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 .
Information Disclosure Statement
An IDS has not been filed in the instant application.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/756419 filed 11/06/2018 is acknowledged.
Claim Election/Restriction
Election without Traverse
Applicant’s election without traverse of Group 1 (claims 1-7 and 23-35) in the reply filed on 11/04/2024 is acknowledged.
Claims 8-22 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 11/04/2024.
Status of Claims
Amendments to the claims are acknowledged. Claims 36-38 are new.
Claims 1-7 and 23-38 are under examination.
Claims 8-22 are withdrawn.
Claim Rejections - 35 USC § 112-2nd paragraph
The rejection of claim 35 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ),
second paragraph, is withdrawn in view of Applicant’s amendments.
The instant rejection is maintained and modified in view of Amendments filed10/10/2025.
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 23-34 and 37-38 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 pre-AIA the applicant regards as the invention.
Claim 30 recites “the DNA binding molecule.” There is insufficient antecedent basis for this limitation. Claim 23 from which claim 30 depends does not recite binding any specific molecule to DNA or “a DNA binding molecule.” Therefore it is unclear what “the DNA binding molecule” is referring to.
Claim 23 recites that the physical occlusion comprises a single strand polynucleotide overhang “(ss overhang).” It is unclear if “(ss overhang)” is intended to limit the claim. It is unclear if the claim requires that the overhang be an “ss overhang.” It is suggested that the parenthesis be removed and “ss overhang” be directly recited.
Claim 38 recites “the oligonucleotide” and “the binding protein.” There is insufficient antecedent basis for these limitations. The claims from which this claim depends recite “polynucleotide” and “the binding molecule.” The claims do not provide antecedent basis for an oligonucleotide or binding protein.
Response to Arguments
Applicant's arguments filed 10/10/2025 have been fully considered but they are not persuasive.
In the previous Office Action, claim 30 was mistakenly rejected for lack of antecedent basis support for “the DNA binding molecule.” However, “a DNA binding molecule” was recited in line 2 of claim 30. Applicants should not have deleted lines 1-3 of claim 1 because by doing so, the antecedent basis support for “the DNA binding molecule” was deleted.
Furthermore, an issue of indefiniteness has been introduced into claim 23 wherein it is unclear if “(ss overhang)” is intended to limit the claim. Claim 38 is also indefinite.
Claim Rejections - 35 USC § 103
The rejection of claims 23-34 under 35 U.S.C. 103(a) as being unpatentable over Loehrlein et al. (US 2002/0160361) in view of Rutten (Nature Reviews Chemistry vol 2 (2018) 365-381). The newly applied rejection of Loehrlein et al. in view of Rutten and further in view of Dekker et al. is necessitated by Applicant’s amendments.
The following rejection is maintained for reasons of record from the Office Action filed 10/10/2025.
The following is a quotation of 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 of this title, 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 negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 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 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Claims 1-7 and 35-36 are rejected under 35 U.S.C. 103(a) as being unpatentable over Loehrlein et al. (US 2002/0160361) in view of Rutten (Nature Reviews Chemistry vol 2 (2018) 365-381).
Loehrlein et al. teach methods of gene expression analysis wherein information is stored on DNA (Abstract)(i.e. a database of data filed which are DNA’s).
Loehrlein et al. teach (par. 0162) contacting labeled DNA with beads bearing avidin or antibody, wherein the labeled DNA is labeled with biotin and antigen that binds of the avidin or antibody on the bead; Loehrlein teach (par. 0050) that a detectable moiety is synonymous with a label used to distinguish a particular nucleic acid (i.e. the DNA is labeled with a chemical moiety); Loehrlein et al. teach that the beads may be magnetic beads (par. 0162) (i.e. contacting the database with a magnetic bead comprising a corresponding chemical group that binds to the moiety), as in claims 1 and 35.
