Apparatus for the synthesis of oligonucleotides and process for the preparation thereof

A method of assembling an oligonucleotide chain in automated fashion by repeated cycles of building block coupling, wherein the following steps 1 through 6 are carried out anew in each of the cycles of building block coupling:

• 1. providing a n-mer oligonucleotide, where n is an integer equal to or larger than 1, bound to a solid support and comprising a first reactive group free to extend the oligonucleotide backbone by reaction with a second reactive group comprised in a building block to be incorporated;
• 2. providing the building block to be incorporated, which comprises the second reactive group free to react with the first reactive group of the n-mer oligonucleotide, and which further comprises a first reactive group blocked by an acid sensitive temporary protecting group;
• 3. contacting the n-mer oligonucleotide with the building block to be incorporated under conditions that allow for binding of the first reactive group of n-mer oligonucleotide to the second reactive group of the building block to be incorporated, and generating a protected, extended n-mer oligonucleotide, which is blocked from further extension by the acid sensitive temporary protecting group;
• 4. preparing an acidic deprotection reagent by mixing at least two liquid compositions, wherein the composition of the acidic deprotection reagent is defined individually for each coupling cycle, and wherein the composition of the acidic deprotection reagent is different between at least two coupling cycles;
• 5. contacting the protected, extended n-mer oligonucleotide of step 3 with the acidic deprotection reagent of step 4, thereby cleaving the acid sensitive temporary deprotecting group from the extended n-mer oligonucleotide;
• and
• 6. removing the deprotection reagent and soluble cleavage product from the extended n-mer oligonucleotide, which may then be used as the n-mer oligonucleotide in step 1 of the following coupling cycle.