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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-20, in the reply filed on 11/24/2025 is acknowledged.
Claims 21, 30, and 43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-21, 30, and 43 are pending.
Claims 1-20 are under examination on the merits.
Priority
This application 18/062,918 filed on 12/07/2022claims the benefit of provisional U.S. Patent Application No. 63/286,717, filed on 12/07/2021.
The priority date of claim 1 and its dependent claims 2-20 is determined to be 12/07/2021, the filing date of provisional U.S. Patent Application No. 63/286,717.
Claim Objections
Claim 1 step a) part i) recites the limitation ” a first cleavage region --- wherein the first cleavage region is capable of forming a first cleavage site when double stranded”. Claim 1 step a) part ii) recites the limitation ”a first cleavage region at the 5' end, wherein at least a portion of the fourth region 3' of the first cleavage region is complementary to the first region of the first activation probe, wherein the first cleavage region is capable of forming a first cleavage site when double stranded”
Later instances reciting the “first cleavage region” recite ”the first cleavage region of the first activation probe” or “the first cleavage region of the first cleavable probe” (claim 1 step b, claim 10, claim 13) . Similarly, later instances reciting the “first cleavage site” recite ”the first cleavage site of the first activation probe” or “ first cleavage site of the first cleavable probe” (claim 1 step b, claim 10, claim 13).
It is suggested to amend “a first cleavage region” and “a first cleavage site” in step a, parts (i) and (ii) to clarify the limitation.
Claim 15 step d) part i), recites the limitation “a first cleavage region, wherein the second region is complementary to the second target nucleic acid, wherein the first cleavage region is capable of forming a first cleavage site when double stranded”. Claim 15 step d) part ii) recites the limitation “a first cleavage region at the 5' end, wherein at least a portion of the fourth region 3' of the first cleavage region is complementary to the first region of the second activation probe, wherein the first cleavage region is capable of forming a first cleavage site when double stranded”.
Later instances reciting the “first cleavage region” recite ”the first cleavage region of the second activation probe” or “first cleavage region of the second cleavable probe” (claim 15 step e). Similarly, later instances reciting the “first cleavage site” recite ”the first cleavage site of the first activation probe” or “ first cleavage site of the first cleavable probe” (claim 15 step e).
It is suggested to amend “a first cleavage region” and “a first cleavage site” in step d, parts (i) and (ii) to clarify the limitation.
Claim 18 step d) part i), recites the limitation “a first cleavage region, --- wherein the first cleavage region is capable of forming a first cleavage site when double stranded”.
Later instances in claim 18 reciting the “first cleavage region” recite ”the first cleavage region of the second activation probe” or “the first cleavage region of the first cleavable probe” (claim 18 step e). Similarly, later instances reciting the “first cleavage site” recite ”the first cleavage site of the first activation probe” or “ the first cleavage site of the first cleavable probe” (claim 18 step e).
It is suggested to amend “a first cleavage region” and “a first cleavage site” in step d, part (i) to clarify the limitation.
Claim Interpretation
Claim 15 step (e), part (ii) includes the term “optionally” to describe limitations. Claim scope is not limited by claim language that makes optional but does not require specific structural features. MPEP 2111.04.
Claim Rejections - 35 USC § 112(b)
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 1-20 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.
Claim 1 step (b) part (ii) recites the limitation “the first cleavage region of the activation probe”. There is insufficient antecedent basis for this limitation in the claim. It is suggested to change the limitation to “the first cleavage region of the first activation probe”.
Claims 2-20 are similarly indefinite because they directly or indirectly depend from claim 1.
Claim 20 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. Claim 20 recites the limitation “detecting the presence of the first target nucleic acid or a second distinct target nucleic acid in the sample by detecting the presence of the first hairpin probe”. Claim 12 sequentially depends from claim 1 and recites “wherein the reagents contacting the sample include a second activation probe having a 5' first region that is not complementary to the first or second target nucleic acid and is the same as the 5' first region of the first activation probe, and a second region comprising a first cleavage site, wherein the second region of the second activation probe is complementary to the second target nucleic acid”. The omitted steps in claim 1 and its dependent claim 20 appear to be: steps causing the second activation probe to react with the first hairpin probe. Claims should clearly delineate all active steps required for performing the claimed methods.
