TAGGED-BASE DNA SEQUENCING READOUT ON WAVEGUIDE SURFACES
A method of tagged-base DNA sequencing readout on waveguide surfaces includes immobilizing, a surface of a waveguide, a nucleotide fragment, exposing the nucleotide fragment to a first plurality of capped nucleotides, wherein the first plurality of capped nucleotides include a first plurality of nucleotide types, each distinct nucleotide type has a distinct capping agent, and each distinct capping agent has a distinct optical signature, severing base pair connections between the at least a nucleotide fragment and the first plurality of capped nucleotides, wherein the nucleotide fragment remains attached and a first single nucleotide, of the first plurality of capped nucleotides, remains immobilized on a nucleotide binding locus adjacent to the first nucleotide sequence, and detecting a first distinct optical signature of a first distinct capping agent of the first single nucleotide using the waveguide.
1 . A method of tagged-base DNA sequencing readout on waveguide surfaces, the method comprising:
immobilizing, a surface of a waveguide, a nucleotide fragment;
exposing the nucleotide fragment to a first plurality of capped nucleotides, wherein:
the first plurality of capped nucleotides include a first plurality of nucleotide types;
each distinct nucleotide type has a distinct capping agent; and
each distinct capping agent has a distinct optical signature;
severing base pair connections between the at least a nucleotide fragment and the first plurality of capped nucleotides, wherein:
the nucleotide fragment remains attached; and
a first single nucleotide, of the first plurality of capped nucleotides, remains immobilized on a nucleotide binding locus adjacent to the first nucleotide sequence; and
detecting a first distinct optical signature of a first distinct capping agent of the first single nucleotide using the waveguide.
2 . The method of claim 1 , wherein the first fragment is a fragment of a nucleotide sample.
3 . The method of claim 2 , wherein immobilizing the first fragment further comprises:
dividing the nucleotide sample into a plurality of fragments; and
selecting the first fragment from the plurality of fragments.
4 . The method of claim 1 , wherein the first distinct optical signature is a fluorescent signature.
5 . The method of claim 1 , wherein detecting the first distinct optical signature further comprises:
exciting the first distinct capping agent using an out of plane light source; and
detecting the fluorescent signature as a function of the exciting.
6 . The method of claim 1 , wherein detecting the first distinct optical signature further comprises:
exciting the first distinct capping agent using a waveguide light source; and
detecting the fluorescent signature as a function of the exciting.
7 . The method of claim 1 , wherein the first distinct optical signature is an absorption signature.
8 . The method of claim 5 , wherein detecting the first distinct optical signature further comprises:
passing a broadband light through the waveguide; and
determining an attenuation frequency of the broadband light.
9 . The method of claim 6 , wherein the waveguide is composed of material having a broad transmission window.
10 . The method of claim 6 , wherein passing the broadband light through the waveguide further comprises generating the broadband light using a tunable laser.
11 . The method of claim 1 , wherein detecting a first distinct optical signature further comprises detecting the first distinct optical signature using at least a spectrometer.
12 . The method of claim 1 , wherein detecting the first distinct optical signature further comprises propagating, using the waveguide, an evanescent wave from the surface, and detecting the first distinct optical signature as a function of the evanescent wave.
13 . The method of claim 1 further comprising removing the first distinct capping agent from the first single nucleotide.
14 . The method of claim 14 , wherein removing the first distinct capping agent further comprises irradiating the first distinct capping agent using the waveguide.
15 . The method of claim 14 , wherein removing the first distinct capping agent further comprises removing the first distinct capping agent using a chemical agent.
16 . The method of claim 14 further comprising performing at least a detection iteration, wherein each detection iteration further comprises:
exposing the nucleotide fragment to a second plurality of capped nucleotides;
severing base pair connections between the at least a nucleotide fragment and the second plurality of capped nucleotides, wherein:
the nucleotide fragment remains attached; and
a second single nucleotide, of the second plurality of capped nucleotides, remains chained to the first single nucleotide; and
detecting a second distinct optical signature of a second distinct capping agent of the second single nucleotide using the waveguide.
17 . The method of claim 17 , wherein each detection iteration is performed after removal of a capping agent from a previous detection iteration.
18 . The method of claim 1 further comprising:
locally amplifying the nucleotide fragment; and
generating a cluster of identical nucleotide fragments immobilized on the surface of the waveguide as a function of the local amplification.
19 . The method of claim 1 , wherein the first plurality of nucleotide types includes all deoxyribonucleic acid nucleotide types.
20 . The method of claim 1 , wherein the first plurality of nucleotide types includes all ribonucleic acid nucleotide types.