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 .
Specification
The disclosure is objected to because of the following informalities:
The specification has been found to comprise nucleotide sequences that are not accompanies with the requisite SEQ ID NO. See, for example, pages 25, 27, and 29.
The use of the term TWEEN 20, which is a trade name or a mark used in commerce, has been noted in this application. Se, for example, page 25 of the disclosure. 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.
Appropriate correction is required.
Claim Objections
Claim 2 is objected to because of the following informalities: Claim 2 comprises what appears to be is a typo “ina” . Appropriate correction is required.
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.
Claim(s) 1-9 and 11-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 2012/0156678 A1 (Le et al.) in view of US 5,262,299 (Evangeliste et al.), US 2007/0009974 A1 (Alderete et al.), and US 2014/0315190 A1 (Bornarth et al.).
Le et al., at paragraph [0085], teach:
[0085] In another embodiment, a detection system of the invention may be used to detect a target molecule, forming a binding-induced hairpin as follows: see FIG. 3: (A). A first probe 10 and a second probe 20 are used to bind to target molecule 30. Target molecule 30 may be a single molecule or two or more associated molecules. In this embodiment, the free end of the oligonucleotide of the first probe 10 further comprises regions of complementarity 15 and 16 that allow the end of the oligonucleotide to fold back and base-pair to form a hairpin loop 14 and stem 15+16. Targeting molecules 13 and 23 are merely depicted as antibodies, but may be any targeting molecule as described herein. In the absence of targets, the first and second probes are typically present separately. The length of stem sequences may be short enough so that the free probes typically do not hybridize together. (B) In the presence of target molecules, a first probe and a second probe bind to a single target molecule (or to two or more associated molecules), placing the two probes in proximity. (C) As a result, nucleotides at the free end 22 of the oligonucleotide of the second probe 20 may hybridize to complementary nucleotides near the free end 12 of the oligonucleotide of the first probe 10, forming a hairpin stem 41, thereby forming a binding-induced hairpin structure 40. In this embodiment, 16 is at the end of the oligonucleotide of the first probe; and 12 is near the free end of the oligonucleotide of the first probe. The term "near" is not limited by any specific distance away from the end of the oligonucleotide. A nucleotide that is near the end of the oligonucleotide may be at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70 or more nucleotides away from the last (terminal) nucleotide at the free end of an oligonucleotide. Typically, "near" refers to nucleotides that are adjacent to the pre-existing hairpin of a probe. The nonhybridized portions of the first and second probes 11 and 21, together with the targeting molecules 13 and 23, and the target molecule (or the two or more associated molecules) bound thereto 30, form the hairpin loop 42 of the binding-induced hairpin. In this embodiment, the oligonucleotide of the first probe comprises a pre-existing hairpin, i.e. loop 14, and stem 15+16. Thus hybridization of nucleotides at the free end 22 of the oligonucleotide of the second probe 20 to complementary nucleotides near the free end 12 of the oligonucleotide of the first probe 10 results in the formation of two hairpin loops (14 and 42) with a common hairpin stem (15, 16 and 41). (D) The formation of the binding-induced hairpin places the free end 16 of the first probe adjacent to the free end 22 of the second probe, both complementary to the other arm, allowing these free ends to be joined by enzymatic DNA ligation (e.g. by a ligase, such as T4 DNA ligase). This approach does not require, for example, the presence of a connector molecule in order to ligate the ends of the first and second probes. This results in a binding-induced hairpin comprising a single oligonucleotide 50. Detection of new oligonucleotide correlates with the presence of the target molecule.
