Structured substrates for optical surface profiling

An optical detection apparatus comprising:

• (i) a light source, wherein said light source produces an illumination beam comprising one or more wavelength(s);
• (ii) a reflective substrate comprising capture molecules bound to an uppermost surface, wherein the illumination beam is directed onto the reflective substrate;
• (iii) a flow cell into which the reflective substrate is incorporated to allow delivery of target molecules to the capture molecules in a fluid environment;
• and
• (iv) a photodetector array operably linked to a central processor capable of measuring an intensity of light from the illumination beam reflected from the reflective substrate.

A method for measuring target molecule binding to a microarray, the method comprising:

• (a) illuminating the microarray with an illumination beam, the illumination beam directed onto the microarray in a direction substantially perpendicular to the plane of the microarray comprising capture molecules on a surface of the microarray, wherein:
• the microarray is incorporated within a flow cell, allowing for delivery of target molecules to the microarray;
• (b) delivering, via the flow cell, target molecules to the microarray in a fluid environment;
• (c) imaging light from the illumination beam reflected from the surface of the microarray onto a photodetector array thereby recording one or more image(s) of the microarray surface;
• and
• (d) using the recorded image(s) of the microarray surface to assess binding of the target molecules to the capture molecules on the microarray surface.