DETAILED ACTION
Preliminary Amendment
The preliminary amendment filed on March 5, 2024 has been entered. The claims pending in this application are claims 96-114 and 116.
Specification
The disclosure is objected to because of the following informalities: (1) since case 16/841,450 has been patented, applicant is required to update this information in paragraph [0001] of the specification; and (2) since several US application in paragraphs [0210] and [0229] have been patented, applicant is required to update these information in paragraphs [0210] and [0229].
Appropriate correction is required.
Claim Objections
Claim 96 is objected to because of the following informalities: (1) “which array regions” in line 2 should be “wherein the array regions”; (2) “which biotin-binding protein” in line 5 should be “wherein the biotin-binding protein”; (3) “or less” in line 5 should be “less than -20”; and (4) “the biotin or biotin analog” in line 6 should be “the biotin or biotin analog on the array regions”.
Claim 100 is objected to because of the following informality: “which polymerase” should be “wherein the nucleic acid polymerase”.
Claim 101 is objected to because of the following informality: “a bis-biotin tag through which the polymerase is bound to the biotin-binding protein” should be “a bis-biotin tag which is bound to the biotin-binding protein”.
Claim 104 is objected to because of the following informality: “or less” should be “less than -44”.
Claim 105 is objected to because of the following informality: “or less” should be “less than -60”.
Claim 106 is objected to because of the following informality: “or less” should be “less than -80”.
Claim 114 is objected to because of the following informality: “free biotin-binding protein” should be “a biotin-binding protein”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Description
Claims 96-114 and 116 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.
Applicant is referred to the interim guidelines on written description published on December 21, 1999 in the Federal Register at Volume 64, Number 244, pp.71427-71440.
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111 (Fed. Cir. 1991), clearly states that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” Vas-Cath Inc. v. Mahurkar, 19USPQ2d at 1117. The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed”. Vas-Cath Inc. v. Mahurkar, 19USPQ2d at 1116.
The specification provides adequate written description for wild type core streptavidin, wild type streptavidin with N terminal and C terminal precursor sequences, 24 streptavidin mutants, and different modified streptavidins which include SG1-modifiied streptavidin, succinylated streptavidin, SGC-modified streptavidin clicked with SG1-BCN, streptavidin-(mPEG9)n, streptavidin-(SGC-PEG9-OH)n, streptavidin-(PEG8-PEG8-SG1)n, streptavidin-(PEG8-BCN-SG1)n, streptavidin-(3,5-disulfobenzamide)n, streptavidin-(SGA-SG1)n, and streptavidin-(2-sulfobenzamide)n (see Table 1 and SEQ ID Nos: 1-26 in pages 14-16 and Figure 1-3 and 5-11 of US 2024/0191287 A1, which is US publication of this instant case). However, the specification fails to adequately describe: (1) any kind of biotin binding protein having a calculated net charge of -20 or less than -20 at pH 7.4 as recited in claims 96-102, 107-114, and 116; (2) any kind of streptavidin mutant or modified streptavidin having a calculated net charge of -20 or less than -20 at pH 7.4 as recited in claim 103; (3) any kind of biotin binding protein having a calculated net charge of -44 or less than -44 at pH 7.4 as recited in claim 104; (4) any kind of biotin binding protein having a calculated net charge of -60 or less than -60 at pH 7.4 as recited in claim 105; and (5) any kind of biotin binding protein having a calculated net charge of -80 or less than -80 at pH 7.4 as recited in claim 106. The claimed inventions as a whole are not adequately described if the claims require essential or critical elements which are not adequately described in the specification and which are not conventional in the art as of Applicants effective filing date. Possession may be shown by actual reduction to practice, clear depiction of the invention in a detailed drawing, or by describing the invention with sufficient relevant identifying characteristics (as it relates to the claimed inventions as a whole) such that a person skilled in the art would recognize that the inventor had possession of the claimed invention. Pfaff v. Wells Electronics, Inc., 48 USPQ2d 1641, 1646 (1998).
