Apparatus for single-molecule detection

A method of sequencing a nucleic acid, comprising the steps of:

• providing a detection apparatus comprising:
• a waveguide comprising:
• a core layer;
• and
• a first cladding layer made of a dielectric material;
• wherein
• at least one nanowell is formed in at least the first cladding layer, and
• an upper opening of the at least one nanowell is larger than a bottom of the at least one nanowell;
• a first opaque protection layer arranged over the first cladding layer without extending into the at least one nanowell;
• a second opaque protection layer arranged below the waveguide, the second opaque protection layer having a nanostructured metal pattern;
• and
• at least one light detector;
• providing at least one nucleic acid molecule;
• locating the at least one nucleic acid molecule individually within the at least one nanowell;
• performing single molecule sequencing-by-synthesis of the at least one nucleic acid molecule, wherein the single molecule nucleic acid sequencing-by-synthesis leads to emission of light correlated to the identity of at least one base in the nucleic acid;
• detecting the light with the detector, resulting in an output signal;
• and
• processing the output signal to determine an identity of at least one base comprised by the nucleic acid.