Status of the Claims
The Amendment filed 03/27/2026 has been entered. Claims 21, 24-27, 43-44, 46, and 49-52 have been amended. Amended claims 25, 44, and 51 are withdrawn as being drawn to a non-elected species as outlined below. Claims 21, 24-28, and 41-54 are currently pending and claims 21, 24, 26-28, 41-43, 45-50, and 52-54 are examined herein.
Status of the Rejection
Applicant’s amendments to the Claims have overcome each objection and 112(b) rejections previously set forth in the Non-Final Office Action mailed 11/28/2025.
New grounds of objections are necessitated by the amendments as outlined below.
New grounds of rejection under 35 U.S.C. § 112(a), and under 35 U.S.C. § 112(b) are necessitated by the amendments as outlined below.
All 35 U.S.C. § 102 and 103 rejections from the previous office action are withdrawn in view of the Applicant’s amendment.
New grounds of rejection under 35 U.S.C. § 103 are necessitated by the amendments as outlined below.
Election/Restrictions
Upon consideration of the amended claims and the elected species A, claims 25, 44, and 51 are drawn to Species B since these claims have been amended to recite the limitation “further comprising: identifying, by the processing system via a sensor, individual components of the molecule during the first and second movements of the first and second portions of the molecule”, which is drawn to Species B, the embodiment of Fig. 20, as outlined in the restriction mailed on 09/20/2024 and 05/20/2025 and the instant specification which disclose “a device is provided, comprising: …at least two electrical terminals..and at least one sensor capable of identifying individual components of the macromolecule during movement” [Para. 000136 of the instant specification] and “in one embodiment, the device comprises a two terminal device with two pores and two controlling electrical terminals (see, e.g., FIG. 20) [Para. 00076 of the instant specification]. Species B includes one or more of components 2008A, 2008B, 2008C that can (individually or in combination with the others) recognize (or otherwise sense, detect, or identify) information encoded in the translocated molecules; the component(s) of the system for controlling translocation direction and/or speed and/or for recognizing, sensing, detecting or identifying the chemical structure of the analyte molecule (see, e.g., the dashed rectangles in FIG. 20 (2008A, 2008B, 2008C) [Paras. 00076-00077 of the instant specification]. Species A, the embodiment of Fig. 1A, does not include components 2008A, 2008B, 2008C which are used for identifying the individual components of the molecule during movement, and does not include two electrode terminals with at least one sensor for identifying individual components of the macromolecule during movement. Therefore, Claims 25, 44, and 51 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to non-elected Species B, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 11/20/2024 and 09/22/2025. See 37 CFR 1.142(b) and MPEP § 821.03.
Claim Objections
Claims 26-27, 46, and 50 are objected to because of the following informalities:
Claim 26, lines 1-2: please amend “DNA and further comprising:” to – DNA; [[and]] the method further comprising:—.
Claim 27, line 2: please amend “planar and wherein” to – planar; and wherein:—.
Claim 46, line 2: please amend “membrane and further comprising:” to – membrane; [[and]] the method further comprising:—.
Claim 50, line 4: please amend “membrane; and further comprising:” to – membrane; [[and]] the method further comprising:—.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 21, 24, 26-28, 41-43, 45-50, and 52-54 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, 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.
Regarding claim 21, claim 21 has been amended to recite “wherein a third portion of the molecule does not enter the first pore”. Applicant argues on page 10 that Gershow appears to be describing the entire molecule passing all the way through the pore of the membrane, which is distinct from the claimed features including where a third portion of the molecule does not enter the first pore. Applicant then refers to Fig. 2B of the instant specification for teaching “a third portion of the molecule does not enter the first pore”. However, it is clear from stage V on Fig. 2B that the entire molecule passes all the way through the first pore of the membrane, indicated by the arrow pointing left, the first pore being on the left side as it is the pore in which the first and second portion of the molecule first enter [see Figs. 2A and 2B and Para. 00045 of the instant specification which states “In FIG. 2B the DNA molecule enters the first nanopore in a folded conformation (I), subsequently traverses the first nanopore in single-file fashion (II), whereupon a different part of the molecule is captured by the second nanopore (III) in a folded fashion. Finally, the DNA reaches the trapped state (IV), and eventually slides out (V)”]. Therefore, the instant specification and the drawings do not support “wherein a third portion of the molecule does not enter the first pore” because the entire molecule, and thus all portions, enter/translocate through the first pore and slide out. Therefore, claim 21 is new matter. Claims 24, 26-28, and 41-42 are further rejected by virtue of its dependence upon claim 21.
Regarding claim 26, claim 26 has been amended to recite “facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane”. However, there is no mention of a third movement or third portion in the instant specification. Applicant appears to be combining the embodiments of Figs. 30 and 31 as Fig. 30 discloses “setting a second physical characteristic in a vicinity of the second pore to cause a second end of the molecule to be moved through the second pore” (see step 3004 of FIG. 30 ) and Fig. 31 discloses “responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore” (see step 3106 of FIG. 31). Therefore, the instant specification and the drawings do not support “facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane” in combination with “responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore” as required by the independent claim 21. Therefore, claim 26 is new matter. Claim 27 is further rejected by virtue of its dependence upon claim 26.
Regarding claim 43, claim 43 has been amended to recite “wherein a third portion of the molecule does not enter the first pore”. Applicant argues on page 10 that Gershow appears to be describing the entire molecule passing all the way through the pore of the membrane, which is distinct from the claimed features including where a third portion of the molecule does not enter the first pore. Applicant then refers to Fig. 2B of the instant specification for teaching “a third portion of the molecule does not enter the first pore”. However, it is clear from stage V on Fig. 2B that the entire molecule passes all the way through the first pore of the membrane, indicated by the arrow pointing left, the first pore being on the left side as it is the pore in which the first and second portion of the molecule first enter [see Figs. 2A and 2B and Para. 00045 of the instant specification which states “In FIG. 2B the DNA molecule enters the first nanopore in a folded conformation (I), subsequently traverses the first nanopore in single-file fashion (II), whereupon a different part of the molecule is captured by the second nanopore (III) in a folded fashion. Finally, the DNA reaches the trapped state (IV), and eventually slides out (V)”]. Therefore, the instant specification and the drawings do not support “wherein a third portion of the molecule does not enter the first pore” because the entire molecule, and thus all portions, enter/translocate through the first pore and slide out. Therefore, claim 43 is new matter. Claims 45-48 are further rejected by virtue of its dependence upon claim 43.
