Nucleic acid affinity columns

A nucleic acid affinity matrix that reduces known nucleic acid molecules in a sample, said affinity matrix comprising a multiplicity of at least 20 different predetermined nucleic acid probes, wherein:

• there exists in said affinity matrix a probe complementary to each of said nucleic acid molecules or a subsequence thereof;
• said at least 20 different predetermined probes do not include every possible probe having the same length as said predetermined probes;
• and
• wherein the probes comprising said multiplicity of probes are preselected by the steps of:
• i) determining an allowable Tm interval;
• ii) determining a mismatch Tm threshold;
• iii) identifying all nucleic acid sequences of a preselected length complementary to a known nucleic acid molecule whose Tm to said known nucleic acid molecule is within said allowable Tm interval;
• iv) determining the likelihood of each of said nucleic acid sequences complementary to said known nucleic acid molecule also occurring in an unknown message;
• v) sorting said sequences in order of likelihood with the least likely sequence first;
• vi) selecting the first nucleic acid sequence whose Tm to all other known nucleic acid molecules in said sample is below said mismatch Tm;
• vii) repeating step vi) until a desired number of nucleic acids that specifically hybridize, under stringent conditions, to said known nucleic acid molecule are obtained;
• viii) repeating steps iii) through vii) until at least one nucleic acid sequence that hybridizes specifically under stringent conditions to each known nucleic acid molecule is selected.

A nucleic acid affinity matrix that reduces known nucleic acid molecules in a sample, said affinity matrix comprising a multiplicity of at least 20 different predetermined nucleic acid probes, wherein:

• there exists in said affinity matrix a probe complementary to each of said nucleic acid molecules or a subsequence thereof;
• and
• said at least 20 different probes do not include every possible probe having the same length as said predetermined probes;
• and
• wherein said affinity matrix is prepared according to a method that comprises
• providing a nucleic acid amplification template array comprising a surface to which are attached at least 20 template nucleic acid probes having different predetermined nucleic acid sequences, wherein:
• i) each different template probe is localized in a known location of said surface;
• ii) the density of said template probes is greater than about 60 different template probes per 1 cm2;
• and
• iii) said different template probes have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence;
• and
• amplifying said multiplicity of oligonucleotides at least about 10 fold to provide a nucleic acid pool from which the at least 20 different predetermined nucleic acid probes are obtained.