DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because:
The margins are not of proper size in Figure(s) 3-6 and 8B. See 37 CFR 1.84(g).
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.
INFORMATION ON HOW TO EFFECT DRAWING CHANGES
Replacement Drawing Sheets
Drawing changes must be made by presenting replacement sheets which incorporate the desired changes and which comply with 37 CFR 1.84. An explanation of the changes made must be presented either in the drawing amendments section, or remarks, section of the amendment paper. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). A replacement sheet must include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of the amended drawing(s) must not be labeled as “amended.” If the changes to the drawing figure(s) are not accepted by the examiner, applicant will be notified of any required corrective action in the next Office action. No further drawing submission will be required, unless applicant is notified.
Identifying indicia, if provided, should include the title of the invention, inventor’s name, and application number, or docket number (if any) if an application number has not been assigned to the application. If this information is provided, it must be placed on the front of each sheet and within the top margin.
Annotated Drawing Sheets
A marked-up copy of any amended drawing figure, including annotations indicating the changes made, are required by the examiner. The annotated drawing sheet(s) must be clearly labeled as “Annotated Sheet” and must be presented in the amendment or remarks section that explains the change(s) to the drawings.
Timing of Corrections
Applicant is required to submit acceptable corrected drawings within the time period set in the Office action. See 37 CFR 1.85(a). Failure to take corrective action within the set period will result in ABANDONMENT of the application.
If corrected drawings are required in a Notice of Allowability (PTOL-37), the new drawings MUST be filed within the THREE MONTH shortened statutory period set for reply in the “Notice of Allowability.” Extensions of time may NOT be obtained under the provisions of 37 CFR 1.136 for filing the corrected drawings after the mailing of a Notice of Allowability.
Claim Interpretation
Attention is directed to MPEP 904.01 [R-08.2012].
The breadth of the claims in the application should always be carefully noted; that is, the examiner should be fully aware of what the claims do not call for, as well as what they do require. During patent examination, the claims are given the broadest reasonable interpretation consistent with the specification. See In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis.
It is noted with particularity that narrowing limitations found in the specification cannot be inferred in the claims where the elements not set forth in the claims are linchpin of patentability. In re Philips Industries v. State Stove & Mfg. Co, Inc., 186 USPQ 458 (CA6 1975). While the claims are to be interpreted in light of the specification, it does not follow that limitations from the specification may be read into the claims. On the contrary, claims must be interpreted as broadly as their terms reasonably allow. See Ex parte Oetiker, 23 USPQ2d 1641 (BPAI, 1992). In added support of this position, attention is directed to MPEP 2111 [R-11.2013], where, citing In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969), is stated:
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.
Additionally, attention is directed to MPEP 2111.01 [R-01.2024], wherein is stated:
II. IT IS IMPROPER TO IMPORT CLAIM LIMITATIONS FROM THE SPECIFICATION
“Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment.” Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).
Attention is also directed to MPEP 2111.02 II [R-07.2022]. As stated herein:
II. PREAMBLE STATEMENTS RECITING PURPOSE OR INTENDED USE
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The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation")… (Emphasis added)
Attention is directed to MPEP 2111 [R-10.2019]. As stated therein:
During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added).
Attention is directed to MPEP 2173.04 [R-10.2019]. As stated therein:
Breadth of a claim is not to be equated with indefiniteness. In re Miller, 441 F.2d 689, 169 USPQ 597 (CCPA 1971); In re Gardner, 427 F.2d 786, 788, 166 USPQ 138, 140 (CCPA 1970) ("Breadth is not indefiniteness."). A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim). (Emphasis added)
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 5, 9, 13, 14, 16, 22, and 27 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, 12, 13, 16, and 18 of U.S. Patent No. 11,702,662 B2 (Jacobson et al.). Although the claims at issue are not identical, they are not patentably distinct from each other because the patented “method of assembling a polynucleotide” fairly discloses the claimed method of “producing a target nucleic acid having a predefined sequence”. As seen in claim 1 of the ‘662 patent, the method requires the use of “blunt-end double-stranded nucleic acid fragments” that are subjected to digestion with the same Type IIS restriction enzymes and are subsequently ligated with the same types of ligases, and forming nucleic acids that can have the same lengths.