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.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Johnson et al. (US PGPub 2016/0040219) and Roth et al. (US PGPub 2014/0315747).
Regarding claim 1, Johnson teaches methods for the detection of nucleic acids. Regarding step (a) part (ii), Johnson teaches contacting a sample with a cleavable probe comprising a first sequence region comprising a label; a second sequence region; and a sequence that is the reverse complement of the second sequence region; and a sequence (a fourth region comprising a first cleavage region) that is complementary to a first region on a nucleic acid and cleavable after hybridization, i.e. when double-stranded (para 9). Johnson further teaches the cleavable probe may further comprise a loop sequence of one or more nucleotides between the second sequence region and the sequence that is the reverse complement of the second sequence region, with a loop sequence that comprises one or more polymerase extension blocking moieties (para 12).
Regarding step (a) part (iii), Johnson teaches the use of endoribonucleases (Abstract and para 9).
Regarding step (b), Johnson teaches forming a hairpin probe (para), having a first Tm (Table 2 and para 173). Johnson teaches hybridizing the cleavable probe with a target nucleic acid; cleaving the hybridized probe to form a truncated probe; extending the hairpin probe and allowing the truncated probe to hybridize to itself to form a hairpin probe (paras 9-11), which reads on parts (iv) – (vi).
Regarding step (c), Johnson teaches detecting the signal (presence) of the hairpin probe to detect the target nucleic acid (paras 9-11).
Regarding step (a) part (i), Johnson does not teach (I) the recited first activation probe. Regarding step (a) part (ii), Johnson teaches that the sequence of the cleavable probe is complementary to a first region of a target nucleic acid, but does not teach (II) that the nucleic acid is a first region of a first activation probe.
Roth teaches (I) a bifunctional mediator probe (activation probe) comprising, from 5’ to 3’, a mediator region (first region) and a probe region (second region). The probe region has affinity to a template molecule (target nucleic acid) and the mediator probe is cleaved at a cleavage site between the regions during an amplification process (i.e. when double stranded), wherein interaction of the cleaved mediator region with a detection molecule triggers a detectable signal (para 36). The mediator region does not have any affinity for the template molecule (para 37) and has affinity to a detection molecule (para 36).
Roth further teaches (II) at the 3′ end, the detection molecule also contains a mediator hybridization site that is complementary to the mediator region (para 118).
Regarding step (b), Johnson does not teach parts (i) – (iii) directed towards the first activation probe.
Roth teaches a reaction comprising binding the probe region of the mediator probe to a sequence of the template molecule (target nucleic acid), cleaving and splitting off the mediator probe at the cleavage site (releasing a first flap probe) and binding of the cleaved mediator region of the mediator probe to the detection molecule (para 97). Roth further teaches after adding the mediator region onto a sequence region of the unpaired 3' sequence segment, the mediator region is preferably elongated by a polymerase, which also reads on part (iv) of step (b).
Roth states that the use of a mediator probe separate from the detection molecule (hairpin) allows design of the detection molecule to be designed independently of the target molecule, making it possible to detect multiple target molecules in a sample and adapting the reaction inexpensively (para 62). Roth further states that the mediator probe is advantageous for multiplexing (para 146).