Loehrlein et al. teach a magnetic platform to precipitate the DNA bound to the beads (par. 0252) wherein the magnetic separation is performed with a moiety (par. 0044)(i.e. extracting the one or more polynucleotide strands bearing the data file using a magnet), as in claims 1 and 35.
Loehrlein et al. does not specifically teach providing an oligonucleotide primer that selectively binds a polynucleotide strand bearing a datafile, wherein the primer is labeled with a chemical moiety.
Rutten et al. however teach encoding information into polymers and using DNA as an alternative for data storage (Abstract and pages 2-4). Rutten et al. teach data storage in DNA where DNA strands that encode the data have attached forward and reverse primers (page 5, Figure 1)(i.e. providing an oligonucleotide primer that selectively binds a polynucleotide strand bearing a datafile), as in claims 1 and 35.
Rutten et al. teach a forward primer and a primer “key” (Figure 1)(i.e. chemical moiety or which also reads on a “physical occlusion”), as in claims 1 and 35.
It would have been obvious to one of ordinary skill in the art at the time the invention was made to have applied the method of attaching magnetic beads and moieties to separate DNA as taught by Loehrlein et al. to the method of storing information in DNA as taught by Rutten et al. Loehrlein et al. teach attaching primers to target sequences (par. 0005) wherein the primers may be forward and reverse primers (par. 0006) and that the primers may be coupled with a moiety (par. 0168). Rutten et al. teach forward and reverse primers and a “key” primer attached to the information carrying DNA sequence (i.e. data file). At the time of invention, a practitioner could have added a moiety with a magnetic bead as taught by Loehrlein et al. to the DNA data file as taught by Rutten et al. The predictable result of datafile DNAs with magnetic bead labeled moieties would be achieved. Such a combination is merely a "predictable use of prior art elements according to their established functions." One of ordinary skill could have also substituted the concept of having a primer “key” of Rutten et al. with a magnetic bead carrying moiety as taught by Loehrlein et al. Such would be a simple substitution of one known element for another to obtain predictable results. KSR Int’l 7, 127 S. Ct. at 1740.
Regarding dependent claims 2-7
Loehrlein et al. teach DNA (par. 0005), as in claim 2.
Loehrlein et al. teach biotin and antibody moieties (par. 0162) and streptavidin (par. 0179) and streptavidin coated magnetic beads (par. 0252), as in claim 3..
Loehrlein et al. teach amplification (par. 0004-0005), as in claim 4.
Loehrlein et al. teach sequencing (par. 0003 and 0076), as in claim 5.
Rutten et al. sequencing and error correction (page 5, section “Error correction”) (i.e. performing error analysis of sequencing data), as in claims 6.
Rutten et al. teach that storing information in DNA polymers is “durable” (Abstract and page 1, par. 1) and DNA can be copied (page 3, par. 2), as in claims 7.
Both Loehrlein et al. and Rutten et al. generally teach a system for use in carrying out a process as set forth in claim 35.
Loehrlein et al. teach double stranded polynucleotides (par. 0049), as in claim 36.
The following rejection is necessitated by Applicant’s amendments filed 10/10/2026.
Claims 23-34 and 37-38 are rejected under 35 U.S.C. 103(a) as being unpatentable over Loehrlein et al. (US 2002/0160361) in view of Rutten (Nature Reviews Chemistry vol 2 (2018) 365-381) and further in view of Dekker et al. (Nucleic Acid Research vol. 32 (2004) pages 1-8).
Loehrlein et al. teach methods of gene expression analysis wherein information is stored on DNA (Abstract)(i.e. a database of data filed which are DNA’s).
Loehrlein et al. teach (par. 0162) contacting labeled DNA with beads bearing avidin or antibody, wherein the labeled DNA is labeled with biotin and antigen that binds of the avidin or antibody on the bead; Loehrlein teach (par. 0050) that a detectable moiety is synonymous with a label used to distinguish a particular nucleic acid (i.e. the DNA is labeled with a chemical moiety); Loehrlein et al. teach that the beads may be magnetic beads (par. 0162) (i.e. contacting the database with a reagent that selectively binds a location on one or more polynucleotide strands not occluded by the physical occlusion), as in claim 23 and 25.