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Le et al., at paragraph [0083] teach:
[0083] In one embodiment, a detection system of the invention may be used to detect a target molecule, forming a binding-induced hairpin as follows: see FIG. 1: (A). A first probe 10 and a second probe 20 are used to bind to target molecule 30. Target molecule 30 may be a single molecule or two or more associated molecules. In the absence of targets, the first and second probes are typically present separately. The length of stem sequences may be short enough so that the free probes typically do not hybridize together. Targeting molecules 13 and 23 are merely depicted as antibodies, but may be any targeting molecule as described herein. (B) In the presence of target molecules, a first probe and a second probe bind to a single target molecule (or to two or more associated molecules), placing the two probes in proximity. (C) As a result, nucleotides at the free end 22 of the oligonucleotide of the second probe 20 may hybridize to complementary nucleotides at the free end 12 of the oligonucleotide of the first probe 10, forming a hairpin stem 41, thereby forming a binding-induced hairpin structure 40. Because this hairpin structure is induced upon the binding of probes to the target molecule, it is termed as binding-induced hairpin. Unlike a traditional nucleotide hairpin, the binding-induced hairpin is a complex structure. Indeed, the nonhybridized portions of the probes 11 and 21, together with the targeting molecules 13 and 23, and the target molecule (or the two or more associated molecules) bound thereto 30, form the hairpin loop 42 of the binding-induced hairpin. (Emphasis added)
Le et al., at page 5 disclose:
Targeting Molecule
[0055] A detection system of the invention comprises first and second probes, each comprising an oligonucleotide and a targeting molecule. A targeting molecule of the invention may be any molecule that may be used to bind to, or associate with, a target molecule. In embodiments of the invention, the targeting molecule may be, without limitation, an aptamer, a ligand, a receptor or an antibody. (Emphasis added)
[0063] A targeting molecule of the invention may be prepared according to standard techniques know to the skilled person. For example, the targeting molecule may be produced synthetically, recombinantly or may be isolated from a source. In one embodiment, the source may be a biological source, preferably from a microorganism (e.g. a bacteria or a virus), an animal (e.g. a mouse, a rat, a rabbit, a goat, or a human), or a plant.
[0064] A detection system of the invention may comprise one or more types of targeting molecules. In one embodiment first and second probes may comprise the same type of targeting molecule. For instance, the targeting molecule of the first probe and that of the second probe may both be antibodies. In another embodiment, the first probe and the second probe may comprise distinct types of targeting molecules. For instance, the targeting molecule of the first probe may be an antibody; whereas the targeting molecule of the second probe may be an aptamer, or any molecule other than an antibody.
[0065] A detection system of the invention may comprise targeting molecules that bind to one or more target molecules. In one embodiment, the targeting molecule of the first probe and that of the second probe may bind to the same target molecule. In this instance, the targeting molecule of the first and second probes may bind to adjacent sites or distal sites on the same target molecule.
[0066] In another embodiment, the targeting molecule of the first probe and that of the second probe may bind to separate target molecules. In one instance, the targeting molecule of the first probe and that of the second probe may bind to separate but identical target molecules, provided the separate but identical target molecules may interact and/or associate with each other (e.g. homodimers or protein aggregates). In another instance, targeting molecule of the first probe and that of the second probe may bind to separate and distinct target molecules, provided the separate and distinct target molecules may interact and/or associate with each other (e.g. heterodimers, molecules of one of the following exemplary relationships: substrate/enzyme; and ligand/receptor). In a further instance, the targeting molecule of the first probe and that of the second probe may bind to separate and distinct target molecules, where the separate and distinct target molecules do not directly interact and/or associate with each other. In this regard, the separate and distinct target molecules may interact via one or more intermediate molecule.
[0068] A detection system of the invention comprises a first probe and a second probe, each of which comprises a targeting molecule attached to an end of an oligonucleotide. The oligonucleotide may be attached directly or indirectly to a targeting molecule. In one embodiment, an oligonucleotide is attached directly to a targeting molecule, e.g. by a chemical bond. In another embodiment, an oligonucleotide is attached indirectly to a targeting molecule via a linker. As used herein, a "linker" may also refer, without limitation, to linking of an oligonucleotide to a targeting molecule by chemical cross-linking.