Neither Johnson nor Roth teach the released probe comprises at least one nucleotide of the second region of the first activation probe as in part b step (ii).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention. The modification would have entailed using the mediator probe of Roth to hybridize to the target nucleic acid instead of the cleavable probe directly and release a mediator (flap) probe region and designing the sequence that is complementary to a first region on a target nucleic acid on the cleavable probe of Johnson to be complementary to the nucleic acids of the first region of the mediator probe of Roth. Alternatively the modification would have entailed using the cleavable probe of Johnson as the detection molecule of Roth. The modification would further have entailed following the method of Roth to bind the cleavable probe of Johnson to form the hairpin probe for detecting the target nucleic acid. Both Johnson and Roth are silent regarding the released probe comprises at least one nucleotide of the second region of the first activation probe. This modification would have been a matter of routine modification and optimization as varying lengths of probes was well known in the art at the time as evidenced by the multiple examples of different probes and varying cleavage sites in both Roth and Johnson. One would have been motivated to combine the elements of Roth and Johnson in order to decrease costs and increase multiplex detection potential, a stated goal of both, with the sensitivity of detection provided by the cleavable probe of Johnson. Further, a two part system as in Roth provides added flexibility in terms of design and cost. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 2, Johnson teaches amplification of a target sequence. The amplification can be performed during the cleavage and extension of the cleavable probes (para 61).
Regarding claim 3, Johnson teaches the label can comprise one non-natural nucleotide labeled with a first member of a reporter-quencher pair and extension of the hairpin probe results in the incorporation of a complementary non-natural nucleotide labeled with a second member of the reporter-quencher pair (para 9).
Regarding claim 4, Johnson teaches a label that comprises one non-natural nucleotide labeled with a first member of a reporter-quencher pair and a complementary non-natural nucleotide labeled with a second member of the reporter-quencher pair (para 9).
Regarding claim 5, Johnson teaches a non-natural nucleotide is an isobase, such as iso-guanine (isoG) or iso-cytosine (isoC) (para 20).
Regarding claim 6, Johnson teaches the cleavable probe comprises both a fluorophore (F) and a quencher (Q) with a confirmation such that when the probe is single-stranded the proximity of the fluorophore to the quencher results in detectable quenching of the signal from the fluorophore. And that extension of the cleaved probe onto the first sequence region creates a double-stranded molecule having a conformation that places the fluorophore at a greater distance from the quencher such that a detectable change in the signal can be observed (para 177 and Fig. 16).
Regarding claim 7, Johnson teaches performing a melt analysis on the hairpin probe (paras 9-11, 57).
Regarding claim 8, Johnson teaches detecting a signal by detecting a change in the signal from the reporter when increasing the temperature above or decreasing the temperature below the melt point of the hairpin (para 63).
Regarding claim 9, Johnson does not teach the first activation probe is cleaved by an invader assay cleavage event. Roth teaches the use of an invader assay but does not use the method for cleavage of the mediator probe (activation probe).
However, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention. The modification would have entailed substituting a different method of cleaving the mediator probe of Roth once bound to the target in order to release the mediator region (flap probe). Determining an appropriate means of cleavage is deemed a matter of judicious selection and routine optimization which is well within the purview of the skilled artisan. One of ordinary skill in the art would have been motivated to try different temperatures in order optimize conditions of cleavage and probe release. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 10, Johnson teaches the use of an endoribonuclease for cleavage of probes that comprise a ribonucleotide position (Abstract, para 76). However, Johnson teaches that the cleavable region that comprises at least one ribonucleotide and is cleaved by an endoribonuclease is within the cleavable probe.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention. The modification would have entailed performing the method of Johnson with the mediator probe of Roth which comprises a probe region complementary to the target nucleic acid. The inclusion of ribonucleotides in the cleavage region of the mediator probe and use of an endoribonuclease for cleavage would have been a simple substitution and constitutes a routine optimization. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 11, Johnson teaches an endoribonuclease can be RNase HII (para 76, claim 3).
Regarding claim 12, Johnson teaches using a polymerase possessing 5′ nuclease activity thereby cleaving the probe that is hybridized with target nucleic acid (paras 57, 58).
Regarding claim 13, Johnson teaches a cleavable probe with a fourth sequence comprising one or more ribonucleotide base that is complimentary to a first region on a first strand of the target nucleic acid, that is cleaved with an endoribonuclease (para 9), and the endoribonuclease can be RNase HII (para 76, claim 3). However, Johnson teaches that the cleavable probe complementary region is complementary to a target nucleic acid.
