DENSLEY-PACKED ANALYTE LAYERS AND DETECTION METHODS

1 .- 99 . (canceled)

100 . 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:

(a) treating the two molecules with an attractant or a repellant;

(b) placing the two molecules onto a 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.

101 . The method of claim 100 , wherein the repellant or the attractant comprises zwitterionic features.

102 . The method of claim 100 , wherein the repellant or the attractant comprises PEG, a polysaccharide, ampholine ampholytes, sulphobetaine, BSA, or any combination thereof.

103 . 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.

104 . The method of claim 103 , further comprising removing the shell of the two molecules prior to imaging the substrate.

105 . The method of claim 100 , wherein the placing of the two molecules onto the substrate comprises dragging or pulling the two molecules.

106 . 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.

107 . The method of claim 106 , wherein the gas-liquid interface is an air-water-interface.

108 . The method of claim 100 , wherein the two molecules comprise concatemers.

109 . The method of claim 108 , wherein the concatemers are hybridized to ssDNA hairs.

110 . 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.

111 . The method of claim 108 , wherein the concatemers comprise an actively extending end.

112 . The method of claim 111 , wherein the actively extended away is raised above the substrate.

113 . The method of claim 100 , wherein the two molecules are proteins or peptides.

114 . The method of claim 100 , wherein the substrate comprises a patterned surface.

115 . The method of claim 100 , wherein the substrate comprises an unpatterned surface.

116 . 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.

117 . The method of claim 100 , wherein the center-to-center distance between the two molecules is less than 400 nm.

118 . The method of claim 100 , wherein the center-to-center distance between the two molecules is less than 300 nm.

119 . 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:

(i) contacting the plurality of analytes with a plurality of probes, a probe of the plurality of probes comprising a detectable label; 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;

(b) determining a peak location of an analyte of the plurality of analytes from each of the plurality of optical signals; and

(c) identifying the analyte from the detectable label of the plurality of probes at the peak location across the plurality of cycles.