In this instant case, although the specification describes that wild type core streptavidin consists of SEQ ID No: 1 and “[T]he modification strategies described herein can be combined with the mutation strategies detailed below. Thus, in one class of embodiments, the biotin-binding protein comprises one or more amino acid substitutions relative to a parental biotin-binding protein, e.g., one or more amino acid substitutions that decrease its calculated net charge relative to the parental biotin-binding protein, improve biotin binding by the modified protein, introduce additional modification sites, and/or the like. Similarly, the biotin-binding protein can include one or more exogenous feature, e.g., a polyglutamate, polyaspartate, polylysine, or other tag as described below”, “[T]he modifications can increase or, preferably, decrease the calculated net charge. For example, the modifications can decrease the net charge of the modified biotin-binding protein relative to the parental biotin-binding protein, e.g., altering the calculated net charge by -4 or less, e.g., -8 or less, -10 or less, -12 or less, -16 or less, -20 or less, -30 or less, -40 or less, -50 or less, -60 or less, -70 or less, or even -80 or less, e.g., at pH 7.4. In some embodiments, the modified biotin-binding protein has a calculated net charge of −20 or less at pH 7.4, e.g., -30 or less, -40 or less, -50 or less, -60 or less, -70 or less, or even -80 or less”, “[T]he net charge of the resulting modified protein can be experimentally determined as known in the art. For example, relative net charge can be assessed, e.g., by measuring retention time on an ion exchange column. The net charge can also be calculated at a desired pH, e.g., given the known amino acid sequence of the protein, modifications employed, and average pKa's of various ionizable groups. Calculated net charge at pH 7.4 can be conveniently determined by assuming a charge of +1 for each arginine side chain, lysine side chain, and free N-terminal amino group and a charge of -1 for each aspartate side chain, glutamate side chain, and C-terminal carboxylate group. Histidine's side chain carries little positive charge on average at pH 7.4 and so is counted as having zero charge. A sulfonate group contributes a charge of -1. Charges of other ionizable groups can be readily determined by one of skill (e.g., -2 for phosphate, etc.). The calculated net charge of SEQ ID NO:1 would thus be -1 (four arginines, four lysines, the N-terminal amine, four aspartates, five glutamates, and the C-terminal carboxylate: +4+4+1-4-5-1=-1); the calculated net charge of a streptavidin tetramer including four copies of SEQ ID NO:1 would be -4”, “[A]ccordingly, in one class of embodiments, one or more positively charged residues in the parental biotin-binding protein are covalently modified, e.g., one or more lysine residues and/or free N-terminal amines. For example, lysine side chains and/or free N-terminal amines can be reacted with an N-hydroxysuccinimide ester of 3,4,5-tris(3-sulfopropoxy)benzoic acid (SG1-NHS). Reaction of a free primary amino group (e.g., on a lysine side chain or free N-terminus) with SG1-NHS is schematically illustrated in FIG. 1A. FIG. 1B
shows a model of streptavidin in which lysine residues have been modified with SG1. While modification of only a single amino group is shown in FIG. 1A for clarity, it will be understood that multiple amino groups (per monomer and/or in different monomers) of the streptavidin can be modified in a single reaction. From one to all of the available primary amino groups can be modified. Each lysine or N-terminal amine (produced, e.g., by removal of an N-formyl methionine, protease removal of an N-terminal tag, etc.) that is modified with SG1 results in a -4 change in calculated net charge at pH 7.4. Modification of all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO: 1 with SG1 would thus change the calculated net charge at pH 7.4 by -80 (four lysines and one N-terminal amine per monomer× four monomers×-4 per SG1-modified amine). As another example, primary amino groups in lysine side chains and/or N-termini can be reacted with succinic anhydride, as shown in FIG. 2. (While tyrosine, histidine, cysteine, serine, and threonine side chains also react with succinic anhydride, these modifications are not stable at high pH.) Again, from one to all of the available primary amino groups can be modified. Each primary amine that is succinylated results in a -2 change in calculated net charge at pH 7.4. Modification of all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO:1 with succinic anhydride