Patent ID: 8721969

Claim:
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.