Regarding claim 46, claim 46 has been amended to recite “facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane, wherein the third movement of the third portion of the molecule results from adjusting a second physical characteristic in a vicinity of the second pore to cause the third portion of the molecule to enter the second pore”. However, there is no mention of a third movement or third portion in the instant specification. Applicant appears to be combining the embodiments of Figs. 30 and 31 as Fig. 30 discloses “setting a second physical characteristic in a vicinity of the second pore to cause a second end of the molecule to be moved through the second pore” (see step 3004 of FIG. 30 ) and Fig. 31 discloses “responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore” (see step 3106 of FIG. 31). Therefore, the instant specification and the drawings do not support “facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane, wherein the third movement of the third portion of the molecule results from adjusting a second physical characteristic in a vicinity of the second pore to cause the third portion of the molecule to enter the second pore” in combination with “responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore” [as required by the independent claim 43]. Therefore, claim 46 is new matter.
Regarding claim 49, claim 49 has been amended to recite “wherein a third portion of the molecule does not enter the first pore”. Applicant argues on page 10 that Gershow appears to be describing the entire molecule passing all the way through the pore of the membrane, which is distinct from the claimed features including where a third portion of the molecule does not enter the first pore. Applicant then refers to Fig. 2B of the instant specification for teaching “a third portion of the molecule does not enter the first pore”. However, it is clear from stage V on Fig. 2B that the entire molecule passes all the way through the first pore of the membrane, indicated by the arrow pointing left, the first pore being on the left side as it is the pore in which the first and second portion of the molecule first enter [see Figs. 2A and 2B and Para. 00045 of the instant specification which states “In FIG. 2B the DNA molecule enters the first nanopore in a folded conformation (I), subsequently traverses the first nanopore in single-file fashion (II), whereupon a different part of the molecule is captured by the second nanopore (III) in a folded fashion. Finally, the DNA reaches the trapped state (IV), and eventually slides out (V)”]. Therefore, the instant specification and the drawings do not support “wherein a third portion of the molecule does not enter the first pore” because the entire molecule, and thus all portions, enter/translocate through the first pore and slide out. Therefore, claim 49 is new matter. Claims 50 and 52-54 are further rejected by virtue of its dependence upon claim 49.
Regarding claim 49, claim 49 has been amended to recite “facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane, wherein the third movement of the third portion of the molecule results from adjusting a second physical characteristic in a vicinity of the second pore to cause the third portion of the molecule to enter the second pore”. However, there is no mention of a third movement or third portion in the instant specification. Applicant appears to be combining the embodiments of Figs. 30 and 31 as Fig. 30 discloses “setting a second physical characteristic in a vicinity of the second pore to cause a second end of the molecule to be moved through the second pore” (see step 3004 of FIG. 30 ) and Fig. 31 discloses “responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore” (see step 3106 of FIG. 31). Therefore, the instant specification and the drawings do not support “facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane, wherein the third movement of the third portion of the molecule results from adjusting a second physical characteristic in a vicinity of the second pore to cause the third portion of the molecule to enter the second pore” in combination with “responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore”. Therefore, claim 49 is new matter. Claims 50 and 52-54 are further rejected by virtue of its dependence upon claim 49.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 43, 45-48, and 50 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 43, claim 43 recites the limitation "the second pore" in the last line of the claim. There is insufficient antecedent basis for this limitation in the claim. Furthermore, it is unclear if the adjusting of the first physical characteristic is in the vicinity of the first pore, the second pore, or both, as claim 43 previously recited “adjusting a first physical characteristic in a vicinity of the first pore”. Therefore, the scope of claim 43 is indefinite. Claims 45-48 are further rejected by virtue of its dependence upon and because it fails to cure the deficiencies of claim 43.
Regarding claim 50, claim 50 has been amended to recite “applying opposing forces”. However, the scope of the term opposing forces is unclear, especially in light of the specification which shows the force applied in the same direction. The term “opposing” means opposite, however it is unclear how opposing forces are applied if they are both applied in the same direction [shown as going down]. Furthermore, it is unclear if the “first physical characteristic” and “second physical characteristic” of claim 49, on which claim 50 depends, is the same as the claimed “opposing forces” or different. Furthermore claim 50 recites “resulting in the molecule being taut against the membrane”. However, claim 49 previously recited “a first portion of the molecule”, “a second portion of the molecule”, and “a third portion of the molecule”. It is unclear if claim 50 refers to the first, second, and/or third portion of the molecule, where the entire molecule is taut against the membrane or only a portion.Therefore, the scope of claim 50 is indefinite.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 21, 24, 26, 28, 41-43, 45-47, 49-50, and 52-53 is/are rejected under 35 U.S.C. 103 as being unpatentable over Royyuru et al. (US20150316504A1) in view of Sigalov et al. (Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor, Nano Letters, 2008, 8, 1, Pages 56-63) and Gershow et al. (US20090136958A1).
Regarding claim 21, a method (Royyuru teaches a method [see e.g., Abstract, Para. 0003, Fig. 2 and 4]) comprising:
detecting by a processing system including a processor a first entry, into a first pore located in a membrane, of a first portion of a molecule (Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018]. Royyuru further teaches measuring “detecting” the tunneling current via ammeter 205a a first entry into a first nanopore 102 [the ammeter is controlled by the computer 500, and thus the computer detects the first entry by measuring the tunneling current via the ammeter] located in a membrane 101, of a base “first portion” on the single strand 105 of the double strand molecule 107 to identify and sequence each individual base “portion” passing/translocating through the first nanopore 102 [Paras. 0037-0040 and 0054, Fig. 2 and Fig. 5]),
wherein the membrane has a first side and a second side (Royyuru teaches the membrane 101 has a first side [source side] and a second side [sink side] [Fig. 2, Paras. 0037-0041]), and
wherein the first pore extends from the first side of the membrane to the second side of the membrane (Royyuru teaches the first nanopore 102 extends from the first side [source side] to the second side [sink side] of the membrane 101 [Fig. 2, Paras. 0037-0041]);
detecting by the processing system a second entry, into the first pore, of a second portion of the molecule (Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018]. Royyuru further teaches measuring “detecting” the tunneling current via ammeter 205a a second entry into a first nanopore 102 as the single strand 105 passes through and translocates through the first nanopore 102 [the ammeter is controlled by the computer 500, and thus the computer detects the second entry by measuring the tunneling current via the ammeter] located in a membrane 101, of another individual base “second portion” on the single strand 105 of the double strand molecule 107 to identify and sequence each individual base “portion” passing/translocating through the first nanopore 102 [Paras. 0037-0041 and 0054, Fig. 2 and Fig. 5])
wherein the first portion and the second portion are portions of the molecule that is a single molecule (Royyuru teaches each individual base of the single strand 105, which includes a first “base” portion and second “base” portion as outlined in the rejection above, are portions of the double strand molecule 107 that is a single molecule [Fig. 2, Paras. 0037-0041])
wherein a third portion of the molecule does not enter the first pore (Royyuru teaches a base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 and does not enter/pass through the first nanopore 102 [Fig. 2, Paras. 0037-0040]; and
Royyuru does not explicitly disclose responsive to the detecting of the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule.
