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 .
Claim Status
Claims 1-7, 9-14, 17-23 are currently pending and are examined herein.
Priority
Acknowledgment is made of applicant’s claim for domestic priority based on US provisional application No. 63/147,173 filed on 08 February 2021.
Specification
The use of the term AmpureTM ([[00013], [000390], [000395], [000396], [000405]), which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 11 is objected to because of the following informalities: claim 11 recites “T7 promotor” and should read “T7 promoter”. Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claim 13 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.
Claim 13 recites the limitation "the operation of the microfluidic path device". There is insufficient antecedent basis for this limitation in the claim. It is not clear which operation of the microfluidic path device this limitation is referring to. It is not clear whether it is referring to the operation of transporting reagents to the first reactor, controlling a temperature, or transporting reagents out of the first reactor. It is not clear whether it is referring to the operation of one of these functions, a combination, all, or the entire microfluidic path device that further comprises additional functions not recited in claim 1.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-7, 9-14, 17-19, 21-23 are rejected under 35 U.S.C. 103 as being unpatentable over Derrick et al (WO 2013/071047 A1; Published Date: 16 May 2013; Cited on IDS received on 08/07/2023), in view of Enzelberger et al (US 2014/0141498 A1; Published Date: 22 May 2014)
Regarding claim 1, Derrick teaches a method of making nucleic acid constructs (i.e., a synthetic product) comprising open reading frames for in vitro transcription ([0005]), and an open reading frame can be…synthetic DNA sequence (i.e., a synthetic DNA template suitable for in vitro transcription) ([00182]). Derrick teaches the method, referred as “Addition of poly-(A) tail by PCR” or “Tail PCR” ([0095]), comprises reagents including diluted ORF plasmid (i.e., a synthetic gene of interest), KAPA PCR Ready Mix (i.e., a polymerase and a buffer), XU-F1 and XU-T120 primers ([00338]). Regarding XU-F1 primer, Derrick teaches it is “a forward universal primer comprising at its 3’ end a sequence…of the IVT template” ([0095] and FIG. 1C) (i.e., a first primer having a first region specific to the synthetic gene of interest). Regarding XU-T120 primer, Derrick further teaches it is “a reverse universal primer sequence comprising a sequence complementary to the…IVT template at its 3’ end and a poly-T sequence at the primer’s 5’end” ([0095] and FIG. 1C) (i.e., a second primer comprising a poly-T sequence and a second region that is specific to the synthetic gene of interest). The sequences of these two primers are disclosed in [00333], and Derrick teaches that “the universal reverse primer can comprise a poly-T sequence of, typically 50-5000 T nucleotides” ([00178]). Lastly, Derrick teaches Tail PCR comprises of aliquoting the reagents into PCR tubes (i.e., transporting reagents), running Tail PCR with optimized temperatures and conditions (i.e., controlling a temperature to perform a PCR), and purifying the Tail PCR product (i.e., transporting the synthetic product) ([00339]-[00345], and [00378]).
However, Derrick teaches conducting the method using a PCR thermocycler ([00334]) rather than a microfluidic path device.
Enzelberger teaches using microfluidic devices to perform “template extension reactions that involve thermal cycling…include…exponential amplifications (extension reactions conducted with both forward and reverse primers…e.g., PCR)” ([0057]). Enzelberger further teaches a method of conducting amplification reactions comprising the following:
reagents are introduced into the central loop 106 (i.e., transporting reagents to a first reactor) ([0087] and FIG. 1),
reagents are circulated around the central loop 106 comprising three different temperature regions 118, 120, and 122 programmed according to particular amplification step (i.e., . controlling a temperature of the first reactor of the microfluidic path device to perform a PCR) ([0087] and FIG. 1), and
the control valve 112 of the outlet 108 is opened so solution can be removed from the central loop 106, and the solution that is withdrawn can then be transported via a flow channel in fluid communication with the outlet 108 (i.e., transporting the synthetic product out of the first reactor) ([0084] and FIG. 1).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Derrick’s method to conduct Tail PCR in microfluidic devices as taught by Enzelberger’s because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage taught by Enzelberger that is conducting PCR amplifications “at a relatively high speed because it is not necessary to heat and cool the heaters” compared to “time domain approach in which the amplification reaction mixture is kept stationary and the temperature is cycled” ([0006]). One would have had a reasonable expectation of success in doing so because both Derrick and Enzelberger teach methods of nucleic acid amplifications.