For convenience, claims 1, 8, 12, 13, 16, and 18 of the ‘662 patent are reproduced below.
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In view of the above presentation, the identified claims of the ‘662 patent are deemed to fairly suggested the claimed method as set forth in the identified claims. Accordingly, and in the absence of convincing evidence to the contrary, claims 1, 5, 9, 13, 14, 16, 22, and 27 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, 12, 13, 16, and 18 of U.S. Patent No. 11,702,662 B2 (Jacobson et al.).
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1-7, 9, 11-16, 19, 22, 25, and 27-29 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over US 2009/0155858 A1 (Blake).
Blake disclose “methods for assembling nucleic acid molecules” (abstract).
Blake, at paragraph [0009] teaches:
[0009] Aspects of the invention can be used in combination with one or more multiplex nucleic acid assembly techniques in order to assemble a long nucleic acid product from small starting nucleic acids (e.g., from a plurality of oligonucleotides)… It should be appreciated that in some embodiments an assembly procedure is hierarchical in that it involves a plurality of converging iterative assembly reactions wherein a first plurality (e.g., N) of pair-wise assembly reactions produces a first plurality of products that are combined in a pair-wise fashion in a second plurality (e.g., N/2) of assembly reactions to generate a second plurality of products. This procedure can be repeated with the number of assembly reactions (and resulting assembly products) being twofold less at each consecutive stage (e.g., until a single final product is generated). In some embodiments, the sizes of the nucleic acid products at each stage are about twofold greater than the sizes at the prior stage (assuming that the initial nucleic acid inserts had similar sizes). Accordingly, this hierarchical assembly procedure can produce a long insert that increases exponentially in size as a function of the number of consecutive assembly steps. However, it also should be appreciated that iterative assembly procedures can be used in a linear assembly procedure. For example, at each consecutive step one product of a prior assembly may be combined with a second nucleic acid insert that was not generated from a prior iterative assembly procedure. In some embodiments, the second nucleic acid insert at each step may be a oligonucleotide (e.g., a double-stranded pair of oligonucleotides) or a relatively short nucleic acid assembled in a multiplex assembly reaction (e.g., about 500 nucleotides long). Accordingly, the nucleic acid being assembled in this linear procedure grows linearly by the length of the second nucleic acid added at each consecutive step. It should be appreciated that an iterative assembly of the invention may involve a combination of one or more linear and one or more exponential assembly steps and is not limited to either a hierarchical assembly or a linear assembly.
Blake, at paragraph [0098], teaches that the nucleic acid fragments that are ultimately to be ligated to one another can initially have a blunt ends. As stated therein:
In some embodiments, one or more nucleic acid fragments being assembled may have blunt ends. In some embodiments, double-stranded blunt ends may have overlapping identical sequences on nucleic acid fragments that are designed to be adjacent to each other on an assembled nucleic acid product. (Emphasis added)
The above showing is deemed to meet a limitation of both independent claim 1.