Sigalov teaches back-and-forth motion of DNA strands through a pore and a strategy for sequencing DNA in a nanopore using an electric field that alternates in a silicon membrane by applying an external electric bias across the membrane to drive a single DNA molecule strand back and forth through the pore [Abstract, Fig. 1 and Page 56, Col. 2, Para. 1]. Figures 2a-g illustrate DNA’s back-and-forth motion during one translocation cycle, where an alternating electric field [e.g., voltage bias: V+ = 20 V switched to V- = -20 V, Fig. 2h] can force DNA to move by exactly n nucleotides back and forth and when applied to a DNA fragment, produce repetitive motion of that fragment “portion” back-and-forth through the pore’s constriction [corresponding to a first movement of a first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule] [Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph].
Gershow teaches a molecular capture and recapture system with data analysis to select a nucleotide fragment “first portion” to be sequenced and the number of times that fragment is sequenced. The molecular capture and recapture system enables the repeated analysis of a selected nucleotide fragment “first portion” a selected number of times by a capture-recapture sequence [corresponding to a first movement of the first portion of the molecule back out of the first pore], followed by a repeated analysis of a next nucleotide fragment “second portion” [corresponding to a second movement of the second portion of the molecule back out of the first pore], until all nucleotide fragments “portions” in a solution under study have been analyzed [Para. 0077, 0073]. With real-time data analysis, the system can be controlled to initiate and continue a molecule's analysis, to terminate a molecule's analysis, or to re-initiate a molecule's analysis [Para. 0077]. Gershow further teaches it is well known that certain sequences in the genome are more difficult to read, and produce a lower quality read-out, than other sequences in general, and if an initial number of molecular fragment translocations, of an individual nucleotide fragment “portion” is determined by real-time software to have produced an incomplete or a poor-quality read-out [corresponding to responsive to the detecting of the first entry into the first pore and the second entry into the first pore], the recapture system can be controlled to promptly recapture that fragment to be re-sequenced a number of additional times as-required to produce a desired read-accuracy [corresponding to facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore], where a molecule can be recaptured by, e.g., reversing the voltage bias between the reservoirs [the applied voltage bias corresponding to wherein the first and second movement are based on application of force on the molecule] [Para. 0076, 0072]. One of ordinary skill in the art would recognize that a software would inherently include a processing system with a processor wherein the software is stored and installed for facilitating/executing the software’s programmed instructions. To recapture the molecule, the driving force across the nanopore is reversed and the recaptured molecule, now having translocated the nanopore in the reverse of its original direction, can then be captured a third time by restoring the driving voltage to its original polarity, producing an electrophoretic force again toward the nanopore [Fig. 1A-1F and Para. 0027-0030].
Given the teachings of Sigalov regarding sequencing DNA in a nanopore using an electric field that alternates in a silicon membrane to force DNA to move by exactly n nucleotides back and forth through a nanopore, it would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify the method, including voltage source 115 with electrodes 111 and 112, and processing system, which detects the first and second entry into the first pore, of Royyuru, such that responsive to the detecting of the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule, by reversing the voltage bias applied by the voltage source at the electrodes, as taught by Gershow and Sigalov, since Gershow teaches it would be beneficial because it is well known that certain sequences in the genome are more difficult to read, and produce a lower quality read-out, than other sequences in general and promptly recapturing a fragment to be re-sequenced a number of additional times as-required produces a desired read-accuracy [Para. 0076 of Gershow]. Furthermore, the use of a known technique (i.e., responsive to detecting entry of a first and second portion/nucleotide into a nanopore, facilitating by software re-sequencing and recapture of the first and second nucleotides back out of the first pore, taught by Gershow, and repeated back-and-forth motion of DNA nucleotides by alternating voltage bias, taught by Sigalov) to improve methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143 [I][C]).
Regarding claim 24, the method of claim 21, wherein the force results from adjusting a first physical characteristic in a vicinity of the first pore to cause the first portion of the molecule to be backed out of the first pore and the second portion of the molecule to be backed out of the first pore (Modified Royyuru as outlined in the rejection of claim 21 above yields the force results from reversing a voltage bias “adjusting a first physical characteristic” by the voltage source 115 including electrodes 111 and 112 in the reservoirs to cause the first portion and second portion of the molecule to be backed out of the first pore 102/translocate in the reverse direction to be recaptured and re-sequenced, and this adjusting of the electric field “physical characteristic” is in a vicinity of the first pore 102, because the voltage bias is applied to the reservoirs through the electrodes 111 and 112, and the first pore 102 joins the two reservoirs, and thus is in a vicinity of/near the first pore 102 as seen in Fig. 2 of Royyuru [see rejection of claim 21 above; Royyuru: Fig. 2 and Para. 0024, 0026; Sigalov: Abstract; Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph; Gershow: Para. 0076-0077, 0072-0073; 0027-0030; Fig. 1A-1F]. The examiner notes the electric field/voltage bias is the same physical characteristic disclosed in the instant specification [see e.g., Para. 000123 of the instant specification which states a physical characteristic in a vicinity of a pore can be an electric field that is changed near the pore]).
Regarding claim 26, the method of claim 21, wherein the molecule comprises DNA (Royyuru teaches the double strand molecule is double strands of DNA [Para. 0002, 0004, 0064-0065]) and further comprising:
facilitating, by the processing system, a third movement of the third portion of the molecule into a second pore of the membrane (Modified Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018 of Royyuru]. Modified Royyuru as outlined in the rejection of claim 21 above yields the first and second movements [see rejection of claim 21 above]. Modified Royyuru further teaches the base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 [corresponding to a third movement] of the membrane 101 and this is facilitated by the processing system which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a third portion the molecule into the nanopore 103] [Fig. 2 and 5, Paras. 0037-0040, 0054-0063, 0026, 0018 of Royyuru]).
Regarding claim 28, the method of claim 21, wherein the membrane is a solid-state membrane (Royyuru teaches the membrane 101 may be silicon, silicon dioxide or any insulating material, and thus is a solid-state membrane as seen in Fig. 2 [Para. 0017 and Fig. 2]).
Modified Royyuru does not explicitly disclose that comprises SiN.
Gershow teaches a nanopore formed in a solid-state membrane where the membrane can be provided as, e.g., a nitride, such as SiNx [corresponding to silicon nitride], an oxide, or other insulating structure that achieves electrical insulation between the two reservoirs, and in example 1 discloses a SiN membrane [Para. 0094-0095 and Fig. 1].
