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 with traverse of species (option) II in the reply filed on 03/13/2026 is acknowledged. The traversal is on the ground(s) that species (option) III is encompassed by species (option) II and therefore should be examined along with species (option) III because there would be no serious search and/or examination burden of both species. This is found persuasive. After further review, however, it appears that each of options I-V can be practiced simultaneously in one (extremely complex) method. Therefore, the requirement for election of species is withdrawn in its entirety.
Claim Objections
Claims 1-24 are objected to because of the following informalities: the claims contain periods in the enumeration of separate steps and/or elements of the claims (e.g., “I.”, “a.”, “i.”, etc.).
In addition, claim 1 appears to contain a period at the end of step b of the “fourth set of steps”.
As set forth in MPEP 608.01(m), “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations.” Appropriate correction is required.
Claim 1 is objected to because of the following informalities:
In III.a.i.2. line 2, “the first strand” should read “the first nucleic acid first strand” for consistency in terminology.
In III.b.i. line 4, “substantially identical to” should read “substantially complementary to”.
In IV.a.i. line 2, “linked to first nucleic acid” should read “linked to a first nucleic acid”.
In IV.a.i.1. line 5, “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in IV.a.i.2.
In IV.a.ii. line 6, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
In IV.b.i. line 3, “to a blocking probe nucleic acid” should read “to a first blocking probe nucleic acid”.
In V.a.i.1. line “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in V.a.i.2.
In V.a.ii. line 6, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
In V.b.i. line 3, “to a blocking probe nucleic acid, wherein the blocking probe nucleic acid” should read “to a first blocking probe nucleic acid, wherein the first blocking probe nucleic acid”.
In V.d. line 2, “dTNP” should read “dNTP”.
Claim 2 is objected to because of the following informalities:
In a.i.2. lines 2 and 3, “the first strand” should in each case read “the first nucleic acid first strand” for consistency in terminology.
Claim 3 is objected to because of the following informalities:
In a.i.1. line 2, “comprising single-stranded toehold domain” should read “comprising a single-stranded toehold domain”.
In a.ii. line 5, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
Claim 4 is objected to because of the following informalities:
In a.i.1. line 3, “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in a.i.2.
In a.ii. line 4, “pairing domain (x)” should read “toehold domain (x)” for consistency in terminology.
In a.ii. line 5, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
Claim 13 is objected to because of the following informalities:
In III.a.2. line 2, “the first strand” should read “the first nucleic acid first strand” for consistency in terminology.
In III.b. line 4, “substantially identical to” should read “substantially complementary to”.
In IV.i.1. line 5, “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in IV.i.2.
In IV.ii. lines 9-12, “and wherein binding of the target to the first reporter probe inhibits the first reporter probe and the first blocking probe from forming a complex; and wherein binding of the target to the first reporter probe inhibits the formation of the complex” should be amended to remove redundancy.
In V.i.1. line 5, “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in V.i.2.
Claim 15 is objected to because of the following informalities:
In line 7, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
Claim 17 is objected to because of the following informalities:
In line 7, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
Claim 19 is objected to because of the following informalities:
In III.a.2. line 2, “the first strand” should read “the first nucleic acid first strand” for consistency in terminology.
In III.b. line 4, “substantially identical to” should read “substantially complementary to”.
In IV.i.1. line 5, “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in IV.i.2.
In IV.ii. lines 9-12, “and wherein binding of the target to the first reporter probe inhibits the first reporter probe and the first blocking probe from forming a complex; and wherein binding of the target to the first reporter probe inhibits the formation of the complex” should be amended to remove redundancy.
In V.i.1. line 5, “an end distal” should read “a first end of the double stranded nucleic acid distal”. This provides context for “at a second end of the double-stranded nucleic acid” referred to in V.i.2.
Claim 21 is objected to because of the following informalities:
In line 7, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
Claim 23 is objected to because of the following informalities:
In line 7, “first reporter probe; a second nucleic acid” should read “first reporter probe; and a second nucleic acid”.
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because many of the figures contain text that is too small or too faint for legibility. See 37 CFR 1.84(a)(1), (l), and (p)(3). Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
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 1-12 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.
In IV.c. (the “fourth set of steps”), claim 1 recites “thereby producing a nucleic acid record of an interaction between the first nucleic acid and the second nucleic acid”. Similarly, in V.d. (the “fifth set of steps”), claim 1 recites “thereby producing a nucleic acid record of an interaction between the first nucleic acid and the second nucleic acid”.
These limitations render the scope of claim 1 unclear, as the nature of this “record” is not recited. This is in contrast to the “first set of steps”, the “second set of steps”, and the “third set of steps”, each of which sets forth the nature of the recited “nucleic acid record”.
