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 and Formal Matters
This action is in response to papers filed 7/23/226 and supplemental amendment filed 8/20/2026.
Claims 1-2, 4-5, 7, 11, 13-16, 18, 21-22, 24-25 and 28 are pending.
Claims 4, 11, 13-14, have been amended.
The response of 7/23/2026 is not compliant with 37 CFR 1.121 as claims 14 has been amended, but is identified as previously presented. Further claim 5 in the instant response has been amended to be limited to an ammonium ligand, however the claims of 7/23/2026 encompassed potassium or ammonium, but is marked as previously presented. In order to promote compact prosecution and customer service the instant response will be examined. However future amendments which are non-compliant with 37 CFR 1.121 may not be entered or examined.
Applicant’s election without traverse of group 2, in the reply filed on least 60 percent of the nucleotides are guanine nucleotides; SEQ ID NO: 26; iCy3 and a shift in fluorescence wavelength. is acknowledged.
Claims 1-2, 16-18, 21-22, 24-25 and 28 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 6/24/2024.
Claims 4-5, 7, 11, 13-15 are being examined.
Priority
The instant application was filed 03/22/2021 and is a national stage entry of PCT/IB2019/058058 with an international filing date: 09/23/2019 and claims priority from provisional application 62734694 , filed 09/21/2018 and claims priority from provisional application 62774648 , filed 12/03/2018.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
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 4-5, 7, 11, 13-15 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.
As set forth in In re Alonso 88 USPQ2d 1849 (Fed. Cir. 2008), at 1851:
The written description requirement of 35 U.S.C. § 112, ¶ 1, is straightforward: “The specification shall contain a written description of the invention ….” To satisfy this requirement, the specification must describe the invention in sufficient detail so “that one skilled in the art can clearly conclude that the inventor invented the claimed invention as of the filing date sought.” Lockwood v. Am. Airlines, Inc., 107 F.3d 1565, 1572 [41 USPQ2d 1961] (Fed. Cir. 1997); see also LizardTech, Inc. v. Earth Res. Mapping, Inc., 424 F.3d 1336, 1345 [76 USPQ2d 1724] (Fed. Cir. 2005); Eiselstein v. Frank, 52 F.3d 1035, 1039 [34 USPQ2d 1467] (Fed. Cir. 1995).
Alonso at 1852:
A genus can be described by disclosing: (1) a representative number of species in that genus; or (2) its “relevant identifying characteristics,” such as “complete or partial structure, other physical and/or chemical properties, functional characteristics when coupled with a known or disclosed correlation between function and structure, or some combination of such characteristics.” Enzo, 323 F.3d at 964.
In applying the test as set forth in Alonso, it is noted that applicant is A reporter-containing oligonucleotide, comprising (a) a nucleotide sequence selected from the group consisting of:AGGAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 26);GGAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 27);AGGAGGGACGG/X/GGCAGGAGGA (SEQ ID NO: 28);GAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 29);GGAGGGACGG/X/GGCAGGAGGA (SEQ ID NO: 30);AGGAGGGACGG/X/GGCAGGAGG (SEQ ID NO: 31);AGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 32);GAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 33);GGAGGGACGG/X/GGCAGGAGG (SEQ ID NO: 34);AGGAGGGACGG/X/GGCAGGAG (SEQ ID NO: 35);GGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 36);AGGGACGG/X/GGCAGGAGGA (SEQ ID NO: 37);GAGGGACGG/X/GGCAGGAGG (SEQ ID NO: 38); GGAGGGACGG/X/GGCAGGAG (SEQ ID NO: 39);AGGAGGGACGG/X/GGCAGGA (SEQ ID NO: 40);GGGACGG/X/GGCAGGAGGA (SEQ ID NO: 41);AGGGACGG/X/GGCAGGAGG (SEQ ID NO: 42);GAGGGACGG/X/GGCAGGAG (SEQ ID NO: 43);GGAGGGACGG/X/GGCAGGA (SEQ ID NO: 44);GGGACGG/X/GGCAGGAGG (SEQ ID NO: 45);AGGGACGG/X/GGCAGGAG (SEQ ID NO: 46);GAGGGACGG/X/GGCAGGA (SEQ ID NO: 47);GGGACGG/X/GGCAGGAG (SEQ ID NO: 48);AGGGACGG/X/GGCAGGA (SEQ ID NO: 49);GGGACGG/X/GGCAGGA (SEQ ID NO: 50);wherein X is a fluorophore comprising a polymethine bond ,wherein the fluorophore is covalently incorporated in the oligonucleotide by two covalent linkages between the flurophore and each phosphate group of two neighboring nucleotide, wherein the reporter-containing oligonucleotide has between 14 and 22 nucleotides.
