3‘-Nitrophenylpropyloxycarbonyl (NPPOC) Protecting Groups for High-Fidelity Automated 5‘ → 3‘ Photochemical DNA Synthesis

Abstract

[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.

Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy

“…227 This group was further modified to increase the absorbance, such as in the 2-(3,4-methylenedioxy-6-nitrophenyl)propoxycarbonyl (MNPPOC; 114 ) 204,228 or analogous 3-(4,5-dimethoxy-2-nitrophenyl)-2-butyl (DMNPB, section 9) 229 derivatives, but 113 was applied in automated light-directed olgonucleotide synthesis (DNA-chips). 230 Amino acids 231 and carbohydrates were protected with NPPOC at the 6-position, including thiophenyl glycoside donors. 232 NPPOC derivatives are themselves relatively inefficient in two-photon deprotections; however, in the presence of sensitizers (section 8) (it has been shown by Wöll and co-workers that NPPOC can be sensitized), 166,233 the cross section can reach useful levels for several applications.…”

Photolabile Protecting Groups: Structure and Reactivity

“…With benzylic methyl substitution, the α‐methyl NPE group, that is, the 2‐(2‐nitrophenyl)propyl (NPP) group, is more than an order of magnitude faster than the NB group in releasing the substrate, and it has a considerably improved quantum yield ( Φ =0.35) 18. 34 The macroscopic rate of the 2‐(3,4‐methylenedioxy‐6‐nitrophenyl)propyl group ( t 1/2 =11 s, Φ =0.037) is fivefold faster than MeNP ( t 1/2 =54 s, Φ =0.0075) and 20‐fold faster than NV ( t 1/2 =216 s, Φ =0.0013) in releasing carbonates at 365 nm 32. In releasing cyclic guanosine monophosphate (cGMP) at 333 nm, the NPE group is more efficient than NV under the same conditions 35…”

Neue Aspekte der molekularbiologischen Diagnostik Array-Technologie und Expressionsprofile für die Charakterisierung rheumatischer Erkrankungen

“…Das Auslesen erfolgt mittels hochauflösenden konfokalen Laserscannern. Alternativ zum Spotting wurden photolithographische Methoden entwickelt, die eine Synthese der Oligonucletidsequenzen direkt auf dem Träger ermöglichen, eine höhere Dichte bis zu mehreren 100 000 Spots pro Quadratzentimeter zulassen und ein hohes Maß an Reproduzierbarkeit in der Fertigung liefern (5, 18,44). Bei der am weitesten entwickelten Technologie werden für die Genexpressionsanalyse mehrere Oligonukleotide des selben Gens verwendet und gleichzeitig kombiniert mit einem bis auf eine Punktmutation identischen Oligonukleotid.…”