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 .
Status of claims: 100-119 are pending below.
Response to Arguments
Applicant's arguments filed July 1st 2026 have been fully considered but they are not persuasive.
Applicant’s remarks – (page 5) Applicant remarked First, the Office's assertion that Klein is in the field of "image analysis" appears incorrect. Please see the Remarks for further detail.
Examiner’s response – Examiner respectfully disagree. Klein is combined with the new Staker et al and Hesselberth together to teaches the mapped claim. Furthermore, Klein does teach the use of image in 0009 using imaging for diagnostic, 0067, 0078, 0562/photography in figures 1A-B, Figures 14A-E and paragraph 0072, figures 15 and 0073, as part of carrying out the claim invention. Examiner also note that the claims gives the choice to select between a repellent or attractant, thus arguing the lack of repellent is moot a choice was given. Please amend if the core inventive concept requires repellent only.
Applicant remark – (page 5-6) Applicant remarks Second, while the Office points to paragraph 0311 of Klein as disclosing "measurement of centers," this excerpt appears to have nothing to do with controlling a center-to-center distance of two molecules on a substrate. Please see remarks for further detail.
Examiner response – Examiner respectfully disagree. Klein is combined with the new Staker et al and Hesselberth together to teaches the mapped claim. Where different cite prior art teaches different parts of the claim invention as mapped below.
Applicant remark – (page 7) Applicant remarks Staker does not teaches the claim invention, where the cited paragraphs of Staker do not disclose the recited repellant. Please see Remarks for further detail.
Examiner response – Examiner respectfully disagree. Staker et al discloses stripping/removal/cleaving/spacing/reagent (cause repel) are all view as repellant between molecules for imaging/photography analysis.
Claim Rejections - 35 USC § 103
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.
Claims 100-118 are rejected under 35 U.S.C. 103 as being unpatentable over Staker et al (US 2018/0274028) in view of KLEIN et al (US 2017/0128365) and Hesselberth (US 2015/0087526).
Claim 100:
Staker et al (US 2018/0274028) teaches the following subject matter:
A method of controlling a center-to-center distance of two molecules on a substrate, wherein the substrate is coupled to an optical system, the method comprising (0176):
(b) placing the two molecules onto a substrate (figure 10c and figure 11, paragraph 0176 detail various molecules on substrate); and
(c) imaging the substrate; wherein the center-to-center distance of the two molecules in an image is less than a diffraction limit of the optical system (0176).
Staker et al teaches all the subject matter above, but not the following:
(a) treating the two molecules with an attractant or a repellant.
KLEIN et al (US 2017/0128365) teaches the following subject matter:
(a) treating the two molecules with an attractant or a repellant (0315 detail use of zwitterion as an electrostatic attraction).
Staker et al and KLEIN et al are both in the field of image analysis, especially analysis of molecules on a substrate regarding measurement of centers (KLEIN et al detail in 0311) such that the combine outcome is predictable.
Therefore it would have been obvious to one having ordinary skill before the effective filing date to modify Staker et al by KLEIN et al regarding attractant or repellant prove an effect highly effective lubrication hydrated charged groups as disclosed by KLEIN et al in 0312.
Staker et al and KLEIN et al both teaches all the subject matter above, but not the following:
Separate from each other.
Hesselberth (US 2015/0087526) teaches the following subject matter: Separate from each other (0124 detail step (c) attaching each of said plurality of peptides to a surface such that each peptide is spatially separated enough to allow single-molecule detection, which is before (d) imaging each of said plurality of peptides using single-molecule detection, and 0129 and 0135).
Staker et al and KLEIN et al and Hesselberth are all in image analysis, especially imaging molecules with optical system on substrate for processing such that the combine outcome is predictable.
Therefore it would have been obvious to one having ordinary skill before the effective filing date to modify Staker et al and KLEIN et al by Hesselberth enables to determined by bioinformatic analysis based on the encoded amino acid sequence further provides peptide derivatization and immobilization strategies to enable the sequencing and identification of a single peptide or a plurality of peptides as disclosed by Hesselberth in 0136.
Claim 101:
KLEIN et al teach:
The method of claim 100, wherein the repellant or the attractant comprises zwitterionic features (0315).
Claim 102:
KLEIN et al teach:
The method of claim 100, wherein the repellant or the attractant comprises PEG (0443), a polysaccharide (0342), ampholine ampholytes, sulphobetaine, BSA, or any combination thereof.
