Device for measuring nanometer level pattern-dependent binding reactions

A method of identifying the presence of an analyte from a fluid sample, the method comprising

• (a) providing a device comprising a substrate having a surface;
• the surface comprising regions, each region comprising an ordered, two-dimensional array of post sets over the surface, where the pitch between adjacent posts within each post set within a region is uniform, wherein each post is coated with a ligand, and wherein the pitch between adjacent posts each post set is less than about 100 nm;
• the regions comprising a gradient of pitch values designed for measuring the spatial dependence of binding of one analyte molecule to a ligand-coated post set, wherein the pitch is the distance between center points of adjacent posts in a post set and the gradient is a gradual change in the pitch values between the regions;
• (b) contacting the surface of the device with a fluid sample;
• and
• (c) determining whether or not one analyte in the fluid sample simultaneously interacts or binds to a set of the ligand-coated posts in a region, thereby identifying the presence of the analyte in the fluid sample.

A kit for determining the presence or absence of an analyte in a sample or for determining a subject's risk for developing a disease or for monitoring the status of a disease in a subject which comprises a device comprising

• (a) a substrate having a surface;
• and
• (b) regions on the surface, each region comprising an ordered, two-dimensional array of post sets over the surface, where the pitch between adjacent posts of a post set within a region is uniform, wherein each post is coated with a ligand, and wherein the pitch between adjacent posts of a post set is less than about 100 nm;
• the regions comprising a gradient of pitch values designed for measuring the spatial dependence of binding of one analyte to a post set;
• wherein sets of the ligand-coated posts can specifically bind to an analyte in an amount effective for detection of an analyte in the sample;
• and wherein the pitch is the distance between center points of adjacent posts of a post set and the gradient is a gradual change in the pitch values from one region to another.

A method for detecting a protein isomer in a mixture, the method comprising

• (a) providing a device comprising a substrate having a surface;
• the surface comprising regions, each region comprising an ordered, two-dimensional array of post sets over the surface, wherein each post is coated with a ligand, and wherein the pitch between adjacent posts in a post set within a region is uniform;
• the pitch between adjacent posts in a post set is less than about 100 nm;
• the regions comprising a gradient of pitch values designed for measuring the spatial dependence of binding of one analyte to a post set;
• and wherein the pitch is the distance between center points of adjacent posts in a post set and the gradient is a gradual change in the pitch values from one region to another;
• (b) contacting the surface of the device with a mixture;
• and
• (c) determining whether or not a protein isomer in the mixture interacts or binds to ligand-coated post sets in a region, thereby detecting the protein isomer in the mixture.

A method for detecting a microorganism in a fluid sample, the method comprising

• (a) providing a device comprising a substrate having a surface;
• the surface comprising regions, each region comprising an ordered, two-dimensional array of post sets over the surface, wherein each post is coated with a ligand, and wherein the pitch between adjacent posts in a post set within a region is uniform and is less than about 100 nm;
• the regions comprising a gradient of pitch values designed for measuring the spatial dependence of binding of one analyte to a post set;
• and wherein the pitch is the distance between center points of adjacent posts in a post set and the gradient is a gradual change in the pitch values from one region to another;
• (b) contacting the surface of the device with a fluid sample;
• and
• (c) determining whether or not a microorganism in the fluid sample interacts or binds to ligand-coated post sets in a region, thereby detecting the microorganism in the fluid sample.