Blake, at paragraph [0172], teaches that the oligonucleotides (applicant’s “nucleic acid fragments”) can be synthesized on any of a variety of solid supports and can have virtually any desired size/length and that the length of the oligonucleotides that are subject to ligation may be multiples of a common length or may have different lengths. As stated therein:
[0172] Oligonucleotides may be synthesized using any suitable technique. For example, oligonucleotides may be synthesized on a column or other support (e.g., a chip). Examples of chip-based synthesis techniques include techniques used in synthesis devices or methods available from Combimatrix, Agilent, Affymetrix, or other sources. A synthetic oligonucleotide may be of any suitable size, for example between 10 and 1,000 nucleotides long (e.g., between 10 and 200, 200 and 500, 500 and 1,000 nucleotides long, or any combination thereof). An assembly reaction may include a plurality of oligonucleotides, each of which independently may be between 10 and 200 nucleotides in length (e.g., between 20 and 150, between 30 and 100, 30 to 90, 30-80, 30-70, 30-60, 35-55, 40-50, or any intermediate number of nucleotides). However, one or more shorter or longer oligonucleotides may be used in certain embodiments. (Emphasis added)
Blake, in paragraph [0165], teaches that the assembly reaction (ligation reaction) can be performed on solid supports. As stated therein:
[0165] As with other assembly reactions described herein, support-bound ligase reactions (e.g., those illustrated in FIG. 4B) that generate a full length predetermined nucleic acid fragment also may generate a distribution of smaller fragments resulting from the assembly of subsets of the oligonucleotides. A support used in any of the assembly reactions described herein (e.g., polymerase-based, ligase-based, or other assembly reaction) may include any suitable support medium. A support may be solid, porous, a matrix, a gel, beads, beads in a gel, etc. A support may be of any suitable size. A solid support may be provided in any suitable configuration or shape (e.g., a chip, a bead, a gel, a microfluidic channel, a planar surface, a spherical shape, a column, etc.). (Emphasis added)
Blake, at paragraph [0066], teaches that the nucleic acid fragments can be ligated via any number of ways, including the use of a ligase such as T4. As stated therein:
[0066] It should be appreciated that any suitable technique (e.g., chemical or enzymatic) may be used to digest the nucleic acids at the appropriate sites as described herein for iterative assembly. Similarly, any suitable technique may be used for connecting nucleic acids (e.g., chemical or enzymatic ligation--e.g., using a suitable ligase such as T4 ligase or other ligase, or in vivo recombination as described herein for concerted assembly). (Emphasis added)
The above showing is deemed to meet limitations of claims 1 and 22.
Blake, in paragraph [0181], teaches that the oligonucleotides may be amplified either while they are still connected to the solid support, or may be amplified following their release from the support. As stated therein:
The oligonucleotide may be synthesized on a support such as a chip (e.g., using an ink-jet-based synthesis technology). In some embodiments, the oligonucleotide may be amplified while it is still attached to the support. In some embodiments, the oligonucleotide may be removed or cleaved from the support prior to amplification.
The above showings are deemed to satisfy limitations of claim 25.
Blake, at paragraph [0174], teaches that the oligonucleotides can comprise not just a primer binding site, but that they may have a common, or universal, binding site, which in turn would allow for amplification of multiple different nucleic acid fragments with a common set of primers. As stated therein:
[0174] In some embodiments, an oligonucleotide may be amplified using an appropriate primer pair with one primer corresponding to each end of the oligonucleotide (e.g., one that is complementary to the 3' end of the oligonucleotide and one that is identical to the 5' end of the oligonucleotide). In some embodiments, an oligonucleotide may be designed to contain a central assembly sequence (designed to be incorporated into the target nucleic acid) flanked by a 5' amplification sequence (e.g., a 5' universal sequence) and a 3' amplification sequence (e.g., a 3' universal sequence). Amplification primers (e.g., between 10 and 50 nucleotides long, between 15 and 45 nucleotides long, about 25 nucleotides long, etc.) corresponding to the flanking amplification sequences may be used to amplify the oligonucleotide (e.g., one primer may be complementary to the 3' amplification sequence and one primer may have the same sequence as the 5' amplification sequence). The amplification sequences then may be removed from the amplified oligonucleotide using any suitable technique to produce an oligonucleotide that contains only the assembly sequence.
The above showing is deemed to meet a limitation of claim 4.