Le et al., at paragraph [0075], teach:
0075] As used herein, a "target molecule" may include, but is not limited to, lipids, polysaccharides, glycans, proteins, oligonucleotide sequences, cells or fragments thereof, and drugs. A preferred group of target molecules are proteins, which include without limitation, enzymes, toxins, cell receptors, ligands, viral or bacterial proteins or antigens, signal transducing agents, cytokines, antibodies, prions and growth factors (e.g. PDGF). The target molecule may include natural and non-naturally occurring modifications thereof. For example, modifications of the target molecule may include in vivo and/or in vitro chemical derivatization of polypeptides, e.g., acetylation, carboxylation, phosphorylation, or glycosylation; such modifications may occur during polypeptide synthesis or processing or following treatment with isolated modifying enzymes. (Emphasis added)
Le et al., at paragraph [0120], teach:
[0120] Kits and commercial packages comprising the detection system described herein are contemplated. Such a kit or commercial package may contain instructions regarding use of the included detection system, for example, to detect a target molecule in a sample in accordance with the methods described herein. The kit or commercial package may also contain reagents' suitable for using a detection system of the invention. Suitable reagents may include, but are not limited to, buffers (e.g. PBS, buffers and reagents suitable for PCR or real time PCR, a buffer suitable for an enzymatic reaction, such as ligation by DNA ligase); pharmaceutically acceptable carriers, diluents and excipients (e.g. as described in Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)); adjuvants; blocking agents; ligases (e.g. T4 DNA ligase); and preservatives. (Emphasis added)
Le et al., at paragraph [0033], teach:
Complementary portions of two single-stranded nucleic acid molecules may comprise a sequence of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16 or more complementary nucleotides. Typically, the stem sequence should have at least 3 base-pairs; however the number suitable base-pairs may vary depending on the design of the probe and in consideration of the target molecule at issue.
The above presentation is deemed to fairly suggest limitations of claims 1, 3, 4, 5,8, 9, 11-13, and 16-20.
Le e al., has not been found to teach detection of the target substance in a well, nor specify the volume of a well, nor the sealing of a well.
Evangelista et al., at column 42, lines 56-60, teach sealing wells used in conjunction with hybridization assays. As disclosed therein:
For hybridization, 100 .mu.L of pre-hybridization solution containing 50 ng/ml or 125 ng/ml (for BCAHAP and FSAP experiments respectively) of biotinylated probe (Enzo pBR322 BioProbe) was added, the wells were sealed, and incubated overnight at 42.degree. C.
The above showing is deemed to fairly suggest limitations of claims 6, 7, 14 and 15.
Evangelista et al., like Le et al., has not been found to specify the volume of the wells.
Alderete et al., at paragraph [0068], teaches performing ELISA for three different proteins wherein 100 pL of assay mixture are added to wells.
Bornarth et al., in paragraph [0133], teach:
[0133] Another advantage provided by the methods disclosed herein is that the methods provide for the use of miniaturized assay volumes (e.g., 1-5 pL), which facilitates the use of high density microplate assay arrays of 16.times.24 (384 well), 32.times.48 (1536 well), or further customized arrays. Only about 5 to 40 picomole of protein may be required (0.1 pg to 1.011 g for a 25 kDa protein) per assay well, for a final protein concentration of about 1 to 4 uM. Thus, 1.0 mg of protein may be used to conduct 10.sup.3 to 10.sup.4 assays in the miniaturized format.
The above presentation is deemed to fairly suggest limitations of claim 2.
In view of the above presentation, it would have been quite obvious to one of ordinary skill in the art at the time of the invention to have applied the teachings of Le et al., and Evangelista et al., for to do so would enhance the reproducibility of the assay as the use of such small volumes presents an issue of evaporation and non-functionality. Said ordinary artisan would have also been motivated to have incorporated the teachings of Alderete et al., and Bornarth et al., for to use such small reaction volumes in places that comprise wells of like sizes speaks to not only lower costs due to use of lesser amounts of reactants, but also the ability to run a significant number of assays in a simultaneous manner.
In view of the well-developed state of the art and the applicability of the assay to the detection of a very broad genus of target substances, said ordinary artisan would have been amply motivated and would have had a most reasonable expectation of success.