It would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to substitute the insulating material of the solid-state membrane of Modified Royyuru with silicon nitride, as taught by Gershow, since Gershow teaches this suitable alternative material for forming a solid-state membrane with a nanopore and it would be beneficial for achieving electrical insulation between the two reservoirs [Para. 0094-0095 of Gershow]. Furthermore, the claimed limitations are obvious because the substitution of one known element for another yields predictable results to one of ordinary skill in the arts (MPEP 2143[I][B]). Additionally, the selection of a known material, which is based upon its suitability for the intended use, is within the ambit of one of ordinary skill in the art [MPEP § 2144.07].
Regarding claim 41, the method of claim 21, wherein the molecule comprises RNA (Royyuru teaches the double strand molecule is double strands of RNA [Para. 0002, 0004, 0064-0065]).
Regarding claim 42, the method of claim 21, wherein the processing system operates in a network environment (Modified Royyuru teaches the computer 500 operates in a network environment [Royyuru: Para. 0062 and Fig. 5]).
Regarding claim 43, a method (Royyuru teaches a method [see e.g., Abstract, Para. 0003, Fig. 2 and 4]) comprising:
detecting by a processing system including a processor a first entry, into a first pore located in a membrane, of a first portion of a molecule (Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018]. Royyuru further teaches measuring “detecting” the tunneling current via ammeter 205a a first entry into a first nanopore 102 [the ammeter is controlled by the computer 500, and thus the computer detects the first entry by measuring the tunneling current via the ammeter] located in a membrane 101, of a base “first portion” on the single strand 105 of the double strand molecule 107 to identify and sequence each individual base “portion” passing/translocating through the first nanopore 102 [Paras. 0037-0040 and 0054, Fig. 2 and Fig. 5]),
wherein the membrane has a first side and a second side (Royyuru teaches the membrane 101 has a first side [source side] and a second side [sink side] [Fig. 2, Paras. 0037-0041]),
wherein the first pore extends from the first side of the membrane to the second side of the membrane (Royyuru teaches the first nanopore 102 extends from the first side [source side] to the second side [sink side] of the membrane 101 [Fig. 2, Paras. 0037-0041]),
wherein the membrane is planar (Royyuru teaches the membrane 101 is planar as seen in Fig. 2 [Fig. 2]), and
wherein the first side of the membrane is parallel to the second side of the membrane (Royyuru teaches the first side [source side] of the membrane 101 is parallel to the second side [sink side] of the membrane 101 as seen in Fig. 2 [Fig. 2, Paras. 0037-0041]);
detecting by the processing system a second entry, into the first pore, of a second portion of the molecule (Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018]. Royyuru further teaches measuring “detecting” the tunneling current via ammeter 205a a second entry into a first nanopore 102 as the single strand 105 passes through and translocates through the first nanopore 102 [the ammeter is controlled by the computer 500, and thus the computer detects the second entry by measuring the tunneling current via the ammeter] located in a membrane 101, of another individual base “second portion” on the single strand 105 of the double strand molecule 107 to identify and sequence each individual base “portion” passing/translocating through the first nanopore 102 [Paras. 0037-0041 and 0054, Fig. 2 and Fig. 5]),
wherein the first portion and the second portion are portions of the molecule that is a single molecule (Royyuru teaches each individual base of the single strand 105, which includes a first “base” portion and second “base” portion as outlined in the rejection above, are portions of the double strand molecule 107 that is a single molecule [Fig. 2, Paras. 0037-0041]),
wherein a third portion of the molecule does not enter the first pore (Royyuru teaches a base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 and does not enter/pass through the first nanopore 102 [Fig. 2, Paras. 0037-0040]);
Royyuru does not explicitly disclose responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore,
Sigalov teaches back-and-forth motion of DNA strands through a pore and a strategy for sequencing DNA in a nanopore using an electric field that alternates in a silicon membrane by applying an external electric bias across the membrane to drive a single DNA molecule strand back and forth through the pore [Abstract, Fig. 1 and Page 56, Col. 2, Para. 1]. Figures 2a-g illustrate DNA’s back-and-forth motion during one translocation cycle, where an alternating electric field [e.g., voltage bias: V+ = 20 V switched to V- = -20 V, Fig. 2h] can force DNA to move by exactly n nucleotides back and forth and when applied to a DNA fragment, produce repetitive motion of that fragment “portion” back-and-forth through the pore’s constriction [corresponding to a first movement of a first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule] [Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph].
Gershow teaches a molecular capture and recapture system with data analysis to select a nucleotide fragment “first portion” to be sequenced and the number of times that fragment is sequenced. The molecular capture and recapture system enables the repeated analysis of a selected nucleotide fragment “first portion” a selected number of times by a capture-recapture sequence [corresponding to a first movement of the first portion of the molecule back out of the first pore], followed by a repeated analysis of a next nucleotide fragment “second portion” [corresponding to a second movement of the second portion of the molecule back out of the first pore], until all nucleotide fragments “portions” in a solution under study have been analyzed [Para. 0077, 0073]. With real-time data analysis, the system can be controlled to initiate and continue a molecule's analysis, to terminate a molecule's analysis, or to re-initiate a molecule's analysis [Para. 0077]. Gershow further teaches it is well known that certain sequences in the genome are more difficult to read, and produce a lower quality read-out, than other sequences in general, and if an initial number of molecular fragment translocations, of an individual nucleotide fragment “portion” is determined by real-time software to have produced an incomplete or a poor-quality read-out [corresponding to responsive to the detecting of the first entry into the first pore and the second entry into the first pore], the recapture system can be controlled to promptly recapture that fragment to be re-sequenced a number of additional times as-required to produce a desired read-accuracy [corresponding to facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore], where a molecule can be recaptured by, e.g., reversing the voltage bias between the reservoirs [the applied voltage bias corresponding to wherein the first and second movement are based on application of force on the molecule] [Para. 0076, 0072]. One of ordinary skill in the art would recognize that a software would inherently include a processing system with a processor wherein the software is stored and installed for facilitating/executing the software’s programmed instructions. To recapture the molecule, the driving force across the nanopore is reversed and the recaptured molecule, now having translocated the nanopore in the reverse of its original direction, can then be captured a third time by restoring the driving voltage to its original polarity, producing an electrophoretic force again toward the nanopore [Fig. 1A-1F and Para. 0027-0030].