Loehrlein et al. teach a magnetic platform to precipitate the DNA bound to the beads (par. 0252) wherein the magnetic separation is performed with a moiety (par. 0044)(i.e. extracting the one or more polynucleotide strands bearing the data file using the reagent), as in claim 23 and 25.
Loehrlein et al. teach a “blocking group” (par. 0039) which reads on a physical occlusion but do not specifically teach that the physical occlusion comprises a single strand polynucleotide overhang (ss overhang) on the one or more double stranded polynucleotide strands bearing the datafile or wherein the physical occlusion comprises a DNA binding molecule, as in claim 23.
Loehrlein et al. does not specifically teach providing a database of a plurality of polynucleotide strands wherein the datafile comprises information encoded into double stranded (ds) polynucleotide strands, as in claim 23 .
Rutten et al. however teach encoding information into polymers and using DNA as an alternative for data storage (Abstract and pages 2-4). Rutten et al. teach data storage in DNA where DNA strands that encode the data have attached forward and reverse primers (page 5, Figure 1)(i.e. providing a database of a plurality of polynucleotide strands wherein the datafile comprises information encoded into double stranded (ds) polynucleotide strands), as in claims 23 and 25.
Rutten et al. teach a forward primer and a primer “key” (Figure 1)(i.e. chemical moiety or which also reads on a “physical occlusion”), as in claim 23 and 25.
Regarding an “overhang” on the double stranded DNA, Dekker et al. teach creating dsRNA molecules with overhangs for efficient hybridization and ligation (Abstract). Dekker et al. teach that the protocols used function on any DNA substrate and allow the user to determine the sequence of the overhangs incorporated; Dekker et al. teach that sticky ends for dsRNA are used for controlled, specific and efficient ligation of dsRNA molecules through hybridization (page 1, col. 1, par. 2).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to have applied the method of attaching magnetic beads and moieties to separate DNA as taught by Loehrlein et al. to the method of storing information in DNA as taught by Rutten et al. Loehrlein et al. teach attaching primers to target sequences (par. 0005) wherein the primers may be forward and reverse primers (par. 0006) and that the primers may be coupled with a moiety (par. 0168). Rutten et al. teach forward and reverse primers and a “key” primer attached to the information carrying DNA sequence (i.e. data file). At the time of invention, a practitioner could have added a moiety with a magnetic bead as taught by Loehrlein et al. to the DNA data file as taught by Rutten et al. The predictable result of datafile DNAs with magnetic bead labeled moieties would be achieved. Such a combination is merely a "predictable use of prior art elements according to their established functions." One of ordinary skill could have also substituted the concept of having a primer “key” of Rutten et al. with a magnetic bead carrying moiety as taught by Loehrlein et al. Such would be a simple substitution of one known element for another to obtain predictable results. KSR Int’l 7, 127 S. Ct. at 1740.
It would have been obvious to one of ordinary skill in the art at the time the invention was made to have combined the method of separating polynucleotides by magnetic beads as taught by Loehrlein et al. wherein the polynucleotides store information as taught by Rutten et al. with the method of creating an overhang on double stranded polynucleotides as taught by Dekker et al. Dekker et al. provide motivation by teaching that the overhang provides for ligation by hybridization (page 1, col. 1, par. 2). One of ordinary skill would have an expectation of success in combining Loehrlein et al. in view of Rutten et al. with Dekker et al. because Loehrlein et al. teach methods of gene expression analysis including the use of hybridization (par. 0039) by double stranded nucleic acid formation (par. 0049).
Regarding claims 24, 26-34 and 37-38
Loehrlein et al. teach double stranded DNA (par. 0049 and 0158) and double or single stranded primers (par. 0133), as in claim 24.