.Thus the claim encompass any of the recited SEQ ID NO which have a length of between 14 and 22 nucleotides. This encompasses SEQ ID NO 26 being truncated to 14 nucleotides for example as well as SEQ ID NO 50 being lengthened to 22 nucleotides. Further the clams requires, “fluorophore comprising a polymethine bond.” Thus it encompasses any fluourophore with any polymethine bond. Further the claim encompasses the fluorophore is covalently incorporated in the oligonucleotide by two covalent linkages between the flurophore and each phosphate group of two neighboring nucleotide. This is an enormous genus of nucleic acid sequences, fluorophores and means of attachment..
It is unclear if the recitation of “wherein X is a fluorophore comprising a polymethine bond as a built-in reporter,wherein the fluorophore is covalently incorporated in the oligonucleotide by two covalent linkages between the flurophore and each phosphate group of two neighboring nucleotides” requires the label to be at the X position or encompasses any position between two nucleotides by linking any phosphate of two neighboring nucleotides. The specification on page 3 states:
AGGAGGGACGG/X/GGCAGGAGGAG SEQ ID NO. 26 GAGGGACGG/X/GGCAGGAGG SEQ ID NO. 38
where X represents a fluorescence dye as the built-in reporter. In a preferred embodiment, the built-in reporter is incorporated into 5 the sugar-phosphate backbone of the aptamers. The built-in reporter may be an environmentally sensitive fluorescence dye, internally coupled to the aptamers. Exemplary environmentally sensitive dyes include cyanine dyes, such as Cy3, Cy3.5, Cy5, Cy5.5, Cy7, Alexa 555, Alexa 647, and derivatives thereof.
The specification teaches, “The singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise. For example, reference to "a 10 compound" includes a plurality of compounds and reference to "the compound" is a reference to one or more compounds and equivalents thereof known to those skilled in the art.” (page 9)
The specification teaches, “"Reporter" or "sensor" as used herein refers to a self-contained analytical device that can provide information about the chemical composition of its environment. For example, it can be a chemical moiety that detects and/or measures a change in the physical property of the environment, the parent molecule, or the overall system, and records, indicates, or otherwise responds to it.” (Page 11). Thus the claims require the reporter can provide information about any chemical in the environment. This is an enormous genus. While the claims comprise the recited sequence, there is no evidence the recited sequences will provide information about any compound, known or unknown.
The specification on pages 12-13 provide potassium ion sensing aptamers, SEQ ID NO 1-25.
The specification on page 26 asserts, “In the presence of 50 mM KCl, the O-328 (22) oligonucleotide containing an internal iCy3 (sequence: AGGAGGGACGG/iCy3/GGCAGGAGGAG) (SEQ ID NO:107) exhibited the longest fluorescence lifetime among the 46 DNA oligonucleotides labeled with iCy3 (Figure 2). Thus, it is evident that the sequence of O-328 is highly specific for K⁺.” Thus th
Dependent claim 5 requires, “wherein the oligonucleotide forms a G-quadruplex upon binding a ligand, wherein the ligand is ammonium..” Thus this is a functional limitation. This dependent claims encompass any ammonium or ammonium ion, this is an enormous genus.
Claim 13 depends from claim 4 and has been amended to require, “wherein the oligonucleotide undergoes a conformational change upon binding to a ligand of the oligonucleotide, wherein the conformational change of the oligonucleotide induces a photophysical change of the fluorophore..” This appears to require the reporter oligonucleotide, furthering the written description issues with any flurophore, any ligand and the funcationl outcome of wherein the oligonucleotide undergoes a conformational change upon binding to a ligand of the oligonucleotide, wherein the conformational change of the oligonucleotide induces a photophysical change of the fluorophor. However review of the specification is limited to the detection of potassium, Na+ and NH4+ by an iCy3 attached internally via phosphoramidite chemistry. Thus is a single species of ligand encompassed by a single species of oligonucleotides encompassed by the claim as well as a single fluorescent label.