Roth teaches the detection molecule (cleavable probe) mediator hybridization site is complementary to the mediator region of the mediator probe (activation probe) (para 118).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention. The modification would have entailed performing the method of Johnson with the mediator probe of Roth which comprises a probe region complementary to the target nucleic acid. The inclusion of ribonucleotides in the cleavage region of the mediator probe and use of an endoribonuclease for cleavage would have been a simple substitution and constitutes a routine optimization. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 14, neither Johnson nor Roth Johnson teaches cleavage of the first cleavable probe is performed by a restriction enzyme or a nicking enzyme.
Roth teaches using a restriction enzyme to cleave the cleavable probe (para 89).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention. The modification would have entailed substituting the restriction enzyme of Roth of the endoribonuclease of Johnson. Such a modification would have been a simple substitution and choosing a particular nuclease for cleaving constitutes a design choice that constitutes routine optimization. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 15, Johnson teaches use of a second cleavable probe comprising, from 5′ to 3′, (i) a first sequence region comprising at least a one non-natural nucleotide labeled with a first member of a reporter-quencher pair; (ii) a second sequence region; (iii) a sequence that is the reverse complement of the second sequence region; and (iv) a sequence comprising one or more ribonucleotide base that is complimentary to a first region on a first strand of a second target nucleic acid (para 55, claim 51), which reads on step (d) part (ii).
Regarding step (d) part (iii), Johnson teaches the use of endoribonucleases (Abstract and para 9).
Regarding step (e) parts (iv)- (vi), Johnson teaches forming a hairpin probe (para), having a first Tm (Table 2 and para 173). Johnson teaches hybridizing the cleavable probe with a target nucleic acid; cleaving the hybridized probe to form a second truncated probe; extending the second hairpin probe and allowing the second truncated probe to hybridize to itself to form a hairpin probe (para 21). Johnson further teaches first and second cleavable probes with distinguishable melting temperatures (paras 21, 49, claim 149).
Regarding step (f), Johnson teaches detecting the signal (presence) of a second hairpin probe to detect a second target nucleic acid (para 21).
Regarding step (d) part (i), Johnson does not teach (I) the recited second activation probe. Regarding step (d) part (ii), Johnson teaches that the sequence of the cleavable probe is complementary to a first region of a target nucleic acid, but does not teach (II) that the nucleic acid is a first region of a first activation probe.
Roth teaches (I) a mediator probe (activation probe) comprising, from 5’ to 3’, a mediator region (first region) and a probe region (second region). The probe region has affinity to a template molecule (target nucleic acid) and the mediator probe is cleaved at a cleavage site between the regions during an amplification process (i.e. when double stranded), wherein interaction of the cleaved mediator region with a detection molecule triggers a detectable signal (para 36). The mediator region does not have any affinity for the template molecule (para 37) and has affinity to a detection molecule (para 36).
Roth further teaches (II) at the 3′ end, the detection molecule also contains a mediator hybridization site that is complementary to the mediator region (para 118).
detecting multiple targets.
Roth teaches the use of "n" different mediator probes for "n" different target molecules (i.e.. a second mediator probe and a second target nucleic acid), wherein the mediator region represents a specific interaction to a defined detection molecule, i.e. a second cleavable probe paired with a second mediator probe (para 146). Roth further teaches the use two different mediator probes (activation probes) and two different detection molecules for detecting different nucleic acids in parallel (para 127),
Regarding step (e), Johnson does not teach parts (i) – (iii) directed towards the second activation probe.
Roth teaches a reaction comprising binding the probe region of the mediator probe to a sequence of the template molecule (target nucleic acid), cleaving and splitting off the mediator probe at the cleavage site (releasing a first flap probe) and binding of the cleaved mediator region of the mediator probe to the detection molecule (para 97). Roth further teaches after adding the mediator region onto a sequence region of the unpaired 3' sequence segment, the mediator region is preferably elongated by a polymerase, which also reads on part (iv) of step (e).