Given the teachings of Sigalov regarding sequencing DNA in a nanopore using an electric field that alternates in a silicon membrane to force DNA to move by exactly n nucleotides back and forth through a nanopore, it would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify the method, including voltage source 115 with electrodes 111 and 112, and processing system, which detects the first and second entry into the first pore, of Royyuru, such that responsive to the detecting of the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule, by reversing the voltage bias applied by the voltage source at the electrodes, as taught by Gershow and Sigalov, since Gershow teaches it would be beneficial because it is well known that certain sequences in the genome are more difficult to read, and produce a lower quality read-out, than other sequences in general and promptly recapturing a fragment to be re-sequenced a number of additional times as-required produces a desired read-accuracy [Para. 0076 of Gershow]. Furthermore, the use of a known technique (i.e., responsive to detecting entry of a first and second portion/nucleotide into a nanopore, facilitating by software re-sequencing and recapture of the first and second nucleotides back out of the first pore, taught by Gershow, and repeated back-and-forth motion of DNA nucleotides by alternating voltage bias, taught by Sigalov) to improve methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143 [I][C]).
wherein the first movement of the first portion of the molecule back out of the first pore and the second movement of the second portion of the molecule back out of the first pore results from adjusting a first physical characteristic in a vicinity of the first pore to cause the first portion of the molecule to be backed out of the first pore and the second portion of the molecule to be backed out of the first pore (Modified Royyuru as outlined in the rejection above yields the first and second movement results from reversing a voltage bias “adjusting a first physical characteristic” by the voltage source 115 including electrodes 111 and 112 in the reservoirs to cause the first portion and second portion of the molecule to be backed out of the first pore 102/translocate in the reverse direction to be recaptured and re-sequenced, and this adjusting of the electric field “physical characteristic” is in a vicinity of the first pore 102, because the voltage bias is applied to the reservoirs through the electrodes 111 and 112, and the first pore 102 joins the two reservoirs, and thus is in a vicinity of/near the first pore 102 as seen in Fig. 2 of Royyuru [see rejection above; Royyuru: Fig. 2 and Para. 0024, 0026; Sigalov: Abstract; Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph; Gershow: Para. 0076-0077, 0072-0073; 0027-0030; Fig. 1A-1F]. The examiner notes the electric field/voltage bias is the same physical characteristic disclosed in the instant specification [see e.g., Para. 000123 of the instant specification which states a physical characteristic in a vicinity of a pore can be an electric field that is changed near the pore]).
wherein the adjusting of the first physical characteristic in the vicinity of the second pore comprises applying a voltage bias (Modified Royyuru as outlined in the rejection above yields reversing a voltage bias “adjusting a first physical characteristic” by the voltage source 115 including electrodes 111 and 112 in the reservoirs [corresponding to applying a voltage bias] and this adjusting of the electric field “physical characteristic” is in a vicinity of a second pore 103, because the voltage bias is applied to the reservoirs through the electrodes 111 and 112, and the second pore 103 joins the two reservoirs, and thus is in a vicinity of/near the second pore 103 as seen in Fig. 2 of Royyuru [see rejection above; Royyuru: Fig. 2 and Para. 0024, 0026; Sigalov: Abstract; Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph; Gershow: Para. 0076-0077, 0072-0073; 0027-0030; Fig. 1A-1F]).
Regarding claim 45, the method of claim 43, wherein the molecule comprises DNA (Royyuru teaches the double strand molecule is double strands of DNA [Para. 0002, 0004, 0064-0065]).
Regarding claim 46, the method of claim 43, wherein the membrane is a solid-state membrane (Royyuru teaches the membrane 101 may be silicon, silicon dioxide or any insulating material, and thus is a solid-state membrane as seen in Fig. 2 [Para. 0017 and Fig. 2]), and further comprising:
facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane (Modified Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018 of Royyuru]. Modified Royyuru as outlined in the rejection of claim 43 above yields the first and second movements [see rejection of claim 43 above]. Modified Royyuru further teaches the base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 [corresponding to a third movement] of the membrane 101 and this is facilitated by the processing system which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a third portion the molecule into the nanopore 103] [Fig. 2 and 5, Paras. 0037-0040, 0054-0063, 0026, 0018 of Royyuru]),
wherein the third movement of the third portion of the molecule results from adjusting a second physical characteristic in a vicinity of the second pore to cause the third portion of the molecule to enter the second pore (Modified Royyuru as outlined in the rejection of claim 43 above yields the first and second movement results from reversing the voltage bias “adjusting a first physical characteristic” by the voltage source 115 including electrodes 111 and 112 in the reservoirs [see rejection of claim 43 above; Royyuru: Fig. 2 and Para. 0024, 0026; Sigalov: Abstract; Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph; Gershow: Para. 0076-0077, 0072-0073; 0027-0030; Fig. 1A-1F]. Modified Royyuru teaches the base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 [corresponding to the third movement] and this results from applying a positive voltage to electrode 112 and negative voltage to electrode 111 for an upward pointing electric field “adjusting a second physical characteristic” by the voltage source 115 in the reservoirs to cause the base “third portion” on the single strand 106 of the double strand molecule 107 to enter the second nanopore 103, and this adjusting of the electric field “physical characteristic” is in a vicinity of the second nanopore 103, because the voltage bias is applied to the reservoirs through the electrodes 111 and 112, and the second nanopore 103 joins the two reservoirs, and thus is in a vicinity of/near the second nanopore 103 as seen in Fig. 2 of Royyuru [see rejection above; Royyuru: Fig. 2 and 5; Para. 0024, 0026, 0043, 0037-0040, 0054-0063, 0018]. The examiner notes the electric field/voltage bias is the same physical characteristic disclosed in the instant specification [see e.g., Para. 000123 of the instant specification which states a physical characteristic in a vicinity of a pore can be an electric field that is changed near the pore]).
Regarding claim 47, the method of claim 43, wherein the molecule comprises RNA (Royyuru teaches the double strand molecule is double strands of RNA [Para. 0002, 0004, 0064-0065]).
Regarding claim 49, a method (Royyuru teaches a method [see e.g., Abstract, Para. 0003, Fig. 2 and 4]) comprising:
detecting by a processing system including a processor a first entry, into a first pore located in a membrane, of a first portion of a molecule (Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018]. Royyuru further teaches measuring “detecting” the tunneling current via ammeter 205a a first entry into a first nanopore 102 [the ammeter is controlled by the computer 500, and thus the computer detects the first entry by measuring the tunneling current via the ammeter] located in a membrane 101, of a base “first portion” on the single strand 105 of the double strand molecule 107 to identify and sequence each individual base “portion” passing/translocating through the first nanopore 102 [Paras. 0037-0040 and 0054, Fig. 2 and Fig. 5]),
wherein the membrane has a first side and a second side (Royyuru teaches the membrane 101 has a first side [source side] and a second side [sink side] [Fig. 2, Paras. 0037-0041]),
wherein the first pore extends from the first side of the membrane to the second side of the membrane (Royyuru teaches the first nanopore 102 extends from the first side [source side] to the second side [sink side] of the membrane 101 [Fig. 2, Paras. 0037-0041]), and
wherein the membrane is a solid-state membrane (Royyuru teaches the membrane 101 may be silicon, silicon dioxide or any insulating material, and thus is a solid-state membrane as seen in Fig. 2 [Para. 0017 and Fig. 2]);
detecting by the processing system a second entry, into the first pore, of a second portion of the molecule (Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018]. Royyuru further teaches measuring “detecting” the tunneling current via ammeter 205a a second entry into a first nanopore 102 as the single strand 105 passes through and translocates through the first nanopore 102 [the ammeter is controlled by the computer 500, and thus the computer detects the second entry by measuring the tunneling current via the ammeter] located in a membrane 101, of another individual base “second portion” on the single strand 105 of the double strand molecule 107 to identify and sequence each individual base “portion” passing/translocating through the first nanopore 102 [Paras. 0037-0041 and 0054, Fig. 2 and Fig. 5]),
wherein the first portion and the second portion are portions of the molecule that is a single molecule (Royyuru teaches each individual base of the single strand 105, which includes a first “base” portion and second “base” portion as outlined in the rejection above, are portions of the double strand molecule 107 that is a single molecule [Fig. 2, Paras. 0037-0041])),
wherein a third portion of the molecule does not enter the first pore (Royyuru teaches a base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 and does not enter/pass through the first nanopore 102 [Fig. 2, Paras. 0037-0040]);
Royyuru does not explicitly disclose responsive to detecting the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore.