would change the calculated net charge at pH 7.4 by -40”, “[C]ovalent modification can be accomplished in multiple steps if desired. For example, primary amino groups in lysine side chains and/or N-termini can be reacted with an N-hydroxysuccinimide ester of 4-(6-azidohexyloxy)-3,5-bis(3-sulfopropoxy)benzoic acid (SGC-NHS) to produce SGC-modified proteins, e.g., SGC-modified streptavidin as shown in FIG. 3. The SGC group includes a clickable azide group. The SGC-modified protein can thus be subjected to a very efficient click reaction modification (Cu-catalyzed or Cu-free) with an acetylene modifier in a second step, to attach any of a variety of desired groups. In the example shown in FIG. 3, the second step clicks an SG1-BCN group to the SGC group; the resulting product has five sulfonate groups at each modified position, resulting in a -6 change in calculated net charge at pH 7.4 per modification. Modification of all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO:1 with SGC-BCN-SG1 would change the calculated net charge at pH 7.4 by -120”, and “[I]n some embodiments, the biotin-binding protein is covalently modified with a moiety that includes polyethylene glycol (PEG) or another hydrophilic group, e.g., a flexible hydrophilic linker. Suitable hydrophilic linker groups include, but are not limited to, PEGs, oligopeptides, and oligomers of glycine, beta-alanine, 4-aminobutyric acid, (2-aminoethoxy)acetic acid, 5-aminopentanoic acid, and 6-aminohexanoic acid, optionally including 1-50 monomer units, e.g., 2-30 or 5-10. Such moieties can, but need not, include a charged group, e.g., one or more negatively charged groups. In one class of embodiments, the biotin-binding protein is covalently modified with a PEG moiety, e.g., a sulfonated PEG moiety. The PEG optionally includes 1-50 monomer units, e.g., 2-30 or 5-10. For example, primary amino groups in lysine side chains and/or free N-terminal amines of streptavidin can be reacted with an N-hydroxysuccinimide ester of a methoxyPEG, e.g., mPEG9-NHS as schematically illustrated in FIG. 5. Again, from one to all of the available primary amino groups can be modified. Each primary amine that is mPEGylated results in a -1 change in calculated net charge at pH 7.4. Modification of all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO: 1 with mPEG9 would change the calculated net charge at pH 7.4 by -20” (see Table 1 and paragraphs [0074], [0075], [0077], and [0094] to [0096] of US 2024/0191287 A1, which is US publication of this instant case), the specification only describes that: (1) a streptavidin having a calculated net charge of -20 at pH 7.4 can be made by modifying all available primary amines in a streptavidin having a streptavidin tetramer including four copies of SEQ ID NO: 1 with mPEG9; (2) a streptavidin having a calculated net charge of -40 at pH 7.4 can be made by modifying all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO:1 with succinic anhydride; (3) a streptavidin having a calculated net charge of -80 at pH 7.4 can be made by modifying all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO: 1 with SG1; and (4) a streptavidin having a calculated net charge of -120 at pH 7.4 can be made by modifying all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO: 1 with SGC-BCN-SG1 and does not provide experimental values of net charges for these modified streptavidins at pH 7.4. Since the biotin-binding protein recited in claims 96-102, 107-114, and 116 is read as any kind of biotin binding protein having a calculated net charge of -20 or less than -20 at pH 7.4, the biotin-binding protein recited in claim 103 is read as any kind of streptavidin mutant or modified streptavidin having a calculated net charge of -20 or less than -20 at pH 7.4, the biotin binding protein recited in claim 104 is read as any kind of biotin binding protein having a calculated net charge of -44 or less than -44 at pH 7.4, the biotin binding protein recited in claim 105 is any kind of biotin binding protein having a calculated net charge of -60 or less than -60 at pH 7.4, and the biotin binding protein recited in claim 106 is read as any kind of biotin binding protein having a calculated net charge of -80 or less than -80 at pH 7.4, claims 96-114 and 116 encompass numerous unknown and unidentified biotin-binding proteins that miss from the disclosure. For example, although biotin-binding proteins include at least avidin, streptavidin, and neutravidin, nowhere in the specification and available arts describe that a modified avidin or a modified neutravidin which is modified by any kind of method has a calculated