Claim 14 continues providing functional limitations of, “wherein the oligonucleotide undergoes a conformational change upon binding to a ligand of the oligonucleotide, wherein the conformational change of the oligonucleotide induces a photophysical change of the fluorophore, wherein the photophysical change of the fluorophore is a shift in the fluorescence wavelength, a change in the fluorescence signal intensity, a change in the fluorescence life time, or combinations thereof.” ..” This appears to require the reporter oligonucleotide, furthering the written description issues with any flurophore, any ligand and the funcationl outcome of wherein the oligonucleotide undergoes a conformational change upon binding to a ligand of the oligonucleotide, wherein the conformational change of the oligonucleotide induces a photophysical change of the fluorophor. However review of the specification is limited to the detection of potassium, Na+ and NH4+ by an iCy3 attached internally via phosphoramidite chemistry. Thus is a single species of ligand encompassed by a single species of oligonucleotides encompassed by the claim as well as a single fluorescent label.
Further claim 15 recites, “wherein the fluorophore is fluorescent-quenched prior to binding of the ligand and becomes fluorescent or fluorescent-enhanced upon binding of the ligand.” This provides the function of being fluorescent and then provides the functional limitation of “non-fluorescent or fluorescent-quenched prior to binding of the ligand and becomes fluorescent or fluorescent-enhanced upon binding of the ligand.” However review of the specification is limited to the detection of potassium by an iCy3 attached internally via phosphoramidite chemistry. Thus is a thress species of ligand encompassed by a the limited species of SEQ ID NO 26 to SEQ ID NO 50 species of oligonucleotides encompassed by the claim as well as a single fluorescent label.
Thus the claims lack adequate written description.
Response to Arguments
The response traverses the rejection asserting, “The specification discloses that the built-in reporter is "covalently incorporated in the sugar-phosphate backbone of the oligonucleotide sequence ... via covalent linkages with the neighboring nucleotides," and, more particularly, that it is "covalently linked to the five-carbon sugar (through the 3'-OH group on the five-carbon sugar) of its neighboring nucleotide from the 5' end and to the phosphate group of its neighboring nucleotide from the 3' end." See
Specification, pages 21, lines 3-15. The specification further provides a representative structure "in which a Cy3 dye is incorporated in the sugar-phosphate backbone of the sequence of an oligonucleotide." Id. As illustrated in the chemical structure reproduced below, the claim language thus corresponds to a specific, well-defined chemical structure in which the fluorophore, such as iCy3, occupies the position designated X and is covalently bonded to its neighboring nucleotides through the sugar-phosphate backbone.“ This argument has been thoroughly reviewed but is not considered persuasive as the claims recite, “reporter containing oligonucleotide,” a fluorophore comprising any polymethine bond, a fluorophore incorporated into the oligonucleotide by any two covalent linkages between the fluorophore and each phosphate on tow neighboring nucleotides. Further the claims encompass shortening and lengthening the oligonucleotides in any manner to get to 14 to 22 nucleotides. These genus still encompass the functional requirement of a reporter of the independent claim and functional limitations of the dependent claims. Thus the claims lack adequate written description.
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.
