[structure: see text]. The most powerful DNA microarrays would be prepared by photolithography with free 3'-ends that could be processed enzymatically. A photoremovable group that could be removed in quantitative yield would ensure high purity of the synthesized probes. We have developed new pyrimidine building blocks for 5' --> 3' DNA synthesis with high cycle yields using the NPPOC (3'-nitrophenylpropyloxycarbonyl) protecting group. These phosphoramidites were proved in automated photochemical DNA synthesis on a modified synthesizer.

Recently, substrate and protein radicals have been recognized as important intermediates in biological reactions.1 Galactose oxidase (GOase) catalyzes the two-electron oxidation of primary alcohols with 02 to produce aldehydes and H202.2 GOase has two one-electron redox centers at the active site. GOase can exist in two stable forms: a one-electron-reduced inactive form and an oxidized active form.3 Spectroscopic data show that the active form has Cu(II)4 and another, non-metal, redox center at the active

Ketyl radical anions with a halogen substitutent on the carbon adjacent to ketyl are known to rapidly rearrange by halide anion ejection. Such a rearrangement is an ideal probe for possible ketyl radical anion intermediates in the catalytic mechanism of the monocopper/tyrosine radical enzyme galactose oxidase (GOase). Turnover of β-fluoro-, β-chloro-, β-bromo-, and β-iodoethanol by GOase leads to mechanism-based inactivation of the enzyme by trapping the enzyme in a catalytically inactive one-electron-reduced form. Presuming that mechanism-based inactivation and turnover proceed through the same reactive intermediates, the data reported here narrow down the possible mechanisms for the substrate oxidation step (the two electron transfer from substrate to enzyme) to two similar possibilities. Either the reaction proceeds through a short-lived ketyl radical anion intermediate or it proceeds through a closely related concerted E2R mechanism with considerable ketyl radical anion character in the transition state.

A high fidelity, surface-based method of nucleic acid analysis has been developed based on DNA polymerase extension of primer-template complexes on DNA microchips. The ability of the method to discriminate against mismatches and provide an almost "digital" signal recommended it for molecular computation. A DNA computer with the capability of solving nondeterministic polynomial time (NP)-complete problems (those whose time-complexity function rises exponentially with the problem size) in polynomial time using this Arrayed Primer EXtension (APEX) method was experimentally demonstrated. An algorithm involving extension of surface-bound primer-template complexes, representing solutions and clauses of a Boolean formula, is described for the solution of two-, three-, and four-variable satisfiability (SAT) problems, including a 3SAT, exploiting the theoretical concepts of Lipton. A discussion of the principles of nondeterministic computing with APEX is also provided.