Method of producing oligonucleotide arrays with features of high purity

A method of making a full length oligonucleotide array from a mixture of pre-synthesized oligonucleotides on a support, the mixture comprising full-length oligonucleotide and shorter-length oligonucleotide each having a 5'-end and a 3'-end, one of the 5'- or 3'-ends being a free-end, the free-end of the full-length oligonucleotide having a protecting group and the free-end of the shorter-length oligonucleotide having a capping group, the other end of each oligonucleotide being the linked-end that is attached to the support, the method comprising the steps of:

• reacting an amine-providing agent with the full-length oligonucleotide to provide an amino group on the free-end of the full-length oligonucleotide;
• cleaving the linked-end of the oligonucleotides in the mixture from the support and simultaneously converting the amino group of the full-length oligonucleotide to a primary amine;
• and
• depositing without separately purifying the oligonucleotide mixture on a surface of an array substrate for attachment to the surface, the primary amine on the free-end of the full-length oligonucleotide preferentially attaching to the surface of the substrate over secondary or tertiary amines present on the full-length and shorter length oligonucleotides of the mixture, thereby forming the full length oligonucleotide array.

A method of making a full length oligonucleotide array having equal to or greater than 90% full-length oligonucleotides from a mixture of pre-synthesized oligonucleotides on a support, the mixture comprising full-length oligonucleotide and shorter-length oligonucleotide each having a 5'-end and a 3'-end, the 5'-end of the full-length oligonucleotide having a protecting group and the 5'-end of the shorter-length oligonucleotide having a capping group, the 3'-end of each oligonucleotide being the linked end that is attached to the support, the method comprising the steps of:

• reacting an amine-providing agent with the full-length oligonucleotide to provide an amino group on the 5'-end of the full-length oligonucleotide;
• cleaving the 3'-end of the oligonucleotides in the mixture from the support and simultaneously converting the amino group of the full-length oligonucleotide to a primary amine;
• depositing without separately purifying the oligonucleotide mixture on a surface of an array substrate for attachment to the surface, the primary amine on the 5'-end of the full-length oligonucleotide preferentially attaching to the surface of the substrate over secondary or tertiary amines present on the full-length and shorter length oligonucleotides of the mixture;
• and
• processing the array of deposited oligonucleotides to remove unattached materials including the capped shorter-length oligonucleotide, thereby forming the full length oligonucleotide tray.