Claims 4-5, 7, 11, 13-15 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 4 recites, “A reporter-containing oligonucleotide, comprising (a) a nucleotide sequence selected from the group consisting of:AGGAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 26);GGAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 27);AGGAGGGACGG/X/GGCAGGAGGA (SEQ ID NO: 28);GAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 29);GGAGGGACGG/X/GGCAGGAGGA (SEQ ID NO: 30);AGGAGGGACGG/X/GGCAGGAGG (SEQ ID NO: 31);AGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 32);GAGGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 33);GGAGGGACGG/X/GGCAGGAGG (SEQ ID NO: 34);AGGAGGGACGG/X/GGCAGGAG (SEQ ID NO: 35);GGGACGG/X/GGCAGGAGGAG (SEQ ID NO: 36);AGGGACGG/X/GGCAGGAGGA (SEQ ID NO: 37);GAGGGACGG/X/GGCAGGAGG (SEQ ID NO: 38); GGAGGGACGG/X/GGCAGGAG (SEQ ID NO: 39);AGGAGGGACGG/X/GGCAGGA (SEQ ID NO: 40);GGGACGG/X/GGCAGGAGGA (SEQ ID NO: 41);AGGGACGG/X/GGCAGGAGG (SEQ ID NO: 42);GAGGGACGG/X/GGCAGGAG (SEQ ID NO: 43);GGAGGGACGG/X/GGCAGGA (SEQ ID NO: 44);GGGACGG/X/GGCAGGAGG (SEQ ID NO: 45);AGGGACGG/X/GGCAGGAG (SEQ ID NO: 46);GAGGGACGG/X/GGCAGGA (SEQ ID NO: 47);GGGACGG/X/GGCAGGAG (SEQ ID NO: 48);AGGGACGG/X/GGCAGGA (SEQ ID NO: 49);GGGACGG/X/GGCAGGA (SEQ ID NO: 50);wherein X is a fluorophore comprising a polymethine bond ,wherein the fluorophore is covalently incorporated in the oligonucleotide by two covalent linkages between the flurophore and each phosphate group of two neighboring nucleotide, wherein the reporter-containing oligonucleotide has between 14 and 22 nucleotides...” The specification teaches, “The singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise. For example, reference to "a compound" includes a plurality of compounds and reference to "the compound" is a reference to one or more compounds and equivalents thereof known to those skilled in the art.” (page 9) The metes and bound are unclear as the sequences with /X/ appear to require a specific location, however the reporter-containing oligonucleotide has between 14 and 22 nucleotides allow for shortening or lengthening any of the sequences in any manner. Thus the metes and bounds are unclear what is encompassed by the claims.
Response to Arguments
The response traverses the previous rejections in view of the amendment. The previous rejections have been withdrawn, however the amendment has introduced numerous issues.
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.
Claim(s) 4-5, 7, 11, 13-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kwok ( Trends in Biotechnol., 35(10):997-1013 (2017)), Tucker(Current Pharmaceutical Design, 2012, 18, 2014-2026), Tippana (Nucleic Acids Research, 2014, Vol. 42, No. 12, 8106–8114), Li (Anal. Chem. 2010, 82, 7576–7580), Schultze (Nucleic Acids Research, 1999, Vol. 27, No. 15, 3018–3028 ) Varizhuk (Mini-Reviews in Medicinal Chemistry, 2016, 16, 1321-1329), Wojczewski (Synlett 1999, No. 10, 1667–1678), Domenyuk (WO2017161357), Bentwich (20070003575), Schierle-Arndt(US 20040118700), Hagen (ACS Omega 2019, 4, 8472−8479), Lee (Nucleic Acids Research, 2014, Vol. 42, No. 9 5967–5977).
Attention is directed to MPEP 2129 [R-6], Admissions as Prior Art, which states in part:
I. ADMISSIONS BY APPLICANT CONSTITUTE PRIOR ART
A statement by an applicant >in the specification or made< during prosecution identifying the work of another as “prior art” is an admission **>which can be relied upon for both anticipation and obviousness determinations, regardless of whether the admitted prior art would otherwise qualify as prior art under the statutory categories of 35 U.S.C. 102. Riverwood Int’l Corp. v. R.A. Jones & Co., 324 F.3d 1346, 1354, 66 USPQ2d 1331, 1337 (Fed. Cir. 2003); Constant v. Advanced Micro-Devices Inc., 848 F.2d 1560, 1570, 7 USPQ2d 1057, 1063 (Fed. Cir.1988).
Further, the courts have held information that an applicant admits is in the prior art "may be considered 'prior art' for any purpose, including use as evidence of obviousness under § 103." In re Nomiya, 509 F.2d 566, 570-71 (CCPA 1975).
The specification on page 15 states:
Additional sequences which can be used to make ligand sensing aptamers with a built-in reporter are the sequences of G-quadruplex forming aptamers, which are known in the art. DNA G-quadruplex forming aptamers are reviewed in Tucker, et al, Current Pharmaceutical Design, 2012, 18, 2014-2026. Exemplary sequences and their targets are listed in Table 1 below. See also Kwok, et al., Trends in Biotechnol., 35(10):997-1013 (2017).
While the claims recite the SEQ ID NO with /X/ at specific positions in the sequences, the claim also limits the reporter oligonucleotide to “wherein the reporter-containing oligonucleotide has between 14 and 22 nucleotides.” Thus the claim appears to allow for truncating the longer SEQ ID NO to get them to 14 nucleotides and adding nucleotides to get to 22 nucleotides in any fashion.