In I.a.ii. (the “first set of steps”), the nature of the “nucleic acid record” is described thusly: “a portion of the first nucleic acid is capable of being extended at least two times to produce a nucleic acid record”. In II.b.i. (the “second set of steps”), the nature of the “nucleic acid record” is described thusly: “a portion of the blocking probe nucleic acid is capable of being extended at least two times to produce a nucleic acid record in the absence of the target”. In III.b.i. (the “third set of steps”), the nature of the “nucleic acid record” is described thusly: “a portion of the blocking probe nucleic acid is capable of being extended at least two times to produce a nucleic acid record in the absence of the target”.
However, for the fourth and fifth sets of steps, as mention above, it cannot be determined what the “nucleic acid record” is, or how it is produced. Therefore, the metes and bounds of the claim is unclear. As claims 2-12 depend ultimately from claim 1, they are similarly indefinite.
Claims 13-18 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 13 recites the limitation "a portion of the second nucleic acid is capable of being extended" in IV.ii. line 13. There is insufficient antecedent basis for this limitation in the claim. Elsewhere, the claims refer to “a second nucleic acid” as a nucleic acid comprised by a “second reporter probe”. However, in claim 13 IV. (the “fourth set of elements”), there is no recitation of any “second reporter probe”, nor any previous introduction of a “second nucleic acid”. Therefore, the metes and bounds of the claim are unclear. A similar problem occurs in V.ii. line 8. The “fifth set of elements” recited in V. does not reference any “second reporter probe”, nor does it adequately introduce any “second nucleic acid”. As claims 14-18 depend ultimately from claim 13, they are rejected for the same reason.
Claims 19-24 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 19 recites the limitation "a portion of the second nucleic acid is capable of being extended" in IV.ii. line 13. There is insufficient antecedent basis for this limitation in the claim. Elsewhere, the claims refer to “a second nucleic acid” as a nucleic acid comprised by a “second reporter probe”. However, in claim 19 IV. (the “fourth set of elements”), there is no recitation of any “second reporter probe”, nor any previous introduction of a “second nucleic acid”. Therefore, the metes and bounds of the claim are unclear. A similar problem occurs in V.ii. line 9. The “fifth set of elements” recited in V. does not reference any “second reporter probe”, nor does it adequately introduce any “second nucleic acid”. As claims 20-24 depend ultimately from claim 19, they are rejected for the same reason.
Claim 7 is 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.
The language “the first target binding ligand and/or the second target binding ligand and the blocking ligand are…” followed by a list of pairs of elements, each of which presumably represents a pair of binding partners (e.g. receptor and ligand, nucleic acid and nucleic acid binding protein, etc.). It is unclear if the language is meant to encompass all three combinations (first target binding ligand and second target binding ligand, first target binding ligand and blocking ligand, second target binding ligand and blocking ligand), or is only intended to encompass two combinations (first target binding ligand and blocking ligand, second target binding ligand and blocking ligand).
In other words, it is unclear whether, e.g., the situation where the first target binding ligand is a “receptor” and the second target binding ligand is a “ligand” would be encompassed by the claim. Or whether, for each pair of recited binding partners (e.g., “receptor”, “ligand”), one has to be either the first or second target binding ligand, and the other has to be the blocking ligand.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2-4 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. In a.iii. lines 1-2, the claim recites “the blocking ligand is capable of directly or indirectly forming a complex with the first target binding ligand and/or the second target binding ligand”. Similarly, in a.iii. lines 7-11, the claim recites “wherein binding of the target to the first reporter probe inhibits the first reporter probe and the blocking probe from forming a complex and/or wherein binding of the target to the second reporter probe inhibits the second reporter probe and the blocking probe from forming a complex”.
However, claim 2 is directed to “the first set of steps” of claim 1. In claim 1, “the first set of steps” requires that the blocking ligand is capable of directly or indirectly forming a complex with the first target binding ligand, and requires that binding of the target to the first reporter probe inhibits the first reporter probe and the blocking probe from forming a complex”. The “and/or” language in claim 2 therefore encompasses the situation where the blocking ligand is not capable of directly or indirectly forming a complex with the first target binding ligand (but rather with the second target binding ligand). Similarly, the “and/or” language in claim 2 encompasses the situation where binding of the target to the first reporter probe does not inhibit the first reporter probe and the blocking probe from forming a complex (but rather inhibits the second reporter probe and the blocking probe from forming a complex).
Thus, claim 2 does not require all the limitations of the claim from which it depends.
A similar problem occurs in claim 3 at a.iii. lines 2 and 8.
A similar problem occurs in claim 4 at a.iii. lines 2 and 8.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Conclusion
The claims are free of the prior art but rejected for other reasons.
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/SAMUEL C WOOLWINE/ Primary Examiner, Art Unit 1681