In view of the above presentation and in the absence of convincing evidence to the contrary, claims 1-9 and 11-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 2012/0156678 A1 (Le et al.) in view of US 5,262,299 (Evangeliste et al.), US 2007/0009974 A1 (Alderete et al.), and US 2014/0315190 A1 (Bornarth et al.).
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 2012/0156678 A1 (Le et al.) in view of US 5,262,299 (Evangeliste et al.), US 2007/0009974 A1 (Alderete et al.), and US 2014/0315190 A1 (Bornarth et al.) as applied to claims 1-9 and 11-20 above, and further in view of US 2020/0318171 A1 (Peterson).
See above for the basis of the rejection as it pertains to the disclosures of Le et al., Evangeliste et al., Alderete et al., and Bornarth et al.
Neither Le et al., Evangeliste et al., Alderete et al., nor Bornarth et al., have been found to teach performing “an invasive cleavage assay”.
Peterson, at paragraph [0230], teaches:
[0230] In some embodiments, the oligomers are for use in performing invasive cleavage assays such as INVADER or INVADER PLUS assays. Such approaches can use a set of detection oligomers, comprising invasive and primary probe oligomers, to form a structure in which the 3′ end of an invasive oligomer competes with the 5′ flap of another oligomer for hybridization to the target sequence, resulting in a complex comprising a partially single-stranded primary probe. A cleavage agent is used that recognizes this structure and cleaves the primary probe, thus liberating the 5′ flap for subsequent detection; this is referred to as an invasive cleavage reaction. In some embodiments, detection occurs by a second invasive cleavage reaction wherein the 5′ flap hybridizes with a double-labeled oligomer (e.g., FRET cassette) and forms a substrate for the cleavage agent. Cleavage of the double-labeled oligomer can separate the two labels and thereby provide a detectable change in label behavior, such as a loss of quenching of a fluorophore. It has been found that this approach is suitable for discrimination of hypervirulent from non-hypervirulent tcdC alleles and also for multiplexing, facilitating a rapid and streamlined approach for assessing whether toxin-producing C. difficile nucleic acid is in a sample, whether the sample contains a tcdC allele associated with hypervirulence, and/or whether it has one, the other, or both of the Pathogenic locus and the Cdt locus.
Peterson, at paragraph [0261], teaches:
[0261] “Cassette,” when used in reference to an INVADER assay and/or invasive cleavage assay or reaction, as used herein refers to an oligomer or combination of oligomers configured to generate a detectable signal in response to cleavage of a detection oligomer in an INVADER assay. In some embodiments, the cassette hybridizes to an cleavage product (e.g., a “flap”) from cleavage of the detection oligomer (e.g., primary probe). In some embodiments, such hybridization results in a detectable change in fluorescence. In some embodiments, such hybridization forms a second invasive cleavage structure, such that the cassette can then be cleaved. In some embodiments, a cassette comprises an interacting pair of labels, e.g., a FRET pair (in which case the cassette is a “FRET cassette”). In some embodiments, a FRET cassette undergoes a detectable change in fluorescence properties upon hybridization to an cleavage product from cleavage of the detection oligomer.
In view of the above presentation, it would have been obvious to one of ordinary skill in the art to incorporate into the target binding assay of Le et al., the aspects of an invasive cleavage assay as both assay systems are based on the use of oligonucleotides to determine, directly and/or indirectly, the presence of a target substance.
In view of the well-developed state of the art and detailed guidance provided, said ordinary artisan would not have been amply motivated, but would have had a most reasonable expectation of success.
In view of the above presentation and in the absence of convincing evidence to the contrary, claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over US 2012/0156678 A1 (Le et al.) in view of US 5,262,299 (Evangeliste et al.), US 2007/0009974 A1 (Alderete et al.), and US 2014/0315190 A1 (Bornarth et al.) as applied to claims 1-9 and 11-20 above, and further in view of US 2020/0318171 A1 (Peterson).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM..
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682
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