net charge of -20 or less than -20 or -44 or less than -44 or -60 or less than -60 or -80 or less than -80 at pH 7.4. Furthermore, although the biotin-binding protein can be streptavidin, nowhere in the specification and available arts describe that a modified a modified streptavidin which is modified by any kind of method has a calculated net charge of -20 or less than -20 or -44 or less than -44 or -60 or less than -60 or -80 or less than -80 at pH 7.4. In addition, it is known that the biotin-binding site of streptavidin is made up of several hydrogen bonding amino acid side-chains (N23, S27, Y43, S45, and D128) as well as several tryptophan residues (W79, W92, W108, and W120 (from a neighboring subunit)) (see page 738 from Trong et al., J. Mol. Biol., 356, 738-745, 2006). Although claims 110 and 111 require that the biotin-binding protein comprises one or more amino acid substitutions that decrease its calculated net charge relative to a parental biotin-binding protein and claim 112 require that the biotin-binding protein comprises one or more amino acid substitutions that replace an uncharged residue in the parental biotin-binding protein with a negatively charged residue, since claims 110-112 do not indicate the locations of the one or more amino acid substitutions on the biotin-binding protein, if the biotin-binding protein is streptavidin and the locations of the one or more amino acid substitutions are located on one or more of N23, S27, Y43, S45, D128W79, W92, W108, and W120, it is unpredictable whether these unknown and unidentified biotin-binding proteins recited in claims 110-112 can still bind to a biotin or a biotin analog. Therefore, the general knowledge and level of skill in the art do not supplement the omitted description because specific, not general, guidance is what is needed.
With limited disclosure provided by the specification, the skilled artisan cannot envision all unknown and unidentified biotin-binding protein recited in claims 96-116 and therefore
conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method used. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of identifying it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991).
One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481, 1483. In Fiddes, claims directed to mammalian FGF’s were found to be unpatentable due to lack of written description for that broad class. The specification provided only the bovine sequence.
Scope of Enablement
Claims 96-114 and 116 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for performing the method recited in claims 96-116 using a biotin-binding protein which can bind to a biotin or biotin analog, does not reasonably provide enablement for immobilizing a complex comprising a nucleic acid and one of unknown and unidentified biotin-binding proteins having a calculated net charge of -20 or less than -20 at pH 7.4 on a surface comprising a plurality of array regions comprising biotin or a biotin analog using the methods recited in claims 96-114 and 116. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
In In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988) the court considered the issue of enablement in molecular biology. The Court summarized eight factors to
be considered in a determination of “undue experimentation”. These factors include: (a) the quantity of experimentation necessary; (b) the amount of direction or guidance presented; (c) the presence or absence of working examples; (d) the nature of the invention; (e) the state of the prior art; (f) the relative skill of those in the art; (g) the predictability of the art; and (h) the breadth of the claims. The Court also stated that although the level of skill in molecular biology is high, results of experiments in molecular biology are unpredictable.
To begin, there is no direction or guidance to show that a complex comprising a nucleic acid and one of unknown and unidentified biotin-binding proteins having a calculated net charge of -20 or less than -20 at pH 7.4 can be immobilized on a surface comprising a plurality of array regions comprising biotin or a biotin analog using the methods recited in claims 96-116. While the relative skill in the art is very high (the Ph.D. degree with laboratory experience), there is no predictability whether a complex comprising a nucleic acid and one of unknown and unidentified biotin-binding proteins having a calculated net charge of -20 or less than -20 at pH 7.4 can be immobilized on a surface comprising a plurality of array regions comprising biotin or a biotin analog using the methods recited in claims 96-114 and 116.