Roth states that the use of a mediator probe separate from the detection molecule (hairpin) allows design of the detection molecule to be designed independently of the target molecule, making it possible to detect multiple target molecules in a sample and adapting the reaction inexpensively (para 62). Roth further states that the mediator probe is advantageous for multiplexing and allows multiparameter analysis (para 146).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention. The modification would have entailed using two mediator probes of Roth to hybridize to two target nucleic acids instead of the cleavable probe directly and release mediator (flap) probe regions specific to two detection molecules (cleavable probes) and designing the sequence that is complementary to a first region on a target nucleic acid on two cleavable probes of Johnson to be complementary to the nucleic acids of the first region of the two mediator probes of Roth, with one mediator probe paired to one cleavable probe. Alternatively the modification would have entailed using the two cleavable probes of Johnson as the detection molecules of Roth. The modification would further have entailed following the method of Roth to bind the cleavable probe of Johnson to form the hairpin probe for detecting the target nucleic acid and performing the same reactions for each pair of mediator and cleavable probes. One would have been motivated to combine the elements of Roth and Johnson and add a second pair of probes in order to increase multiplex target nucleic acid detection, a stated goal of both, with the sensitivity of detection provided by the cleavable probe of Johnson. Further, a two part system as in Roth provides added flexibility in terms of design and cost. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 16, Johnson teaches amplification of a target sequence. The amplification can be performed during the cleavage and extension of the cleavable probes (para 61 and claim 42).
Regarding claim 17, Johnson teaches first and second cleavable probes with the same reporter and distinguishable melting temperatures that differ by 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30° C from one another (paras 21,49) and detecting a signal by detecting a change in the signal from the reporter when increasing the temperature above or decreasing the temperature below the melt point of the hairpin of one more of the primers in the sample (para 63), which reads on steps (g) and (i) and the limitation in step (h) “detecting signal from the reporter at a third temperature that is below the second TM and a fourth temperature that is above the second TM”.
Johnson does not explicitly teach in step (h) wherein the third temperature is equal to or greater than the second temperature.
However, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Johnson and Roth to arrive at the instantly claimed invention. The method of Johnson comprising two cleavable probes is directed to cleavable probes with distinguishable melting temperatures. It would have been obvious to use temperatures that do not overlap (i.e. the third temperature is equal to or greater than the second temperature). Determining an appropriate temperature range is deemed merely a matter of judicious selection and routine optimization which is well within the purview of the skilled artisan. One of ordinary skill in the art would have been motivated to try different temperatures in order to optimize conditions for distinguishing melting temperatures. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 18, step (d) part (ii) Johnson teaches the use of endoribonucleases (Abstract and para 9).
Regarding step (e) parts (iv)- (vi), Johnson teaches forming a hairpin probe (para), having a first Tm (Table 2 and para 173). Johnson teaches hybridizing the cleavable probe with a target nucleic acid; cleaving the hybridized probe to form a second truncated probe; extending the second hairpin probe and allowing the second truncated probe to hybridize to itself to form a hairpin probe (para 21).
Regarding step (e), Johnson teaches detecting the signal (presence) of the first hairpin probe (paras 9-11).
Regarding step (d) part (i), Johnson does not teach the recited second activation probe that has the
Roth teaches a mediator probe (activation probe) comprising, from 5’ to 3’, a mediator region (first region) and a probe region (second region). The probe region has affinity to a template molecule (target nucleic acid) and the mediator probe is cleaved at a cleavage site between the regions during an amplification process (i.e. when double stranded), wherein interaction of the cleaved mediator region with a detection molecule triggers a detectable signal (para 36). The mediator region does not have any affinity for the template molecule (para 37) and has affinity to a detection molecule (para 36).
Roth teaches the use of "n" different mediator probes for "n" different target molecules (i.e.. a second mediator probe and a second target nucleic acid) (para 146)., which reads on a second mediator probe with a probe region complementary to a second target nucleic acid.