Kwok provides a review of G-Quadruplexes: Prediction, Characterization,
And Biological Application (title);. Kwok teaches, “Besides proteins and enzymes, specific G-quadruplex-containing aptamers have also been found to recognize small molecules (Table 1). SELEX was used to identify an aptamer called ‘spinach’ that recognizes 3,5-difluoro-4-hydroxybenzylidene imidazolinone, and produces fluorescence upon ligand binding [14]. Recent crystal structural studies showed that the ligand stacked with the unique G-quadruplex [15] (Figure 2B). Notably, the G-quadruplex was found to be in a special structural scaffold in the spinach aptamer that is essential for the ligand binding and fluorescence [15]. Since then, the spinach aptamer has been modified and applied for live cell imaging to track different biomolecules [16,17]. In addition, the sequence requirement for the fluorescence of spinach RNA aptamer was extensively studied [18], and several other fluorescent RNA aptamers, such as ‘mango’ aptamer and other variants of ‘spinach’, have been shown to contain G-quadruplex structures [19–22], providing structural insights for future design and development of brighter fluorescent RNA for imaging purposes.”(998, 3rd paragraph) Kwok teaches on page 1000, “Thanks to the unusual structure and folding of the G-quadruplex, one can experimentally identify G-quadruplex formation and investigate structural properties using biophysical tech niques (Table 2). For example, the topology of the G-quadruplex structure can be determined by monitoring the positive or negative circular dichroism (CD) signals at specific wavelengths [57]. In general, G-quadruplexes with parallel topology (Figure 1B) have negative and positive CD signals at 240 and 262 nm, respectively, whereas antiparallel topology (Figure 1B) places these signals at 262 and 295 nm, respectively. To verify G-quadruplex formation, one should also perform the CD experiments under non-G-quadruplex stabilizing (Li+) and G-quadruplex stabilizing conditions (such as K+or with G-quadruplex ligands), and scan toward the far-UV region ( 180–230 nm)”
Tucker teaches, “G-quadruplex DNA Aptamers and their Ligands: Structure, Function and Application “ (title) Tucker in table 1 multiple ligands of G-Quadraplexes including potassium. Tucker teaches, “G-quadruplex topology and stability was first understood from the perspective of telomeric sequences, and from these examples some generalities were drawn such as: 1) cation ability to induce quadruplex formation follows the trend K+>Rb+>Na+>Cs+>Li+ with mechanistic differences being the most understood between K+ and Na+, 2) many cations move in and out of the quadruplex core if not obstructed, 3) Ka values for divalent cations are significantly greater than those for monovalent cations and 4) stabilizing abilities of divalent cations relate in the order Sr2+>Ba2+>Ca2+>Mg2+ [40]. A number of studies have investigated the influence of cations on DNA aptamer structure, and TBA is again the most deeply studied model for this aspect of aptamers that can act as a case study. Not only do cations have an important role in stabilizing quadruplex aptamers, but this property has even been exploited for the purpose of cation detection. The TBA aptamer itself has also been used to detect Hg2+ and Pb2+ [75]. As a further example, aptamers have been generated for the detection of K+ using fluorometric and nanosilver resonance scattering methods [76, 77]. To some degree, these detection methods owe their approach to previous work in understanding the relationship between cation and DNA G quadruplex aptamer.” (2019, 2nd column, last full paragraph)
Tippana teaches, “The basic formula of [G3N1–7G3N1–7 G3N1–7 G3] allows four sets of G triplets to form into three layers of G tetrads, mediated by the Hoogsteen base pairing (10). The GQ structures are stabilized by monovalent cations such as potassium or sodium. These ions occupy the central cavity created by the stacks of G tetrads (11–13). GQ DNA can fold into parallel, antiparallel and hybrid conformations depending on its loop length and sequence composition (14). Conventional techniques such ascircular dichroism (CD)and thermal melting curves acquired through UV–visible spectroscopy are often used to distinguish GQ folding in to parallel and antiparallel conformations (15). CD readings will provide either a characteris tic peak at 260 nm for parallel or 295nmfortheantiparallel state. This allows for qualitative comparison among various GQ forming sequences (16). As demonstrated before, the single molecule FRET (smFRET) technique offers several advantages over ensemble methods. First, the fraction of molecules that fold into different conformations (parallel and antiparallel) can be quantified with accuracy. Second, unfolded DNA can be distinguished from folded con formations. Third, the real-time imaging of single molecules allows for the monitoring of molecules undergoing transitions from one state to another, thus enabling kinetic analysis. This approach was applied in studies of telomeric DNA (17–19), modified GQ sequences in various solution condi tions (18), GQbindingligands (20) andprotein interactions with the telomere overhang (21–23).” (8106, 2nd column, full paragraph).
