Presented here is a method for preparing small DNA arrays on aldehyde-bearing glass slides. Immobilization involves reductive amination and employs oligonucleotides with 3¢-terminal lysine residues, obtained in high yield from solid phase syntheses. Spot patterns are produced by protecting selected areas of the aldehyde slides with wax, coating the free surface with a methyl triethylene glycol derivative, and removing the wax with dichloromethane. The DNA arrays give better signal to noise ratios in hybridization experiments than slides without passified background.

The relative reactivity of building blocks is critical for a successful preparation of combinatorial libraries.Here, we present a method for measuring the reactivity of carboxylic acid building blocks in amide-forming reactions. The method involves competitive reactions between a reference and test acid and a tetraphenylporphyrin reaction partner with four reactive sites. Relative reactivities are calculated on the basis of the distribution of substituted porphyrins found in MALDI-TOF mass spectra. Reactivities thus determined were used to prepare reactivity-adjusted building block mixtures. These were reacted with amino-terminal oligonucleotide and peptide scaffolds on solid support, generating small libraries suitable for spectrometrically monitored selection experiments (SMOSE). The rate of building block "drop outs" that fail to couple as expected was not substantially lowered by acquiring spectra from two reactions, performed with different ratios of building blocks, where the effect of a given substituent on the desorption/ionization yield of the porphyrin can be eliminated. Instead, coupling building blocks of similar size together or employing N-hydroxysuccinimide esters rather than activating with a "uronium salt" were found to improve the quality of libraries generated via competitive reactions.

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Abstract:Presented here is a method for rapidly testing the reactivity of carboxylic acids in amide-forming reactions. For this, a mixture of two acids, one a reference compound, and one acid whose reactivity is unknown, are coupled to an aminoacylated tetrakis(paminophenyl)porphyrin under typical peptide coupling conditions. The product distribution in the resulting library is analyzed via MALDI-TOF mass spectrometry to reveal the relative reactivity. This rapid reactivity test requires sub-nanomole quantities of acids, does not involve cleavage from a support or any potentially biasing work-up, and is automatable. Thus, it is well suited for testing building blocks for combinatorial syntheses. Further, it is demonstrated that step-wise coupling can produce near-statistically distributed libraries of porphyrins when acids of very different reactivity are employed.

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