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 .
DETAILED ACTION
Application status
In response to the previous Office action, a non-final rejection (mailed on 02/18/2026), Applicants filed a response and amendment received on 05/07/2026. Said amendment canceled Claims 2, 7-11 and 22, and amended Claim 1. Thus, Claims 1, 3-6, 12 and 21 are at issue and present for examination.
It is noted by the Examiner that Claims 13-20 are withdrawn from further consideration by the Examiner, 37 CFR 1.142(b) as being drawn to a non-elected invention in the previous Office actions, a non-Final rejection (mailed on 04/22/2025).
Claim Rejections - 35 U.S.C. § 112 - WITHDRAWN
The previous rejection of Claim 22 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112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn because Applicants have canceled claim 22.
Claim Rejections - 35 U.S.C. § 103 – MAINTAINED as necessitated by Applicants’ new amendment to claims
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The previous rejection of Claim 1, 3-6 and 12 under 35 U.S.C. 103 as being unpatentable over Berglund et al. (Luminopsins integrate opto- and chemogenetics by using physical and biological light sources for opsin activation, PNAS, 113 (3) E358-E367, published on 01/05/2016) in view of Parag-Sharma et al. (ACS Synth Biol. 2020 January 17; 9(1): 1–9), Tischer (Using optogenetic tools to test the kinetic proofreading model of T cell receptor ligand discrimination, Dissertation, 2017), and an evidentiary reference of Berglund et al. ("Light-Emitting Channelrhodopsin for Combined Optogenetic and Chemical-Genetic Control of Neurons", PLOS ONE, 8(3): e59759-1 - e59759-11, 27 March 2013, see IDS) is withdrawn by virtue of Applicants’ amendment and in favor of a new rejection as shown below.
Claims 1 and 3-6 are rejected under 35 U.S.C. 103 as being unpatentable over
Berglund et al. (Luminopsins integrate opto- and chemogenetics by using physical and biological light sources for opsin activation, PNAS, 113 (3) E358-E367, published on 01/05/2016, previously cited) in view of Nye et al. (Kinetic Control of Histidine-Tagged Protein Surface Density on Supported Lipid Bilayers, Langmuir, 2008, vol 24, no 8, 4145–4149) and Parag-Sharma et al. (ACS Synth Biol. 2020 January 17; 9(1): 1–9).
The instant claims are drawn to a composition of matter comprising a fusion protein attached, via a histidine tag, to a nickel chelating lipid present on the outer surface of a synthetic lipid particle, wherein the fusion protein comprises a light-generating protein, said histidine tag and a light- transducing protein, wherein the fusion protein is encoded by a nucleic acid comprising from 5' to 3', a sequence encoding said histidine tag, a sequence encoding said light generating protein and a sequence encoding said light transducing protein.
Berglund et al. teach various fusion proteins comprising wild-type Gaussia or Renilla luciferase (Gluc) or GLuc variants as a light-generating protein fused to a light-transducing protein, i.e., an opsin: Volvox channelrhodopsin 1 (VChR1) or other light-activated opsins (see Abstract; pg. E358, 1st para of introduction; and Fig. 1). Berglund et al. further teach that said fusion proteins to be lipidated and be expressed on the extracellular surface of transfected HEK cells because VChR1 comprises a cell membrane targeting domain, allowing said fusion protein to be expressed and be translocated to cell membrane (see Abstract; p.359, left column under “Identifying a GLuc Variant That Emits More Light”; Fig. 4. A & D on p. E362).
Claims 3-4 are included in this rejection because Berglund et al. teach that Gaussia or Renilla GLuc is inducible light-generating protein as it is dose-dependently induced to bioluminescence by coelenterazine (CTZ) (see Fig.1 C on pg. E359).
Claim 6 is included in this rejection because GLuc is attached to the N-terminus of ChR2 through a flexible 15 amino-acid linker (see the evidentiary reference of Berglund et al. on page 2, last sentence in left column continued to next column).