Li teaches, “In this work, we utilize circular dichroism (CD), fluorescence, and UV-vis spectroscopy to characterize the DNA structures and monitor the fluorescence and absorbance changes of PPIX in K+ or Na+solution. Interestingly, we find the fluorescence intensity of PPIX can be remarkably enhanced by DNA binding. More importantly, PPIX exhibits a high selectivity for parallel G quadruplexes over the antiparallel and duplex. The selectivity and fluorescence property enable PPIX to indicate DNA structural changes via modulating fluorescence signal readout by its binding and release. This is illustrated by utilizing PPIX as a specific fluorescent probe for a K+ sensor, which is constructed based on an antiparallel-to-parallel conformation transition of the G-quadruplex.” (7577, 1st column, 2nd paragraph).
Varizhuk teaches methods of designing G4 aptamers.
Schultze teaches G quadraplex for binding ammonium ions (title, throughout).
Wojczewski teaches numerous methods of labeling nucleic acids including 5’ end, 3’ end and internal nucleotides.
Domenyuk teaches SEQ ID NO 33524 which provides 35 nucleotides including the re4vers complement of SEQ ID NO 42.
Bentwich teaches SEQ ID NO 185011 which is 64 nucleotides and comprise SEQ ID NO 42 (nucleotides 38-54) and SEQ ID NO 396894 which is 64 nucleotides and comprise SEQ ID NO 42 (5-21).
Schierle-Arndt teaches SEQ ID NO 160118 which comprise the reverse complement of SEQ ID NO 41( nucleotides 18 to 2)
Hagen teaches G-quadraplex (abstract, figures, throughout). Hagen teaches internally labeling of G-quadraplex with Cy3 or Cy5(table 1).
Lee teaches in figure S1.
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Designing and labeling G4, which are equivalents to those of the claims is routine experimentation. The prior art teaches the parameters and objectives involved in the selection of oligonucleotides that function as G4 quadraplexes with internal Cy3 or Cy5 labels as taught by Lee, see Varizhuk, Tucker, Tippana, Li, etc. The prior art is replete with guidance and information necessary to permit the ordinary artisan in the field of G-quadrapelx to design labeled G4 aptamers or G4 quadraplexes. As discussed above, the ordinary artisan would be motivated to have designed and tested new probes to obtain additional oligonucleotides that function to detect specific metal ions and identify oligonucleotides with improved properties. The ordinary artisan would have a reasonable expectation of success of obtaining additional labeled G4 aptamers or G4 quadraplexes. Thus, for the reasons provided above, the ordinary artisan would have designed additional labeled G4 aptamers using the teachings in the art at the time the invention was made. The claimed SEQ ID NOs are obvious over the cited prior art, absent secondary considerations.
With regards to claim 7, Long teaches, “50-Cy5.5-(CH2)6-GGGTGGGTGGGTGGGT-3). Thus long teaches a DNA sequence which is between 14 and 22 nucleotides inclusive.
With regards to claim 11Lee teaches Figure S1
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With regards to claim 13, Li teaches K+ and Na+.
With regards to claim 14, Long teaches a change in fluorescence intensity. (Figure 2).
With regards to claim 15, Long teaches fluorescence is increased upon binding of the ligand to the Pb+, K+ and Na+. Thus the fluorescence was quenched prior to binding of Pb+ relative to after Pb+.
Response to Arguments
The response traverses the rejection asserting none of the prior art contemplate the oligonucleotide defined by claim 4. This argument has been thoroughly reviewed but is not considered persuasive as the metes and bounds of claim 4 are unclear. Further in view of the lack of clarity of the claim the cited prior art at least renders the claims obvious.
The response continues by asserting the claimed oligonucleotide has an unexpected improved fluorescent lifetime. This argument has been thoroughly reviewed but is not considered persuasive as figure 3A and page 29, lines 6-9 are limited to a specific nucleotide sequence with a specific label, which is a species encompassed by the claims, but is not commensurate in scope with the full breadth of the claims.
Thus the rejection is modified in view of the amendment is maintained.
Summary
No claims are allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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/Steven Pohnert/Primary Examiner, Art Unit 1683
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