Regarding claims 2-5, the teachings of Derrick regarding XU-F1 and XU-T120 primers (i.e., the first primer and the second primer) are discussed above and applied to claim 1. Derrick further teaches XU-F1 and XU-T120 primers include end regions of 27 and 30 bp long complementary to the IVT template (i.e., synthetic gene of interest) ([00333]).
Regarding claim 6, it recites "generating greater than 1 uM of an amplified DNA template" but the specification provides no working examples specifying a reaction volume, elution volume, or size of the amplified DNA template. The specification also fails to teach whether this concentration is based on yield prior to or after purification. Derrick teaches generating an IVT DNA template comprising components (a) - (h) ([0090]), as illustrated in FIG. 4, which collectively account for approximately 376 base pairs (bp). Derrick further teaches that a successfully transcribed ORF (SEQ ID NO: 184) encoding a hormone is 504 bp )[00205]) and a poly(A) tail of about 120 bp was added. Accordingly, Derrick's IVT DNA template is about 1,000 bp in length. Derrick further teaches the method generated sufficient yield of 10-15 IVT reactions ([00340]), and each IVT reaction requires 16 µL of 100 ng/µL of PCR product ([00348]). Therefore, Derrick’s method generates 16-24 µg of PCR product. Given that an average molecular weight for a base pair is 660 g/mol, it can be calculated that 1,000 bp has a molecular weight of 660,000 g/mol, and 16-24 µg equals to 24-36 pmol. If Derrick’s PCR product is diluted to 24-36 µL, the concentration will be greater than 1 µM. It is also noted that these calculations are based on the amount of purified PCR products. As is well-understood in the art, purification of PCR products inherently results in material loss. Therefore, Derrick’s method generates more than the calculated amount of PCR product, which further supports that Derrick’s method teaches this claim limitation.
Regarding claim 7, Derrick further teaches adding DpnI enzyme after PCR to digest the methylated plasmid DNA and purifying the PCR products (i.e., synthetic DNA template) using a PCR purification kit ([00343]-[00346]). These steps remove bacterial DNA and endotoxins.
Regarding claims 9 and 11, Derrick does not explicitly teach the first primer includes a promoter region or the first primer having a T7 promoter. However, Derrick teaches the XU-F1 primer (i.e., the first primer) anneals to a region upstream of a T7 promoter (FIG. 1A and 1C) because the DNA template used for PCR amplification already contains a T7 promoter. Derrick further teaches it is advantageous to position an open reading frame under the control of a recombinant or heterologous promoter, including but not limited to SP6 promoter, T7 promoter, and T3 promoter ([00124]-[00126]). Therefore, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Derrick’s XU-F1 primer to contain a T7 promoter or any promoter region because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of introducing recombinant promoters that are not naturally occurring and comprise different transcriptional regulatory elements for enhanced in vitro transcription. One would have had a reasonable expectation of success in doing so because Derrick already teaches a method of making IVT templates comprising such recombinant promoters.
Regarding claim 10, Derrick further teaches PCR amplification comprises of denaturation, primer annealing, and extension that repeats for 25 cycles ([00378]).
Regarding claim 12, the teachings of Derrick regarding the length of poly-T sequence is discussed above and applied to claim 1.
Regarding claim 13, the obviousness of modifying Derrick’s method with the microfluidic device of Enzelberger is discussed above as applied to claim 1. Enzelberger further teaches the microfluidic device can be attached to a translatable stage and scanned under a microscope objective (i.e., sensor), and the acquired signal (i.e., optical sensor data) is routed to a processor (i.e., received in a controller) for signal interpretation and processing (i.e., controller controls the operation of the microfluidic path device) ([0192]).
Regarding claim 14, the obviousness of modifying Derrick’s method with the microfluidic device of Enzelberger is discussed above as applied to claim 1. Enzelberger further teaches solutions (i.e., synthetic product) “are transported the microfluidic device to a separate external device…such as UV/Vis…chromatographic columns…electrophoretic columns and/or mass spectrometry” ([0196]) (i.e., one-dimensional or two-dimensional purification).
Regarding claim 17, the obviousness of modifying Derrick’s method with the microfluidic device of Enzelberger, and the teachings of Enzelberger regarding the temperature regions (i.e., a plurality of fluid depots) in the central loop 106 of the microfluidic device are discussed above as applied to claim 1. Enzelberger further teaches after having injected the reagent mixture into the microchip, the central loop 106 circulation was operated with the Fluid Controller (i.e., power circuit moving reagents between a plurality of fluid depots). ([0304]).
