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Method for the light-controlled synthesis of biochips

Organization name

DKFZ Deutsches Krebsforschungszentrum



The present invention relates to a method for the photolithographic synthesis of biochips in which photolabile protective groups of the 2-(2-nitrophenyl) ethyl type (NPPOC) are used, whereby the irradiation step is carried out in the presence of a base, preferably a secondary or tertiary base.

Development Stage

For DNA chip synthesis, oligonucleotide quality has immense consequences for accuracy, sensitivity and dynamic range. The quality of biochips produced by photolithographic in situ synthesis depends critically on the efficiency of photodeprotection. By means of base-assisted enhancement of this process using NPPOC deoxynucleotide amidites, synthesis yields improved by at least 12% per condensation compared to current chemistries.

Experimental Data

The inventors showed the enhancing effect of adding a base during removal of the NPPOC group, published in Nucleic Acids Research, 2000, Vol. 28, No. 4). A custom built synthesizer with opto-sensors was used for the photolithographic
DNA chip synthesis. For chip production with NPPOC phosphoramidites, irradiation was initially performed in the presence of 10% water in methanol known from in-solution studies. However, only DNA arrays of low quality were obtained. When irradiation took place in the absence of any fluid, as recommended for MeNPOC chemistry, the synthesis gave comparable unsatisfactory results. The inventors found the enhancing effect of adding a base during removal of the NPPOC group, using solutions of piperidine, diisoproyl-ethylamine or DBU in acetonitrile.


What claimed is (claims 1 and 2 of 10):

  1. A method for synthesising a light-controlled biochip comprising the step if carrying out an irradiation step common for photolithographic chip in the presence of a base, wherein photolabile protecting groups of the 2-(2-nitrophenyl)ethyl type are used.
  2. A method, wherein the base is a secondary or tertiary base.


The cleavage of photolabile protecting groups, e.g. NPPOC, in the irradiation step of a common photolithographic chip synthesis is not only applicable for DNA synthesis but also in the synthesis of RNA, PNA and LNA.


  • Improved cleavage of photolabile protecting groups during biochip synthesis by the use ofbases
  • Enhanced quality of oligonucleotide biochip synthesis
  • Applicable for DNA, RNA; PNA and LNA Chip synthesis


The invention was jointly conceived by Markus Beier, Stefan M. Matysiak, Jörg Hoheisel

Intellectual Property

Patents have been granted in the US and Europe (AT, BE, CH, DE, FR, GB, IE).

Commercial Opportunity

We seek industrial partners for commercializing this technology through a licence and/or cooperation agreement.

Further Information

No other public information is currently available, but further information (speaking with the inventors) is available under a signed Confidential Disclosure Agreement (CDA).

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