System and method for patterning flow cell substrates

A method for patterning flow cell substrates, comprising:

• fabricating a planar waveguide flow cell, wherein fabricating the planar waveguide flow cell includes:
• forming light coupling gratings on a glass substrate;
• depositing a core layer on the light coupling gratings;
• depositing a cladding layer on the core layer;
• and
• patterning the cladding layer to include nanowells in the cladding layer and interstitial regions of the cladding layer between the nanowells, wherein each nanowell includes a top portion and a bottom portion;
• silanizing the patterned cladding layer of the planar waveguide flow cell such that both the nanowells and the interstitial regions are silanized;
• coating the silanized cladding layer with a first group of reactants such that both the nanowells and the interstitial regions are coated with the first group of reactants;
• introducing a second group of reactants into the nanowells, wherein the second group of reactants includes at least one target reactant, a copper chelated ligand, and a light-sensitive photoinitiator system;
• and
• directing light internally within the planar waveguide flow cell such that the light coupling gratings and the core layer reflect the light to only the bottom portion of each nanowell for photo-initiating a chemical reaction between the first and second groups of reactants, wherein the photo-initiated chemical reaction covalently binds the at least one target reactant to only the bottom portion of each nanowell and the at least one target reactant is not bound to the interstitial regions.

A method for patterning flow cell substrates, comprising:

• fabricating a planar waveguide flow cell, wherein fabricating the planar waveguide flow cell includes:
• forming light coupling gratings on a glass substrate;
• depositing a core layer on the light coupling gratings;
• depositing a cladding layer on the core layer;
• and
• patterning the cladding layer to include nanowells in the cladding layer and interstitial regions of the cladding layer between the nanowells, wherein each nanowell includes a top portion and a bottom portion;
• silanizing the patterned cladding layer of the planar waveguide flow cell such that both the nanowells and the interstitial regions of the patterned cladding layer are silanized;
• coating the silanized cladding layer with a first group of reactants such that both the nanowells and the interstitial regions of the cladding layer are coated with the first group of reactants, wherein the first group of reactants includes a polymer, azide moieties bound to the polymer, a copper ligand, and a first light-sensitive photoinitiator system;
• directing first light of a predetermined wavelength internally within the planar waveguide flow cell such that the light coupling gratings and the core layer reflect the first light to only the bottom portion of each nanowell for photo-initiating a first chemical reaction between the reactants in the first group of reactants, wherein the photo-initiated first chemical reaction covalently binds the polymer to only the bottom portion of each nanowell and the polymer is not bound to the interstitial regions;
• introducing a second group of reactants into the nanowells, wherein the second group of reactants includes at least one target reactant, a copper ligand, and a second light-sensitive photoinitiator system;
• and
• directing second light of a predetermined wavelength internally within the planar waveguide flow cell such that the light coupling gratings and the core layer reflect the second light to only the bottom portion of each nanowell for photo-initiating a second chemical reaction between the covalently bound polymer and the second group of reactants, wherein the photo- initiated second chemical reaction covalently binds the at least one target reactant to only the bottom portion of each nanowell and the at least one target reactant is not bound to the interstitial regions.