Claim 103:
KLEIN et al teach:
The method of claim 100, wherein the treating the two molecules with the attractant or the repellant comprises encasing the two molecules in a shell of the attractant or the repellant (0499 detail coverage/encasing).
Claim 104:
KLEIN et al teach:
The method of claim 103, further comprising removing the shell of the two molecules prior to imaging the substrate (0458 detail rinsed in de-ionized water to remove; 0551 detail attributed to removal of residual intact).
Claim 105:
KLEIN et al teach:
The method of claim 100, wherein the placing of the two molecules onto the substrate comprises dragging or pulling the two molecules (0315 detail use of zwitterion as an electrostatic attraction).
Claim 106:
Staker et al teach:
The method of claim 100, further comprising exposing the two molecules placed onto the substrate to a gas-liquid interface such that the two molecules form a monolayer across the substrate (0115-0117 teaches air imaging system).
Claim 107:
Staker et al teach:
The method of claim 106, wherein the gas-liquid interface is an air-water-interface (0115-0117 teaches air imaging system).
Claim 108:
Staker et al teach:
The method of claim 100, wherein the two molecules comprise concatemers (0012).
Claim 109:
Staker et al teach:
The method of claim 108, wherein the concatemers are hybridized to ssDNA hairs (0012; figure 2A and 0113; claim 2).
Claim 110:
Staker et al teach:
The method of claim 108, wherein the attractant or the repellant increases an effective exclusion size of the concatemers without altering a size of the concatemers (figure 2A and 0113 detail overfill or project, as well as shorten segment, all view as altering size).
Claim 111:
Staker et al teach:
The method of claim 108, wherein the concatemers comprise an actively extending end (figure 2A and 0113 detail project length).
Claim 112:
KLEIN et al teach:
The method of claim 111, wherein the actively extended away is raised above the substrate (0563).
Claim 113:
Staker et al teach:
The method of claim 100, wherein the two molecules are proteins or peptides (0099-0100).
Claim 114:
Staker et al teach:
The method of claim 100, wherein the substrate comprises a patterned surface (0118-0119 detail patterned).
Claim 115:
Staker et al teach:
The method of claim 100, wherein the substrate comprises an unpatterned surface (0192 detail non-patterned).
Claim 116:
Staker et al teach:
The method of claim 100, wherein a plurality of molecules are disposed on the substrate at a density of about 1 to about 25 molecules per square micron (0023-0025).
Claim 117:
Staker et al teach:
The method of claim 100, wherein the center-to-center distance between the two molecules is less than 400 nm (0119 and 0023).
Claim 118:
Staker et al teach:
The method of claim 100, wherein the center-to-center distance between the two molecules is less than 300 nm (0119 and 0023).
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 119 is rejected under 35 U.S.C. 102(a)(2) as being anticipated by Staker et al (US 2018/0274028)
Claim 119:
Staker et al (US 2018/0274028) anticipated following subject matter:
A method of sequencing a plurality of analytes disposed at high density on a surface of a substrate, comprising:
(a) performing a plurality of cycles of probe binding to a substrate comprising a surface, wherein the surface comprises a plurality of analytes immobilized adjacent to the surface in a monolayer due to, at least in part, a repellant of one or more adjacent analytes and a repellant of an analyte of the plurality of analytes, wherein a cycle of the plurality of cycles comprising (0010, 0017, 0031, 0049-0050):
(i) contacting the plurality of analytes with a plurality of probes, a probe of the plurality of probes comprising a detectable label (0095-0096 detail binding efficient and probe; 0100-0101); and
(ii) imaging a field of the surface with an optical system to detect an optical signal of a plurality of optical signals from each probe of the plurality of probes brought in contact with the plurality of analytes (0132-0133 detail binding with optical detection; 0151; 0173);
(b) determining a peak location of an analyte of the plurality of analytes from each of the plurality of optical signals (0011 detail peak location determined; 0025-0026; 0031); and
(c) identifying the analyte from the detectable label of the plurality of probes at the peak location across the plurality of cycles (0031, 0044-0049, specifically 0049 detail identifying densely packed analytes as well as each analyte; 0156 detail identify position/location).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Marini et al (US 2006/0148104) Detection Of Ion Channel Or Receptor Activity – 0223: The distance between two particles (or other components) can be measured with respect to any fixed points of the particles (or components), e.g., between the centers of two spherical particles, the centers of mass of two irregularly shaped particles or components.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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.
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/TSUNG YIN TSAI/Primary Examiner, Art Unit 2656
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