GSJ: Received Jul. 18-21, 2007: http://wbabin.net/saba/saba87.htm

The present invention teaches support-affixed libraries of polynucleotides with tertiary structure (hereafter termed "aptamers") and the process of their fabrication. Aptamers preferably are single-stranded polynucleotides with tertiary structure which bind a target, and subsequently may or may not catalyze a reaction.

On-chip synthesis of protein microarrays is a proven technology (1, 2, 3). Figure 1 is a general outline of a preferred embodiment of the present invention, wherein aptamers rather than proteins are affixed to a support.

Therein, we start with two different dsDNAs microarrayed on the surface of a microchip as previously described (1,2,3). This is followed with polymerization to form multiple copies of a polynucleotide which affix to the support adjacent to their template dsDNA.

Polymerization could be achieved by means other than a polymerase promoter, for example nick displacement amplification (4).

There are several ways in which the aptamer products can be captured adjacent to their template dsDNA.

One method of capturing the aptamers is to make them chimeric, such that one portion, directed to the target, is different in each aptamer of the library, while another portion is common and binds a molecule such as streptomycin (5) or biotin, previously affixed to the support.

Another solution depicted in Figure 2 would be to polymerize two different modified nucleotides, via unnatural base-pairs (6,7), adjacent to each other such that their combination results in a recognition domain. It should be relatively easy to select for phage which only recognize the combined form.

Yet another alternative is to hybridize a portion of each synthesized aptamer to a support-affixed oligonucleotide as exemplified in Figure 3.

In one form of this, each different aptamer would have a common sequence which hybridizes to a common support-affixed oligonucleotide. However, it could be that each aptamer has a different sequence that hybridizes to a unique and complementary support affixed oligonucleotide.

While it may have been previously described, notice that with this later scheme aptamer synthesis no longer need be done on the chip. That is the different aptamers could be addressed to different oligonucleoties subsequent to batch synthesis.

One potential problem with these hybridization methods is the stability of the hybrids. A reasonable solution to this problem would be to incorporate hybridization-triggered crosslinking nucleotides into the aptamer-capturing oligonucleotides (11, 12).

The support as exemplified in the figures can be essentially any material in any form, but preferably is a microarray biochip or microbead.

These libraries can of course be used in screening for an aptamer which binds a target, and is perhaps catalytic. They could also be composed of previously characterized aptamers useful in parallel detection or quantitation of targets.

Lastly, notice that the protein microarrays of references 1-3 could be fabricated similar to the process delineated in Figure 2. That is during translation, there could be incorporated one or more amino acids whose unnatural side group (9) is bound by a support-affixed receptor specific for the unnatural side group(s).

If it should be that the above invention is indeed novel any patentable rights I may have, I freely give away.

It is hoped that others will honor the invention as delineated above and by the following claims.

Claims