Berglund et al. do not teach attaching the fusion protein to a lipid particle via histidine tag bound to nickel-chelating lipids on the outer surface; and the use of iLID as a light-transducing protein (claim 5).
Nye et al. teach a well-established method for attaching histidine-tagged proteins to the outer surface of synthetic lipid particles. Nye et al. specifically teach supported lipid bilayers and liposomes containing nickel-chelating lipids (Ni-NTA-DOGS) that reversibly bind polyhistidine-tagged proteins on the outer surface of the bilayer (see Abstract; page 4146, left column under “Preparing SLBs with Nickel-Chelating Lipids”; pg. 4146-4147; and Figure 1).
Parag-Sharma et al. a bioluminescence resonance energy transfer (BRET)-activated optogenetics (BEACON), wherein iLID is activated upon bioluminescence of CeNLuc (a fusion of NanoLuc in-frame with a cyan fluorescent protein) which produces ~474 nm (blue-green light) (see Abstract; p. 4, 2nd para; p. 5, 3rd para).
It would have been obvious to a person of ordinary skill in the art (POSITA) prior to the effective filing date of the claimed invention to make and use the fusion protein taught by Berglund et al. and modify it by attaching them to the outer surface of a synthetic lipid particle via an N-terminal histidine tag using the nickel-chelating lipid method taught by Nye et al., while optionally replacing the light-transducing protein VChR 1 with iLID as taught by Parag-Sharma et al. A POSITA would have been motivated to make and use such composition especially in order to create a modular, membrane-displayable platform for lumiopsin-type fusion proteins on fluid synthetic lipid surfaces, enabling localized or autonomous optogenetic/chemogenetic signaling in synthetic cells or in vitro systems, in addition to the following reasons: [1] GLuc produces a blue light (see p. E365, left column, 3rd para of Berglund et al.) which can be used to activate iLID, which is an optimal light-transducing protein for the purposes of BEACON as taught by Parag-Sharma et al., [2] GLuc is much simpler to make (only 169 amino acids long) than CeNLuc, which is a fusion of NanoLuc in-frame with a cyan fluorescent protein, as a light-generating fusion partner, and [3] the his-Ni affinity technique was a standard, well-characterized, reversible, and oriented method routinely used to anchor his-tagged fusion proteins to the outer surface of liposomes and supported lipid bilayers (see Nye et al., Introduction on pg. 4145; Discussion on pg. 4148). A POSITA would have had a reasonable expectation of success to make and use such composition because all of the required biochemical reagents and techniques were readily available and rampantly used as evidenced by Berglund et al., Nye et al. and Parag-Sharma et al. prior to the filing of the instant application.
For the reasons provided herein, the invention as claimed is prima facie obvious over the combined teachings of the prior art.
Applicants’ Arguments:
Applicant submits that the cited art fails to teach or suggest the presently claimed configuration, particularly when the claims are properly construed as requiring a fusion protein whose spatial arrangement is defined by the nucleic acid sequence encoding order. As amended, the nucleic acid encodes, from 5' to 3', the histidine tag, the light-generating protein, and the light-transducing protein, thereby necessarily producing a fusion protein in which the light-generating protein is positioned proximal to the membrane and the light-responsive protein (e.g., iLID) is positioned distally. This sequence-defined orientation dictates the physical presentation of the domains upon attachment to the nickel-chelating lipid and is not taught or suggested in the cited art.
This distal positioning provides significant and unexpected functional advantages. By placing the light-responsive protein away from the membrane surface, steric hindrance is reduced and conformational flexibility upon illumination is enhanced. In the case of iLID, this arrangement facilitates efficient exposure of the buried peptide epitope (e.g., SsrA), enabling high-affinity binding to its cognate partner (e.g., SspB) in solution or on another surface. The result is improved accessibility, binding kinetics, and functional responsiveness - features that would be compromised in membrane-proximal or centrally constrained configurations.