Loehrlein et al. teach biotin and antibody moieties (par. 0162) and streptavidin (par. 0179) and streptavidin coated magnetic beads (par. 0252), as in claim 26.
Rutten et al. teach a single stranded overhand and contacting the database with a key nucleic acid (page 5, Figure 1), as in claim 27.
Rutten et al. teach associating free nucleotides (i.e. an overhang sequence) and polymerizing with a polymerase (page 16-17, connecting par.); (i.e. polynucleotide strand comprises a RNA polymerase promoter sequence, extracting the polynucleotide by extracting the ss overhand using a labeled primer, adding the RNA polymerase), as in claim 28.
Rutten et al. teach that m-RNA acts as a reading template after DNA is copied by the DNA polymerase (page 21, section “Writing by catalytic methods), as in claim 29.
Loehrlein et al. teach a “blocking group” (par. 0039), contacting (i.e. providing a reagent that binds a sequence not occluded by the DNA binding molecule) and target specific primers that include labels such as a “friction moiety” (par. 0010 and 0017) which would aid in magnetic extract like a bead (par. 0044)(i.e. providing a reagent that binds to a sequence not occluded, contacted the data base with the reagent and magnetic bead, and extracting polynucleotide strands), as in claim 30.
Loehrlein et al. teach contacting DNA with a reagent of primers (par. 0006) and polymerase (par. 0018)(i.e. oligonucleotide and/or binding protein), as in claim 31.
Loehrlein et al. teach sequencing (par. 0003 and 0076), as in claim 32.
Rutten et al. sequencing and error correction (page 5, section “Error correction”) (i.e. performing error analysis of sequencing data), as in claims 33.
Rutten et al. teach that storing information in DNA polymers is “durable” (Abstract and page 1, par. 1) and DNA can be copied (page 3, par. 2), as in claims 34.
Regarding archeal histone proteins and guide RNA with dCAS9, as in claims 37-38, these DNA binding molecules are well known in the art as basic proteins that bind to DNA.
Response to Arguments
Applicant's arguments filed 10/10/2025 have been fully considered but they are not persuasive.
Applicants argue (Remarks, page 13, par. 3) that Rutten is a review article and does not teach any solutions to the unsolved problems. Applicants argue that Loehrlein at best attempts to address problems in methods and tools for analyzing genomic DNA and thus Loehrlein in view of Rutten do not teach that “information” outside of the naturally occurring genome is “stored on DNA.”
In response, Applicants appear to be arguing an intended use of the method without reciting active steps or structural limitations delimiting how the intended use is achieved. The claims recite “a polynucleotide strand bearing the datafile.” However, the claims do not recite how the polynucleotide is coded such that it bears information outside the naturally occurring genome. The claims do not recite what the data/information in the data is or how it is represented by the polynucleotides. A naturally occurring genome carries information and in fact reads on “a datafile” of information. Also, a naturally occurring genome can also correspond to information. The instant claims do not recite any algorithms for encoding a specific type of information into a nucleotide strand. However, even so, Rutten et al. teaches synthetic DNA that stores binary code and polymers for data storage (Abstract).
Applicants argue (Remarks, page 13, par. 3) that the claims recite a data file comprising information encoded into one or more polynucleotide strands.
In response, this limitation appears to be an intended use because the claims do not recite any structural difference between the recited polynucleotides and the polynucleotides taught in the prior art of Loehrlein or Rutten et al. Furthermore, Rutten et al. teaches synthetic DNA that stores binary code and polymers for data storage (Abstract). Rutten et al. clearly teaches that DNA can be used as an information storage medium (page 366, col. 1).
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anna Skibinsky whose telephone number is (571) 272-4373. The examiner can normally be reached on 12 pm - 8:30 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Ram Shukla can be reached on (571) 272-7035. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Anna Skibinsky/
Primary Examiner, AU 1635