Blake, at paragraph [0106], teach that the double-stranded nucleic acid fragments can be digested with a type IIS restriction enzyme, which will produce single-stranded overhangs. Depending upon the enzyme used, the overhang may be of different lengths. As stated therein:
[0106] In some embodiments, a double-stranded nucleic acid fragment (e.g., a fragment assembled in a multiplex assembly) may be digested with an appropriate restriction enzyme to generate a terminal single-stranded overhang. In some embodiments, fragments that are designed to be adjacent to each other in an assembled product may be digested with the same enzyme to expose complementary overhangs. In some embodiments, overhangs may be generated using a type IIS restriction enzyme. Type IIS restriction enzymes are enzymes that bind to a double stranded nucleic acid at one site, referred to as the recognition site, and make a single double stranded cut outside of the recognition site. The double stranded cut, referred to as the cleavage site, is generally situated 0-20 bases away from the recognition site. The recognition site is generally about 4-7 bp long… Cleavage generally produces 1-5 nucleotide single-stranded overhangs, with 5' or 3' termini… To date, .about.80 type IIS enzymes have been identified. Examples include but are not limited to BstF5 I, BtsC I, BsrD I, Bts I, Alw I, Bcc I, BsmA I, Ear I, Mly I ( blunt), Ple I, Bmr I, Bsa I, BsmB I, Fau I, Mnl I, Sap I, Bbs I, BciV I, Hph I, Mbo II, BfuA I, BspCN I, BspM I, SfaN I, Hga I, BseR I, Bbv I, Eci I, Fok I, BceA I, BsmF I, BtgZ I, BpuE I, Bsg I, Mme I, BseG I, Bse3D I, BseM I, AclW I, Alw26 I, Bst6 I, BstMA I, Eam1104 I, Ksp632 I, Pps I, Sch I ( blunt), Bfi I, Bso31 I, BspTN I, Eco31 I, Esp3 I, Smu I, Bfu I, Bpi I, BpuA I, BstV2 I, AsuHP I, Acc36 I, Lwe I, Aar I, BseM II, TspDT I, TspGW I, BseX I, BstV1 I, Eco57 I, Eco57M I, Gsu I, and Bcg I. Such enzymes and information regarding their recognition and cleavage sites are available from commercial suppliers such as NEB. (Emphasis added)
The above showing is deemed to meet a limitation of claims 13 and 14.
Blake, in paragraph [0027], teaches that the method can involve multiple rounds of ligation, and that it may result in the production of a nucleic acid of considerable size. As stated therein:
For example, a 100 kb fragment of DNA broken into one hundred 1 kb pieces will require 7 assembly steps (100>64>32>16>8>4>2>1) while the same fragment broken into two hundred 500 bp pieces will require 8 assembly steps (200>128>64>32>16>8>4>2>1). It should be noted that in the first assembly cycle, a subset of pieces may be paired such that the product of this pairing combined with the remaining pieces will yield a total number of pieces for the second round that is a power of two (e.g., 100=72+28; 72/2+28=64).
[0028] It should be appreciated that the nucleic acids that are combined for assembly in each cycle may be obtained from any suitable source. For example, each nucleic acid fragment independently may have been generated in a multiplex nucleic acid assembly reaction, an amplification reaction, a prior cloning procedure, etc., or any combination thereof. In some embodiments, one or two fragments that are combined for assembly each may have been generated in a prior assembly cycle that involved vector-encoded trait activation as described herein. (Emphasis added)
Blake, in paragraph [0032], teach that different restriction enzymes can be used to digest the double stranded nucleic acid fragments so to generate fragments that are uniquely complementary such that only the intended order of ligated fragments would occur. As stated therein:
[0032] Thus, some embodiments of the invention provide methods for assembling nucleic acid segments which include the following steps: digesting a first population of nucleic acids having at least first, second, third and fourth restriction sites, using a first set of restriction enzymes that cleave the nucleic acids at the first and third sites; digesting a second population of nucleic acids having at least first, second, third and fourth restriction sites, using a second set of restriction enzymes that cleave the nucleic acids at the second and fourth sites, where the first and second populations of nucleic acids comprise a first activation sequence located between the first and second restriction sites and a second activation sequence located between the third and fourth restriction sites, and digestion of the first population results in a first population of nucleic acid segments that comprises the first activation sequence but lacks the second activation sequence, and digestion of the second population results in a second population of nucleic acid segments that lacks the first activation sequence and comprises the second activation sequence; combining (optionally in the presence of a ligase) the first and second populations of nucleic acid segments with a first nucleic acid vector that is digested with one or more enzymes to generate overhangs that are compatible with the overhangs generated at the first and fourth site
Blake, in paragraph [0036], each that one can use Type IIS restriction enzymes. As stated therein:
In addition, as discussed in more detail herein, the restriction enzymes used in any of the embodiments disclosed may be type II restriction enzymes or type IIS restriction enzymes. In some embodiments, the same first type IIS restriction enzyme recognition sequence is used for the first and third sites. Similarly, in some embodiments, the same type IIS restriction enzyme recognition sequence is used for the second and fourth sites. Accordingly, a single type IIS enzyme may be used to cut the first and third sites and a different single type IIS enzyme may be used to cut the second and fourth sites. It should be appreciated that in some embodiments, the type IIS recognition sites are located within the flanking regions of the inserts in association with the activating sequences… Also, it should be appreciated that the cleavage overhang sizes and orientations generated by the restriction enzymes used for cutting the second and third sites should be compatible so that they generate complementary sequences for ligation within the overlap region of two inserts designed for subsequent ligation.