None of the cited references recognize or suggest this structurally defined spatial arrangement or its advantages. Berglund et al. disclose fusion proteins but do not address domain orientation relative to a membrane or teach positioning a light- responsive domain distally from a membrane anchor. Parag-Sharma et al. describe light-responsive systems such as iLID but likewise do not teach incorporation into a membrane-bound fusion construct with a defined orientation. Tischer is even further removed, as it does not disclose a fusion protein at all. Instead, Tischer teaches optogenetic systems in which separate proteins are independently attached to a supported lipid bilayer, for example via His-tag/Ni-NTA interactions, and interact upon light activation (see page 72). Thus, Tischer relies on proximity between distinct proteins rather than a covalently linked, sequence-defined fusion architecture. The
Examiner's reliance on Tischer to suggest membrane attachment therefore does not remedy the absence of any teaching or suggestion of a fusion protein in which domain orientation is dictated by nucleic acid sequence and results in a distal light-responsive module.
Accordingly, the proposed combination would not yield the claimed invention but would instead require a fundamental redesign of the prior art systems, including converting separate interacting proteins into a single fusion construct and arranging the domains in a specific sequence-defined order to achieve the claimed distal positioning. There is no teaching, suggestion, or motivation in the art to make such modifications, nor any reasonable expectation that doing so would produce the demonstrated functional advantages. The rejection therefore rests on impermissible hindsight and should be withdrawn.
Examiner’s Explanation:
Applicants’ arguments have been fully considered but are not deemed persuasive for the following reasons.
First, Berglund et al. states that “[e]ach luciferase was fused to the extracellular N terminus of VChR1 and thus expressed on the extracellular surface of transfected HEK cells” (see page E359, left column 2nd para), which emphasizes that the fusion domain organization of the fusion protein taught by Berglund et al. is the same N-to-C terminal order recited in claim 1, i.e., light-generating protein followed by light-transducing protein (italicized for added emphasis).
Second, N-terminal his-tags are extremely common precisely because they frequently provide good accessibility and binding kinetics to Ni-NTA. This is predictable, not unexpected and a general knowledge in the art (see Nye et al. which studies kinetics of his-tagged proteins binding Ni-NTA-DOGS).
Third, trying different positions for the his-tag (N-terminal, C-terminal or internal) is routine optimization in fusion protein design (italicized for added emphasis). A POSITA would have been motivated to test N-terminal placement for better accessibility on the outer surface of liposomes.
Fourth, the claims of the instant application have no functional limitation, which is outside the scope of the claimed invention. Even assuming arguendo that unexpected functions of the claimed fusion protein were true, such functional characteristics would have been expected by a POSITA to be inherent in the fusion protein of Berglund et al. with N-terminal his-tag which has the same N-to-C terminal order as recited in claim 1, and such N-terminal his-tag often provides good accessibility for binding Ni-NTA resins and lipids (see Nye et al.)
Fifth, in response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
For the reasons provided herein, the invention as claimed is prima facie obvious over the combined teachings of prior art.
Allowable
Claim 21 is indicated to be allowable if claim 21 is written as an independent claim (currently claim 21 depends from a rejected claim 1). It is noted by the Examiner that claim 21 has the same language as previously proposed in the Examiner’s amendment for allowance (see interview summary dated 04/22/2025).
Conclusion
Claims 1 and 3-6 are rejected for the reasons as stated above. Claim 21 is indicated to be allowable if claim 21 is written as an independent claim (currently claim 21 depends from a rejected claim 1). Applicants must respond to the objections/rejections in this Office action to be fully responsive in prosecution.
THIS ACTION IS MADE FINAL. 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAE W LEE whose telephone number is (571)272-9949. The examiner can normally be reached on M-F between 9:00-6:00.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath Rao can be reached on (571)272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JAE W LEE/
Examiner, Art Unit 1656
/MANJUNATH N RAO/Supervisory Patent Examiner, Art Unit 1656
Prosecution Insights