Sigalov teaches back-and-forth motion of DNA strands through a pore and a strategy for sequencing DNA in a nanopore using an electric field that alternates in a silicon membrane by applying an external electric bias across the membrane to drive a single DNA molecule strand back and forth through the pore [Abstract, Fig. 1 and Page 56, Col. 2, Para. 1]. Figures 2a-g illustrate DNA’s back-and-forth motion during one translocation cycle, where an alternating electric field [e.g., voltage bias: V+ = 20 V switched to V- = -20 V, Fig. 2h] can force DNA to move by exactly n nucleotides back and forth and when applied to a DNA fragment, produce repetitive motion of that fragment “portion” back-and-forth through the pore’s constriction [corresponding to a first movement of a first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule] [Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph].
Gershow teaches a molecular capture and recapture system with data analysis to select a nucleotide fragment “first portion” to be sequenced and the number of times that fragment is sequenced. The molecular capture and recapture system enables the repeated analysis of a selected nucleotide fragment “first portion” a selected number of times by a capture-recapture sequence [corresponding to a first movement of the first portion of the molecule back out of the first pore], followed by a repeated analysis of a next nucleotide fragment “second portion” [corresponding to a second movement of the second portion of the molecule back out of the first pore], until all nucleotide fragments “portions” in a solution under study have been analyzed [Para. 0077, 0073]. With real-time data analysis, the system can be controlled to initiate and continue a molecule's analysis, to terminate a molecule's analysis, or to re-initiate a molecule's analysis [Para. 0077]. Gershow further teaches it is well known that certain sequences in the genome are more difficult to read, and produce a lower quality read-out, than other sequences in general, and if an initial number of molecular fragment translocations, of an individual nucleotide fragment “portion” is determined by real-time software to have produced an incomplete or a poor-quality read-out [corresponding to responsive to the detecting of the first entry into the first pore and the second entry into the first pore], the recapture system can be controlled to promptly recapture that fragment to be re-sequenced a number of additional times as-required to produce a desired read-accuracy [corresponding to facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore], where a molecule can be recaptured by, e.g., reversing the voltage bias between the reservoirs [the applied voltage bias corresponding to wherein the first and second movement are based on application of force on the molecule] [Para. 0076, 0072]. One of ordinary skill in the art would recognize that a software would inherently include a processing system with a processor wherein the software is stored and installed for facilitating/executing the software’s programmed instructions. To recapture the molecule, the driving force across the nanopore is reversed and the recaptured molecule, now having translocated the nanopore in the reverse of its original direction, can then be captured a third time by restoring the driving voltage to its original polarity, producing an electrophoretic force again toward the nanopore [Fig. 1A-1F and Para. 0027-0030].
Given the teachings of Sigalov regarding sequencing DNA in a nanopore using an electric field that alternates in a silicon membrane to force DNA to move by exactly n nucleotides back and forth through a nanopore, it would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify the method, including voltage source 115 with electrodes 111 and 112, and processing system, which detects the first and second entry into the first pore, of Royyuru, such that responsive to the detecting of the first entry into the first pore and the second entry into the first pore, facilitating by the processing system a first movement of the first portion of the molecule back out of the first pore and a second movement of the second portion of the molecule back out of the first pore, wherein the first and second movement are based on application of a force on the molecule, by reversing the voltage bias applied by the voltage source at the electrodes, as taught by Gershow and Sigalov, since Gershow teaches it would be beneficial because it is well known that certain sequences in the genome are more difficult to read, and produce a lower quality read-out, than other sequences in general and promptly recapturing a fragment to be re-sequenced a number of additional times as-required produces a desired read-accuracy [Para. 0076 of Gershow]. Furthermore, the use of a known technique (i.e., responsive to detecting entry of a first and second portion/nucleotide into a nanopore, facilitating by software re-sequencing and recapture of the first and second nucleotides back out of the first pore, taught by Gershow, and repeated back-and-forth motion of DNA nucleotides by alternating voltage bias, taught by Sigalov) to improve methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143 [I][C]).