Blake, in paragraph [0055], teaches:
Restriction sites 2 and 3 may be different. However, the cleavage patterns (e.g., the type of overhang, 5' or 3', and the overhang length) of the Type IIS restriction enzymes that recognize 2 and 3 may be identical or similar. As a result, the nucleic acid constructs may be designed so that cleavage by Type IIS enzymes specific for sites 2 and 3 generates free ends that are compatible (e.g., cohesive or complementary) for a subsequent ligation reaction. For example, sites 2 and 3 may be located to cause Type IIS cleavage within a sequence region that is common to the fragments being assembled (e.g., in an overlapping sequence region of I and II, or of III and IV, or of II and III illustrated in FIGS. 6 and 7). In some embodiments, the common or overlapping regions are not duplicated after assembly, because the cleavage sites may be designed to cut at a location that results in a single copy of the overlapping or common regions being reassembled upon ligation. It should be appreciated that, in this non-limiting configuration, the cleavage sites for 2 and 3 are within the sequence of the nucleic acid being assembled. (Emphasis added)
Blake, at paragraph [0057], teaches:
[0057] In some embodiments, restriction enzyme digestion and ligation may be performed in the same reaction tube. The use of Type IIS sites that are not regenerated after ligation can drive the reaction towards the correct assembly as described in more detail herein. This also may speed up an assembly reaction by avoiding separate digestion and ligation steps and by avoiding any purification, size separation, or other processing steps in between restriction enzyme digestion and ligation. This aspect also may be readily automated, avoiding additional sample manipulations associated with separate restriction digestion and ligation steps. (Emphasis added)
The above showings is deemed to meet limitations of claims 1, 5, 11, 12, 13, 14, 15.
Blake, at paragraph [0038], teaches that the enzyme recognition sequence can be the same for all the fragments. As stated therein:
[0038] It should be appreciated that in some embodiments described herein all sites 1, 2, 3, and 4 are recognized by the same enzyme (e.g., the same type IIS enzyme). (Emphasis added)
The aspect that “some embodiments” may have the same recognition sequence is deemed to fairly suggest that in some other embodiments it may be different.
The above showing is deemed to meet a limitation of claims 1, 5, 6 and 11.
Blake, paragraph [0073], teaches that the “input nucleic acids” (the sequences to be ligated so to form the polynucleotide, can be produced via any known means, be it synthesis (e.g., solid support) and/or amplification. As stated therein:
[0073] In act 520, the input nucleic acids are obtained. These may be synthetic oligonucleotides that are synthesized on-site or obtained from a different site (e.g., from a commercial supplier). In some embodiments, one or more input nucleic acids may be amplification products (e.g., PCR products), restriction fragments, or other suitable nucleic acid molecules. Synthetic oligonucleotides may be synthesized using any appropriate technique as described in more detail herein.
In paragraph [0074], Blake teaches that the nucleic acid fragments can be joined via use of ligase. As stated therein:
[0074] In act 530, an assembly reaction may be performed for each nucleic acid fragment. For each fragment, the input nucleic acids may be assembled using any appropriate assembly technique (e.g., a polymerase-based assembly, a ligase-based assembly, a chemical assembly, or any other multiplex nucleic acid assembly technique, or any combination thereof). (Emphasis added)
Blake, at paragraph [0066], teaches that the nucleic acid fragments can be ligated via any number of ways, including the use of a ligase such as T4. As stated therein:
[0066] It should be appreciated that any suitable technique (e.g., chemical or enzymatic) may be used to digest the nucleic acids at the appropriate sites as described herein for iterative assembly. Similarly, any suitable technique may be used for connecting nucleic acids (e.g., chemical or enzymatic ligation--e.g., using a suitable ligase such as T4 ligase or other ligase, or in vivo recombination as described herein for concerted assembly). (Emphasis added)
The above showing is deemed to meet limitations of claims 1 and 22.
