Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.

Distinct local environments of the pyrene chromophores in the covalent deoxyribonucleic acid adducts of 9,10-epoxy-9,10,11,12-tetrahydrobenzo[e]pyrene and 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene elucidated by optically detected magnetic resonance

The optically detected magnetic resonance (ODMR) spectra of the covalent DNA adduct of 9,10-epoxy-9,10,11,12-tetrahydrobenzo[e]pyrene (BePE) reveal that the excited triplet state chromophore is perturbed by the nucleic acid and that this perturbation is diminished successively by denaturation and enzymatic hydrolysis of the modified DNA, indicating that the adduct resides in an environment with some quasi-intercalative character. In contrast the covalent adduct of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene shows little ODMR evidence of interaction with the nucleic acid, which, in view of ODMR's sensitivity demonstrated for the BePE adduct, suggests that the chromophore is situated in an environment resembling the bulk solvent. These results demonstrate that ODMR is more sensitive than conventional phosphorescence techniques to interactions between these pyrene-like chromophores and DNA.