As shown in above written description rejection, the specification only describes that: (1) a streptavidin having a calculated net charge of -20 at pH 7.4 can be made by modifying all available primary amines in a streptavidin having a streptavidin tetramer including four copies of SEQ ID NO: 1 with mPEG9; (2) a streptavidin having a calculated net charge of -40 at pH 7.4 can be made by modifying all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO:1 with succinic anhydride; (3) a streptavidin having a calculated net charge of -80 at pH 7.4 can be made by modifying all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO: 1 with SG1; and (4) a streptavidin having a calculated net charge of -120 at pH 7.4 can be made by modifying all available primary amines in a streptavidin tetramer including four copies of SEQ ID NO: 1 with SGC-BCN-SG1 and does not provide experimental values of net charges for these modified streptavidins at pH 7.4. Since the biotin-binding protein recited in claims 96-102, 107-114, and 116 is read as any kind of biotin binding protein having a calculated net charge of -20 or less than -20 at pH 7.4, the biotin-binding protein recited in claim 103 is read as any kind of streptavidin mutant or modified streptavidin having a calculated net charge of -20 or less than -20 at pH 7.4, the biotin binding protein recited in claim 104 is read as any kind of biotin binding protein having a calculated net charge of -44 or less than -44 at pH 7.4, the biotin binding protein recited in claim 105 is any kind of biotin binding protein having a calculated net charge of -60 or less than -60 at pH 7.4, and the biotin binding protein recited in claim 106 is read as any kind of biotin binding protein having a calculated net charge of -80 or less than -80 at pH 7.4, claims 96-114 and 116 encompass numerous unknown and unidentified biotin-binding proteins that miss from the disclosure. For example, although biotin-binding proteins include at least avidin, streptavidin, and neutravidin, nowhere in the specification and available arts describe that a modified avidin or a modified neutravidin which is modified by any kind of method has a calculated net charge of -20 or less than -20 or -44 or less than -44 or -60 or less than -60 or -80 or less than -80 at pH 7.4. Furthermore, although the biotin-binding protein can be streptavidin, nowhere in the specification and available arts describe that a modified a modified streptavidin which is modified by any kind of method has a calculated net charge of -20 or less than -20 or -44 or less than -44 or -60 or less than -60 or -80 or less than -80 at pH 7.4. In addition, it is known that the biotin-binding site of streptavidin is made up of several hydrogen bonding amino acid side-chains (N23, S27, Y43, S45, and D128) as well as several tryptophan residues (W79, W92, W108, and W120 (from a neighboring subunit)) (see page 738 from Trong et al., J. Mol. Biol., 356, 738-745, 2006). Although claims 110 and 111 require that the biotin-binding protein comprises one or more amino acid substitutions that decrease its calculated net charge relative to a parental biotin-binding protein and claim 112 require that the biotin-binding protein comprises one or more amino acid substitutions that replace an uncharged residue in the parental biotin-binding protein with a negatively charged residue, since claims 110-112 do not indicate the locations of the one or more amino acid substitutions on the biotin-binding protein, if the biotin-binding protein is streptavidin and the locations of the one or more amino acid substitutions are located on one or more of N23, S27, Y43, S45, D128W79, W92, W108, and W120, it is unpredictable whether these unknown and unidentified biotin-binding proteins recited in claims 110-112 can still bind to a biotin or a biotin analog. Without knowing these numerous unknown and unidentified biotin-binding proteins, the skilled artisan does not know whether a complex comprising a nucleic acid and one of unknown and unidentified biotin-binding proteins having a calculated net charge of -20 or less than -20 at pH 7.4 can be immobilized on a surface comprising a plurality of array regions comprising biotin or a biotin analog by an interaction between the one of unknown and unidentified biotin-binding proteins and the biotin or the biotin analog such that the methods recited in claims 96-114 and 116 cannot be performed.
Case law has established that “(t)o be enabling, the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation’.” In re Wright 990 F.2d 1557, 1561. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970) it was determined that “[T]he scope of the claims must bear a reasonable correlation to the scope of enablement provided by the specification to persons of ordinary skill in the art”. The amount of guidance needed to enable the invention is related to the amount of knowledge in the art as well as the predictability in the art. Furthermore, the Court in Genentech Inc. v Novo Nordisk 42 USPQ2d 1001 held that “[I]t is the specification, not the knowledge of one skilled in the art that must supply the novel aspects of the invention in order to constitute adequate enablement”.
In view of above discussions, the skilled artisan will have no way to predict the experimental results. Accordingly, it is concluded that undue experimentation is required to make the invention as it is claimed. The undue experimentation at least includes to test whether a complex comprising a nucleic acid and one of unknown and unidentified biotin-binding proteins having a calculated net charge of -20 or less than -20 at pH 7.4 can be immobilized on a surface comprising a plurality of array regions comprising biotin or a biotin analog using the methods recited in claims 96-114 and 116.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph. D., whose telephone number is (571)272-0746. The examiner can normally be reached Monday to Friday, 9 AM to 5 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow, Ph.D., can be reached at 571-272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
July 10, 2026
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