Blake, in paragraph [0190], teach that the nucleic acid to be produced may be that of an entire genome, or a large part thereof, as found in any of a variety of sources. As stated therein:
[0190] Many of the techniques described herein can be used together, applying combinations of one or more extension-based and/or ligation-based assembly techniques at one or more points to produce long nucleic acid molecules. For example, concerted assembly may be used to assemble oligonucleotide duplexes and nucleic acid fragments of less than 100 to more than 10,000 base pairs in length (e.g., 100 mers to 500 mers, 500 mers to 1,000 mers, 1,000 mers to 5,000 mers, 5,000 mers to 10,000 mers, 25,000 mers, 50,000 mers, 75,000 mers, 100,000 mers, etc.). In an exemplary embodiment, methods described herein may be used during the assembly of an entire genome (or a large fragment thereof, e.g., about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more) of an organism (e.g., of a viral, bacterial, yeast, or other prokaryotic or eukaryotic organism), optionally incorporating specific modifications into the sequence at one or more desired locations.
The above showing is deemed to fairly suggest limitations of claims 1 and 9.
Blake, at paragraph [0088], teaches of including one or more forms of quality control. As stated therein:
[0088] It should be appreciated that a quality control procedure may be performed at one or more steps in a multi-stage assembly of the invention. For example, an ION assembly may involve a quality control at one or more intermediate stages. In some embodiments, quality control may be performed at each intermediate stage. A quality control procedure may include one or more techniques designed to distinguish incorrectly assembled intermediates from correctly assembled intermediates. For example, a quality control procedure may include sequencing, amplification (e.g., by PCR, LCR, etc.), restriction enzyme digestion, size analysis (e.g., using electrophoresis, mass spectrometry, etc.), any other suitable quality control technique, or any combination of two or more thereof. (Emphasis added)
The above showing is deemed to fairly meet the limitation of claim 19.
Blake, in paragraph [0009], teaches that the assembly of the fragments so to form the linear polynucleotide, can be hierarchical. As stated therein:
It should be appreciated that in some embodiments an assembly procedure is hierarchical in that it involves a plurality of converging iterative assembly reactions wherein a first plurality (e.g., N) of pair-wise assembly reactions produces a first plurality of products that are combined in a pair-wise fashion in a second plurality (e.g., N/2) of assembly reactions to generate a second plurality of products. This procedure can be repeated with the number of assembly reactions (and resulting assembly products) being twofold less at each consecutive stage (e.g., until a single final product is generated).
The above showing is deemed to fairly suggest the limitations of claim 27.
Blake, at paragraph [0056], teaches:
[0056] In some circumstances, the invention may be useful for generating a library of variants. For example, each insert to be progressively added (e.g., insert I, II, III, and IV as shown in FIGS. 6 and 7) may represent a plurality of nucleic acid variants. For example, insert I may represent a plurality (e.g., a pool) of variants of I, and insert II may represent a plurality (e.g., a pool) of variants of II, and so on. Such variants may include naturally occurring variants (such as SNPs) and other mutations. (Emphasis added)
The above showing is deemed to fairly suggest limitations of claim 28.
Blake, at paragraph [0211], teaches:
[0211] Mixed oligonucleotide pools were prepared as follows: 36 overlapping 50-mer oligonucleotides and two 5' terminal 59-mers were separated into 4 pools, each corresponding to overlapping 200-300 nucleotide segments of the final construct. The total oligonucleotide concentration in each pool was 5 .mu.M. (Emphasis added)
The above showing is deemed to fairly suggest limitations of claim 29.
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 methods of Blake for to do so would enable one of ordinary skill in the art to produce target nucleic acids of known sequences which can have a wide range of lengths.
In view of the well developed state of the art, said ordinary artisan would have mott only been well motivated, but would have also had a most reasonable expectation of success.
In view of the above presentation and in the absence of convincing evidence to the contrary, claims 1-7, 9, 11-16, 19, 22, 25, and 27-29 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over US 2009/0155858 A1 (Blake).
Conclusion
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682
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