Roth further teaches that is possible to use a standardized detection molecule (i.e. a cleavable probe with a region complementary to the identical first mediator probe region and second mediator probe mediator region), which can be produced in large quantities to minimize production costs (para 123). Roth also teaches that coupling between the presence of a target molecule and the detection reaction depends only on the properties of the mediator region and/or the mediator probe and thus allows free coupling between any target molecule and any detection reaction and/or detection molecule (para 37).
Roth states that the detection molecule can therefore be used universally and is not bound to a specific target which greatly reduces cost because the detection molecule need not be tailored to each reaction and each target molecule (para 117).
Regarding step (e), Johnson does not teach parts (i) – (iii) directed towards the first activation probe.
Roth teaches a reaction comprising binding the probe region of the mediator probe to a sequence of the template molecule (target nucleic acid), cleaving and splitting off the mediator probe at the cleavage site (releasing a first flap probe) and binding of the cleaved mediator region of the mediator probe to the detection molecule (para 97). Roth further teaches after adding the mediator region onto a sequence region of the unpaired 3' sequence segment, the mediator region is preferably elongated by a polymerase, which also reads on part (iv) of step (b).
Roth states that the use of a mediator probe separate from the detection molecule (hairpin) allows design of the detection molecule to be designed independently of the target molecule, making it possible to detect multiple target molecules in a sample and adapting the reaction inexpensively (para 62). Roth further states that the mediator probe is advantageous for multiplexing.
Roth does not explicitly teach a second mediator probe with a mediator region identical to the first region of the first activation probe.
However, It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention using two mediator probes capable of binding to the same cleavable probe. The modification would have entailed using two mediator probes of Roth to hybridize to two target nucleic acids and identical mediator regions, releasing mediator (flap) probe regions specific to two detection molecules (cleavable probes) and designing the sequence that is complementary to a first region on a target nucleic acid on the cleavable probe of Johnson to be complementary to the nucleic acids of the first region of the two mediator probes of Roth. The modification would further have entailed following the method of Roth to bind mediator regions from a first and second mediator probe to the cleavable probe of Johnson to form the hairpin probe for detecting the target nucleic acid and performing the same reactions for each pair of mediator and cleavable probes. One would have been motivated to combine the elements of Roth and Johnson and add a second pair of probes in order to increase multiplex target nucleic acid detection, a stated goal of both, with the sensitivity of detection provided by the cleavable probe of Johnson. Further, a two part system as in Roth provides added flexibility in terms of design and cost. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 19, Johnson teaches amplification of a target sequence. The amplification can be performed during the cleavage and extension of the cleavable probes (para 61).
Regarding claim 20, Roth teaches a mediator probe (activation probe) comprising, from 5’ to 3’, a mediator region (first region) and a probe region (second region). The probe region has affinity to a template molecule (target nucleic acid) and the mediator probe is cleaved at a cleavage site between the regions during an amplification process (i.e. when double stranded), wherein interaction of the cleaved mediator region with a detection molecule triggers a detectable signal (para 36). The mediator region does not have any affinity for the template molecule (para 37) and has affinity to a detection molecule (para 36).
Roth teaches the use of "n" different mediator probes for "n" different target molecules (i.e.. a second mediator probe and a second target nucleic acid) (para 146)., which reads on a second mediator probe with a probe region complementary to a second target nucleic acid.
Roth teaches that coupling between the presence of a target molecule and the detection reaction depends only on the properties of the mediator region and/or the mediator probe and thus allows free coupling between any target molecule and any detection reaction and/or detection molecule (para 37). Roth further teaches that is possible to use a standardized detection molecule (e.g. a cleavable probe with a region complementary to the identical first mediator probe region and second mediator probe mediator region), which can be produced in large quantities to minimize production costs (para 123).
Roth states that the detection molecule can therefore be used universally and is not bound to a specific target which greatly reduces cost because the detection molecule need not be tailored to each reaction and each target molecule (para 117).