wherein the first movement of the first portion of the molecule back out of the first pore and the second movement of the second portion of the molecule back out of the first pore results from adjusting a first physical characteristic in a vicinity of the first pore to cause the first portion of the molecule to be backed out of the first pore and the second portion of the molecule to be backed out of the first pore (Modified Royyuru as outlined in the rejection above yields the first and second movement results from reversing a voltage bias “adjusting a first physical characteristic” by the voltage source 115 including electrodes 111 and 112 in the reservoirs to cause the first portion and second portion of the molecule to be backed out of the first pore 102/translocate in the reverse direction to be recaptured and re-sequenced, and this adjusting of the electric field “physical characteristic” is in a vicinity of the first pore 102, because the voltage bias is applied to the reservoirs through the electrodes 111 and 112, and the first pore 102 joins the two reservoirs, and thus is in a vicinity of/near the first pore 102 as seen in Fig. 2 of Royyuru [see rejection above; Royyuru: Fig. 2 and Para. 0024, 0026; Sigalov: Abstract; Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph; Gershow: Para. 0076-0077, 0072-0073; 0027-0030; Fig. 1A-1F]. The examiner notes the electric field/voltage bias is the same physical characteristic disclosed in the instant specification [see e.g., Para. 000123 of the instant specification which states a physical characteristic in a vicinity of a pore can be an electric field that is changed near the pore]); and
facilitating by the processing system a third movement of the third portion of the molecule into a second pore of the membrane (Modified Royyuru teaches a computer 500 including one or more processors 510 for testing and analysis which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a portion the molecule into the nanopore] and voltage sources 210a and 210 b, measurements of the ammeters 205 a and 205 b, and the capabilities of the computer 500 implements features of the embodiments discussed to connect to and/or support any element [Fig. 5 and Para. 0054-0063, 0026, 0018 of Royyuru]. Modified Royyuru as outlined in the rejection above yields the first and second movements [see rejection above]. Modified Royyuru further teaches the base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 [corresponding to a third movement] of the membrane 101 and this is facilitated by the processing system which implements, controls, and/or regulates the voltage of the voltage source 115 [electrodes 111 and 112 connected to voltage source 115 for applying a voltage to induce an electric field to cause entry of a third portion the molecule into the nanopore 103] [Fig. 2 and 5, Paras. 0037-0040, 0054-0063, 0026, 0018 of Royyuru]),
wherein the third movement of the third portion of the molecule results from adjusting a second physical characteristic in a vicinity of the second pore to cause the third portion of the molecule to enter the second pore (Modified Royyuru as outlined in the rejection above yields the first and second movement results from reversing the voltage bias “adjusting a first physical characteristic” by the voltage source 115 including electrodes 111 and 112 in the reservoirs [see rejection above; Royyuru: Fig. 2 and Para. 0024, 0026; Sigalov: Abstract; Fig. 2 and Fig. 2 caption; Page 57, Col. 2, Para. 3; Page 62, Col. 1, Para. 1 and last paragraph; Gershow: Para. 0076-0077, 0072-0073; 0027-0030; Fig. 1A-1F]. Modified Royyuru teaches the base “third portion” on the single strand 106 of the double strand molecule 107 enters the second nanopore 103 [corresponding to the third movement] and this results from applying a positive voltage to electrode 112 and negative voltage to electrode 111 for an upward pointing electric field “adjusting a second physical characteristic” by the voltage source 115 in the reservoirs to cause the base “third portion” on the single strand 106 of the double strand molecule 107 to enter the second nanopore 103, and this adjusting of the electric field “physical characteristic” is in a vicinity of the second nanopore 103, because the voltage bias is applied to the reservoirs through the electrodes 111 and 112, and the second nanopore 103 joins the two reservoirs, and thus is in a vicinity of/near the second nanopore 103 as seen in Fig. 2 of Royyuru [see rejection above; Royyuru: Fig. 2 and 5; Para. 0024, 0026, 0043, 0037-0040, 0054-0063, 0018]. The examiner notes the electric field/voltage bias is the same physical characteristic disclosed in the instant specification [see e.g., Para. 000123 of the instant specification which states a physical characteristic in a vicinity of a pore can be an electric field that is changed near the pore]).
Regarding claim 50, the method of claim 49, wherein the first entry of the first portion of the molecule into the first pore is from the first side of the membrane and wherein the second entry of the second portion of the molecule into the first pore is from the first side of the membrane (Royyuru teaches the first entry of a base “first portion” on the single strand 105 of the double strand molecule 107 into the first nanopore 102 is from the first side [source side] of the membrane 101 and the second entry of another individual base “second portion” on the single strand 105 of the double strand molecule 107 into the first nanopore 102 is from the first side [source side] of the membrane 101 as the double strand DNA molecule 107 is presented on the source side of the membrane 101 and the double strand DNA molecule 107 translocates from the source “first” side of the membrane to the sink “second” side through the nanopores [Paras. 0024, 0037-0041 and 0054, Fig. 2 and Fig. 5]); and further comprising:
applying opposing forces to the molecule resulting in the molecule being taut against the membrane between the first and second pores (Royyuru teaches applying opposing forces to the double strand DNA molecule 107 by applying a positive voltage to electrode 112 and negative voltage to electrode 111, which generates an ionic current through the electrically conductive solution 170, and an upward pointing electric field (resulting in a downward force on the double strand DNA molecule 107). The downward opposing forces translocate the double strand DNA molecule 107 from the source side of the membrane to the sink side through the nanopores 102 and 103 in the membrane 101. As the entire double strand DNA molecule 107 is pulled down by the opposing downward forces, this results in the portion of the molecule indicated as 107 in Fig. 2 on the source side of the membrane to be pulled down against the membrane [corresponding to taut against the membrane] between the first nanopore 102 and the second nanopore 103 as the molecule is presented in an electrically conductive solution 170 and the voltage is applied as outlined above [Para. 0024, 0037-0041, Fig. 2]).
Regarding claim 52, the method of claim 49, wherein the membrane is planar (Royyuru teaches the membrane 101 is planar as seen in Fig. 2 [Fig. 2]) and wherein the first side of the membrane is parallel to the second side of the membrane (Royyuru teaches the first side [source side] of the membrane 101 is parallel to the second side [sink side] of the membrane 101 as seen in Fig. 2 [Fig. 2, Paras. 0037-0041]).
Regarding claim 53, the method of claim 49, wherein the molecule comprises RNA (Royyuru teaches the double strand molecule is double strands of RNA [Para. 0002, 0004, 0064-0065]).
Claim(s) 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Royyuru in view of Sigalov and Gershow as applied to claim 26 above, and further in view of Heller et al. (US20140099726A1).
Regarding claim 27, the method of claim 26, wherein the membrane is planar (Royyuru teaches the membrane 101 is planar as seen in Fig. 2 [Fig. 2]]) and
Modified Royyuru is silent to wherein the first and second pores are of different sizes.
Heller discloses a method for determining the sequence of a polynucleotide comprising a device with two pores defined as a first and second pore with the polynucleotide placed in both pores, wherein the polynucleotide moves across both pores at the same direction to identify a plurality of nucleotides of the polynucleotide using a sensor [Abstract, Para. 0022-0025 and Fig. 3]. Heller teaches each of the pores 111 and 112 independently have a size [corresponding to the first and second pores are of a different size or same size] that allow a small or large molecule or microorganism to pass [Para. 0046].
It would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify the first and second pores of Modified Royyuru, to be provided as different sizes, as taught by Heller, since Heller teaches this suitable alternative configuration for two pores in a nanopore device for determining the sequence of a polynucleotide with the polynucleotide placed in both pores, wherein the polynucleotide moves across both pores at the same direction to identify a plurality of nucleotides of the polynucleotide using a sensor and would be beneficial for allowing a small or large molecule or microorganism to pass [Abstract, Para. 0022-0025 and 0046 of Heller]. Furthermore, the use of a known technique (i.e., independently sizing two pores to be of a different size or same size, taught by Heller) to improve similar methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143 [I][C]).
Claim(s) 48 and 54 is/are rejected under 35 U.S.C. 103 as being unpatentable over Royyuru in view of Sigalov and Gershow as applied to claim 43 and claim 49, respectively, above, and further in view of Aksimentiev et al. (US20140360876A1).
