High yield detritylation of surface-attached nucleosides with photoacid generated in an overlying solid film: roles of translational diffusion and scavenging.

Conventional solid-phase oligonucleotide synthesis overcomes the reversibility of acid-dependent detritylation by washing away the released dimethoxytrityl cations (DMT(+)) with acid. This option is unavailable if the acid is photogenerated in an overlying solid film, as in the photolithographic fabrication of oligonucleotide arrays on planar surfaces. To overcome the resulting reversibility problem we developed methods of achieving >or=98% detritylation of glass-attached 5'-O-DMT-thymidine, a model for 5'-O-DMT-protected oligonucleotides, by the photogeneration of trichloroacetic acid in a solid film. Enhanced intrafilm diffusion, insufficient to degrade the photolithographic resolution but enabling DMT(+) to move from its plane of release into the overlying photoacid-generating film, increased detritylation from or=98%. Inclusion of an intrafilm carbocation scavenger such as a triarylsilane hydride converted the detritylation into a time-dependent irreversible process proceeding to >or=99% detritylation within 60 s following brief photoacid generation. Light sensitivity is high, exceeding direct photodeprotection methods by 15-100 fold.

Substituted 2-nitrobenzyltrichloroacetate esters for photodirected oligonucleotide detritylation in solid films.

Oligonucleotide microarray fabrication by chemical synthesis using photoacid generators in solid films could have advantages over existing methods, but has not matched the accuracy of conventional synthesis where detritylation is performed with acid solutions. To address this problem, we explored the kinetics and equilibria of nucleoside detritylation in solid films, using trichloroacetic acid (TCA) generated by photolysis from its esters with substituted 2-nitrobenzyl alcohols. We synthesised 25 such esters, all alpha-phenyl substituted, and assessed their potential as solid film photoacid generators. They included sets with (i) mono- or dimethoxy-, (ii) 5-halo-, (iii) alkyl- or aryl-substituted 5-amino-, or (iv) 5-aryl-substituents in the 2-nitro- or 2,6-dinitrobenzyl ring. Absorption maxima of their UV spectra ranged from 230 to 410 nm, with quantum yields at 365 nm from < 0.01 to nearly 1.0. The esters formed optically clear solid films on glass slides without added polymer. Kinetics of intrafilm photoacid generation, proton activity changes and detritylation were measured in situ. The most effective esters for light sensitivity and detritylation were 5-chloro-, 5-bromo-, 4,5-dimethoxy-, and 4- or 5-aryl-substituted 2,6-dinitrobenzyl esters. Photoacid-induced increases in proton activity and detritylation were severely inhibited by polymers containing electronegative heteroatoms, but not by polymers lacking them. In solid films, intrafilm detritylation with photogenerated TCA was fast, but stopped at an equilibrium well short of completion. Both experiment and theory emphasise the inadequacy of attempting to force detritylation with high intrafilm acid activity.

Novel photoacid generators for photodirected oligonucleotide synthesis.

Photodirected oligonucleotide synthesis uses either direct or indirect light-dependent 5'-deprotection. Both have been reported to give lower stepwise synthetic yields than conventional methods. The deficiency appears to be due to incomplete deprotection at the oligonucleotide 5'-position and, additionally in the case where photodirection is indirect and uses photogenerated photoacid to effect 5'-detritylation, the depurinating effects of strong acid. We have developed novel photosensitive-2-nitrobenzyl esters that on irradiation with near UV light generate alpha-chloro-substituted acetic acids, such as trichloroacetic acid, which are widely and successfully used in conventional solid-phase oligonucleotide synthesis. alpha-Phenyl-4,5-dimethoxy-2-nitrobenzyltrichloroacetate and alpha-phenyl-4,5-dimethoxy-2,6-dinitrobenzyltrichloroacetate showed appropriate photochemical characteristics and were used for photodirected synthesis of a variety of oligonucleotides, including (T)(5), TATAT, TGTGT, (T)(10), (AT)(5), (CT)(5) (GT)(5), and (TGCAT)(2) on a modified Millipore Expedite DNA synthesizer. The outcomes were compared with those obtained by use of directly added trichloroacetic acid (conventional synthesis). The stepwise yields for the two methods were essentially identical.

Effects of stray light on the fidelity of photodirected oligonucleotide array synthesis.

Fabrication of high density oligonucleotide arrays using metal on glass photolithographic masks is inflexible and expensive. Maskless methods using computer-controlled projection have been proposed and implemented, but associated stray light effects on photodirected oligonucleotide synthesis and their analysis have not been reported. We have developed a theoretical approach: it predicts that the stray light content of the output of digital micromirror devices and other spatial light modulators of similar performance (contrast ratio approximately 400) will cause extensive random base insertions. For example, use of a digital micromirror device for synthesis of a 20mer array will result in the majority of oligonucleotide chains being 21mers or 22mers. This chain lengthening effect of stray light would not be preventable when synthesis involves a directly photosensitive 5'-blocking group. If the 5'-blocking group is acid labile and released with photogenerated acid, the presence of low concentrations of weak base will prevent the effect of stray light. We have demonstrated experimentally the anticipated chain lengthening effect of stray light on photoacid-dependent synthesis of oligonucleotides and prevention of the effect by low concentrations of n-octylamine. The application of these findings should facilitate the development of maskless fabrication and availability of high density and high fidelity user-designed arrays for research applications.

New method for the preparation of 3'- and 2'-O-phosphoramidites of 2'- and 3'-difluoromethyluridine derivatives.

Hydrogenation of 2'-deoxy-2'-difluoromethylene-5'-O-dimethoxytrityluridine (1) and 3'-deoxy-3'-difluoromethylene-5'-O-dimethoxytrityluridine (7), gave the corresponding 2'- and 3'-difluoromethyluridine derivatives 2a and 8a. Detritylation of compounds 2a, 2b and 8a, 8b resulted in the formation of 1-(2-deoxy-2-C-difluoromethyl-beta-D-arabino-pentofuranosyl)uracil (3a) and 1-(3-deoxy-3-C-difluoromethyl-beta-D-xylo-pento furanosyl)- uracil (9a) as well as corresponding minor isomers 3b and 9b. Compounds 3a and 3b were also obtained from 2'-deoxy-2'-difluoromethylene-3',5'-O-(tetraisopropyldisiloxane-1,3-diyl)uridine (4). Finally, phosphitylation of 2a and 8a provided the title 2'- and 3'-O-phosphoramidites 6 and 10.