Methods for testing oligonucleotide arrays
AssigneeAffymetrix, Inc.
InventorGlenn McGall
Life of this patent
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Abstract
Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acids.
Claims17
A method of manufacturing oligonucleotide arrays comprising manufacturing oligonucleotide arrays by spatially directed nucleic acid synthesis in high volume and testing selected arrays wherein the selected arrays are tested for the amount of depurination of oligonucleotides.
A method for determining the amount of depurination of oligonucleotides synthesized on a substrate by spatially directed oligonucleotide synthesis comprising the steps of:
- providing a substrate having a surface with linkers having an active site for oligonucleotide synthesis, the linkers being resistant to cleavage under cleavage conditions;
- synthesizing an ensemble of sequence-specific oligonucleotides in an area of the substrate, the oligonucteotides having active sites for attaching a detectable label;
- attaching a detectable label to the oligonucleotides in the ensemble;
- exposing the ensemble to a test condition;
- exposing the ensemble to cleavage conditions that cause cleavage of depurinated oligonucleotides;
- and
- determining the amount of detectable label in the area, said amount of detectable label being a determination of said amount of depurination.
A method for determining the amount of depurination of oligonucleotides synthesized on a substrate by spatially directed oligonucleotide synthesis comprising the steps of:
- providing a substrate having a surface with linkers having an active site for oligonucleotide synthesis, the linkers being resistant to cleavage under cleavage conditions;
- synthesizing an ensemble of sequence-specific oligonucleotides in an area of the substrate under a test condition, the oligonucleotides having active sites for attaching a detectable label;
- attaching a detectable label to the active sites;
- exposing the ensemble to cleavage conditions that cause cleavage of depurinated oligonucleotides;
- and
- determining the amount of detectable label in the area, said amount of detectable label being a determination of said amount of depurination.
Dependencies are inferred from the claim text.