Methods and compositions for determining the purity of and purifying chemically synthesized nucleic acids

A method of preparing an oligonucleotide microarray comprising the steps of:

• (a) providing, for each oligonucleotide sequence in the oligonucleotide microarray, a synthetic oligonucleotide mixture prepared using organic protecting groups, the mixture comprising fully deprotected synthetic oligonucleotides, partially deprotected synthetic oligonucleotides, and/or fully protected synthetic oligonucleotides, the mixture having at least one partially or fully protected synthetic oligonucleotide with a protecting group covalently bound thereto;
• (b) providing an antibody microarray comprising, for each oligonucleotide in the oligonucleotide microarray, a plurality of antibodies immobilized at a separate discrete location on a first substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto, the plurality of antibodies including at least one antibody that is capable of binding at least one of the partially or fully protected synthetic oligonucleotides;
• (c) separately contacting each synthetic oligonucleotide mixture with the antibodies immobilized at a separate discrete location on the antibody microarray such that at least one of the protected synthetic oligonucleotides from the mixture is bound to at least one of the antibodies immobilized on the antibody microarray, wherein at least a portion of the oligonucleotides in the synthetic oligonucleotide mixture do not bind to the plurality of antibodies;
• (d) separating the unbound synthetic oligonucleotides of each synthetic oligonucleotide mixture from the antibody microarray, thus separating the unbound synthetic oligonucleotides from any partially and/or fully protected synthetic oligonucleotide or oligonucleotides bound to the antibodies immobilized on the antibody microarray;
• and
• (e) immobilizing the unbound synthetic oligonucleotides from each synthetic oligonucleotide mixture at a separate discrete location on a second substrate to form an oligonucleotide microarray.