Regarding claim 18, Derrick further teaches a method of performing in vitro transcription using the tailed-PCR product (i.e., synthetic DNA template) ([00347]) that contains an open reading frame sequence encoding for a protein therapeutic (i.e., therapeutic polynucleotide) (00204]).
Regarding claim 19, Derrick teaches determining the yield using a Nano-drop (i.e., a UV yield detection) ([00372]).
However, Derrick does not teach determining the yield using a UV yield detection window on a microfluidic path device.
Enzelberger teaches solutions (i.e., synthetic product) are “transported from the microfluidic device to a separate external device for further analysis…such as UV-Vis” ([0196]).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Enzelberger’s microfluidic device with a Nano-drop taught by Derrick because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of quantifying the amount of PCR product in the microfluidic device. One would have had a reasonable expectation of success in doing so because Enzelberger teaches a microfluidic device capable of being attached to separate devices such as UV-Vis to perform additional analysis after PCR amplification, and Derrick teaches a routine method quantifying PCR products using a Nano-drop that also provides UV-Vis measurements.
Regarding claim 21, the specification does not teach which additional enzymes are added during the PCR within the microfluidic path device. Therefore, the instant claim is interpreted as adding any enzyme that is active and compatible with the PCR buffer. Derrick further teaches “conditions for the Run Tail PCR can vary depending upon DNA polymerase used…which should be optimized by the use” ([00342]), which positively teaches additional DNA polymerase can be added during PCR reaction to improve amplification efficiency and product yield.
Regarding claims 22 and 23, the methods recited in claims 22, 23, and 1 differ in primer designs wherein the sequence complementary to the synthetic gene of interest are located on different ends (5’ or 3’). Derrick teaches using primers “capable of annealing to a portion of a sequence of a nucleic acid…and providing a 3’end substrate for a polymerase enzyme to produce an enzymatic extension product that is complementary to the nucleic acid to which the primer is annealed” ([0054]). Therefore, the obviousness of modifying Derrick’s method with the microfluidic device of Enzelberger discussed above as applied to claim 1 is also applicable for claims 22 and 23, and a mere reversal of essential workings parts/primers of a PCR reaction involves only routine optimization by one of ordinary skill in the art. One would have been motivated to have done so for the advantage of greater flexibility in primer design for DNA template amplification since PCR primers must satisfy strict sequence and thermodynamic requirements to achieve efficient and successful amplifications. One would have had a reasonable expectation of success in doing so because Derrick teaches a method making DNA template for IVT using similar primers and Enzelberger teaches a method of conducting PCR with microfluidic devices.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Derrick et al (WO 2013/071047 A1; Published Date: 16 May 2013; Cited on IDS received on 08/07/2023), in view of Enzelberger et al (US 2014/0141498 A1; Published Date: 22 May 2014) as applied to claim 1 above, and further in view of Randall et al (WO 2010/141131 A1; Published Date: 9 December 2010).
Regarding claim 20, the obviousness of modifying Derrick’s method with the microfluidic device of Enzelberger is discussed above as applied to claims 1 and 19.
However, neither Derrick or Enzelberger teach the method comprises automatically diluting the synthetic product in the microfluidic path device based on the determined yield.
Randall teaches a microfluidic device that includes a first domain configured for PCR amplification, a second domain for electrophoretic separation (Abstract), and a “post-PCR clean-up/dilution domain” that is fluidically coupled with the first and second domain that can be used for any suitable process after the PCR amplification and before the electrophoretic separation([0029]). Although Randall does not explicitly recite dilution is “based on the determined yield” as recited in the instant claim, Randall teaches dilution of PCR product at ratios from 1:5 to 1:20 (claim 8) and inherently teaches that yield must be known to implement the specific dilution for downstream electrophoretic separation.
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Enzelberger’s microfluidic device with a dilution domain from Randall to conduct the method of Derrick because it would have merely amounted to a simple combination of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of automatically diluting the PCR products for downstream analysis or sequencing. One would have had a reasonable expectation of success in doing so because Randall teaches a method of conducting PCR amplifications and automatically diluting the PCR products for electrophoretic separations using a microfluidic device with a dilution domain.
Conclusion
No claims are allowable.
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QIWEN SU-TOBON
Examiner
Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636