Roth does not explicitly teach a second mediator probe with a mediator region identical to the first region of the first activation probe.
However, It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Johnson and Roth to arrive at the instantly claimed invention using two mediator probes capable of binding to the same cleavable probe. The modification would have entailed using two mediator probes of Roth to hybridize to two target nucleic acids and identical mediator regions, releasing mediator (flap) probe regions specific to two detection molecules (cleavable probes) and designing the sequence that is complementary to a first region on a target nucleic acid on the cleavable probe of Johnson to be complementary to the nucleic acids of the first region of the two mediator probes of Roth. One would have been motivated to combine the elements of Roth and Johnson and add a second pair of mediator probes in order to increase multiplex target nucleic acid detection, a stated goal of both. Further, a two part system as in Roth provides added flexibility in terms of design and cost and a shared detection molecule (cleavable probe) would simplify design by only requiring change to the mediator probe complementary to a second target nucleic acid. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 9,982,291 in view of Johnson et al. (US PGPub 2016/0040219) and Roth et al. (US PGPub 2014/0315747). Although the claims at issue are not identical, they are not patentably distinct from each other because both methods are directed to methods using a cleavable probe that forms a hairpin reporter to detecting a target nucleic acids by detecting a signal and performing melt analysis.
Claim 1 of the ‘291 patent requires (a) contacting a sample with a first cleavable probe, said probe comprising, from 5′ to 3′, (i) a first sequence region comprising at least one non-natural nucleotide labeled with a first member of a reporter-quencher pair; (ii) a second sequence region; (iii) a sequence that is the reverse complement of the second sequence region; and (iv) a sequence comprising one or more ribonucleotide base(s) that is complementary to a first region on a first strand of the target nucleic acid; (b) contacting the cleavable probe with an endoribonuclease, thereby cleaving probe that is hybridized with target nucleic acid to form a truncated cleavable probe; (c) allowing the truncated cleavable probe to hybridize to itself to form a hairpin probe; (d) extending the hairpin probe in the presence of a non-natural nucleotide labeled with a second member of a reporter-quencher pair that is capable of base-pairing with the at least one non-natural nucleotide of the first sequence region; and (e) detecting the target nucleic acid by detecting a change in signal from the label on the cleavable probe and the hairpin probe, which satisfies the requirements of claims 1, 3, 4,5, and 10.
Regarding instant claim 1, claim 5 of the ‘291 patent further requires the cleavable probe further comprises (v) a loop sequence of one or more nucleotide(s) between the second sequence region and the sequence that is the reverse complement of the second sequence region and claim 9 of the ‘291 patent requires the cleavable probe comprises an extension-blocking modification in the loop sequence.
Regarding instant claim 2, claim 12 of the ‘291 patent requires amplifying the target nucleic acid.
Regarding instant claim 6, claims of the ‘291 patent do not require the label comprises a reporter-quencher pair arranged such that the quencher quenches the reporter signal when the first region of the first cleavable probe is single stranded and extension of the hybridized third region separates the reporter and quencher to release the reporter from quenching.
The teachings of Johnson as they relate to these claims are given previously in this office action and are fully incorporated here.
Regarding instant claims 7 and 8, claim 10 of the ‘291 patent requires detecting a change in signal from the label comprises detecting a change in signal from a reporter as the temperature of the sample is changed and claim 11 of the ‘291 patent requires detecting a change in signal from the reporter comprises detecting a change in signal from the reporter as the temperature of the sample is increased above the melt point of the hairpin probe.
Regarding instant claim 11, claim 3 of the ‘291 patent requires the endoribonuclease is RNase HII.
Regarding instant claim 12, claims of the ‘291 patent do not require
The teachings of Johnson as they relate to these claims are given previously in this office action and are fully incorporated here.
Regarding instant claims 9 and 13-20, the claims of the ‘291 patent do not require the recited limitations.
The teachings of Johnson and Roth as they relate to these claims are given previously in this office action and are fully incorporated here.
Conclusion
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682