Regarding claim 48, the method of claim 43, Modified Royyuru does not explicitly teach wherein the processing system operates in a distributed environment.
Aksimentiev discloses a method for controlling materials such as DNA through a through-hole/nanopore, including, but not limited to, applying an electrical potential to an electrolyte solution to apply a transport force on the molecular strand to displace a section of the molecular strand into the nanopore and measuring a signal at the nanopore to identify the section of the molecular strand with reversible stepping of DNA through the membrane system such as a one-nucleotide or larger displacement of the DNA strand through the nanopore [see e.g., Title, Abstract, Figs. 9-10 and 7, Paras. 0046-0047]. Aksimentiev teaches a machine in the form of a computer system 1100 which a set of instructions (e.g., software), when executed, may cause the machine/computer system to perform any one or more of the methods and operations, such as, applying a potential to the solution to apply a transport force on the molecular strand to displace a section of the molecular strand into the through-hole and measuring the signal at the through-hole to identify the section of the molecular strand and the computer system/processing system can be combined with an apparatus including a membrane comprising a through-hole, a first voltage source to apply a first potential to a surface of the membrane, a second voltage source to apply a second potential to a solution having conductive properties, a sensor to measure a signal at the through-hole, and a memory to store instructions; the computer system 1100/processing system including a processor and also stores one or more sets of instructions (e.g., software) that the computer system is capable of executing and in response to executing the instructions, can perform operations as mentioned above [see e.g., Fig. 11 and Paras. 0051-0058]. Aksimentiev further teaches the machine/computer system/processing system may be connected using a network and the machine/computer system/processing system operates in a network environment, such as in a distributed network environment [Para. 0053].
It would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify the processing system of modified Royyuru to operate in a distributed environment, as taught by Aksimentiev, since Aksimentiev teaches this suitable configuration for operating a processing system and teaches it would be beneficial for connecting to other machines using a network [Para. 0053 of Aksimentiev]. Furthermore, the use of a known technique (i.e., operating in a distributed environment, taught by Aksimentiev) to improve similar methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143 [I][C]).
Regarding claim 54, the method of claim 49, Modified Royyuru does not explicitly teach wherein the processing system operates as a peer in a peer-to-peer environment
Aksimentiev discloses a method for controlling materials such as DNA through a through-hole/nanopore, including, but not limited to, applying an electrical potential to an electrolyte solution to apply a transport force on the molecular strand to displace a section of the molecular strand into the nanopore and measuring a signal at the nanopore to identify the section of the molecular strand with reversible stepping of DNA through the membrane system such as a one-nucleotide or larger displacement of the DNA strand through the nanopore [see e.g., Title, Abstract, Figs. 9-10 and 7, Paras. 0046-0047]. Aksimentiev teaches a machine in the form of a computer system 1100 which a set of instructions (e.g., software), when executed, may cause the machine/computer system to perform any one or more of the methods and operations, such as, applying a potential to the solution to apply a transport force on the molecular strand to displace a section of the molecular strand into the through-hole and measuring the signal at the through-hole to identify the section of the molecular strand and the computer system/processing system can be combined with an apparatus including a membrane comprising a through-hole, a first voltage source to apply a first potential to a surface of the membrane, a second voltage source to apply a second potential to a solution having conductive properties, a sensor to measure a signal at the through-hole, and a memory to store instructions; the computer system 1100/processing system including a processor and also stores one or more sets of instructions (e.g., software) that the computer system is capable of executing and in response to executing the instructions, can perform operations as mentioned above [see e.g., Fig. 11 and Paras. 0051-0058]. Aksimentiev further teaches the machine/computer system/processing system may be connected using a network and the machine/computer system/processing system operates in a network environment, such as a server-client user network environment, or as a peer machine in a peer-to-peer network environment [Para. 0053].
It would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify the processing system of modified Royyuru to operate as a peer machine in a peer-to-peer environment, as taught by Aksimentiev, since Aksimentiev teaches this suitable configuration for operating a processing system and teaches it would be beneficial for connecting to other machines using a network [Para. 0053 of Aksimentiev]. Furthermore, the use of a known technique (i.e., operating as a peer in a peer-to-peer environment, taught by Aksimentiev) to improve similar methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143 [I][C]).
Response to Arguments
Applicant's arguments, see Remarks Pgs. 8-11, filed 03/27/2026, with respect to the 35 U.S.C. § 102 and 103 rejections have been fully considered and all 102 and 103 rejections from the previous office action are withdrawn.
Applicant’s Argument #1:
Applicant argues on page 9 that Gershow also does not describe facilitating the first and second movement of the first and second portions of the molecule back out of the first pore responsive to the detecting of the first entry into the first pore and the second entry into the first pore. This is distinct from the claimed features including where the first portion and the second portion are portions of the molecule that is a single molecule, and where a third portion of the molecule does not enter the first pore. Aksimentiev does not make up for the deficiencies on Gershow. Hence, claim 21 is allowable. Claims 24-28 and 41-42 depend from claim 21 are allowable at least by virtue of their dependency.
Examiner’s Response #1:
Applicant’s arguments have been fully considered, but are moot in view of the new grounds of rejection.
Applicant’s Argument #2:
Applicant argues on page 10 that Gershow appears to be describing the entire molecule passing all the way through the pore of the membrane. which is distinct from the claimed features including where the first portion and the second portion are portions of the molecule that is a single molecule, and where a third portion of the molecule does not enter the first pore and from facilitating the first and second movement of the first and second portions of the molecule back out of the first pore responsive to the detecting of the first entry into the first pore and the second entry into the first pore. Aksimentiev does not make up for the deficiencies on Gershow. Hence, claim 43 is allowable. Claims 44-48 depend from claim 43 are allowable at least by virtue of their dependency.
Examiner’s Response #2:
Applicant’s arguments have been fully considered, but are moot in view of the new grounds of rejection.
Applicant’s Argument #3:
Applicant argues on pages 10-11 that Gershow appears to be describing the entire molecule passing all the way through the pore of the membrane. which is distinct from the claimed features including where the first portion and the second portion are portions of the molecule that is a single molecule, and where a third portion of the molecule does not enter the first pore and from facilitating the first and second movement of the first and second portions of the molecule back out of the first pore responsive to the detecting of the first entry into the first pore and the second entry into the first pore. Aksimentiev does not make up for the deficiencies on Gershow. Hence, claim 49 is allowable. Claims 50-54 depend from claim 49 are allowable at least by virtue of their dependency.
Examiner’s Response #3:
Applicant’s arguments have been fully considered, but are moot in view of the new grounds of rejection.
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.
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/S.Y.O./Examiner, Art Unit 1794
/JAMES LIN/Supervisory Patent Examiner, Art Unit 1794
