Assembly Fabrication of Oligonucleotide Arrays

Abstract

In this paper, a simple, reliable and flexible method for fabricating oligonucleotide arrays integrating in in-situ synthesis with a spotting technique is described. In this approach, different oligonucleotide sequences were synthesized on coded modification glass slides using combinatorial chemistry and a mature phosphoramidite chemistry protocol. The slides were then sliced into smaller pieces. Finally, an oligonucleotide array was fabricated by arbitrarily assembling the different coded pieces onto another solid support. A 5 x 5 array including four different sequences of the P16 gene and a control (blank) was successfully assembled. The results indicated that the hybridization fluorescence intensities from the same sequences located at different places on the array were homogeneous and uniform. Background fluorescence was much lower. The fluorescence intensity ratio of a matched sequence to a one-base mismatched sequence, a two-base mismatched sequence and a three-base mismatched sequence was 0.499, 0.236 and 0.04, respectively. The results for the same sequence at different spots in the chip were reproducible with the relative standard deviation ranging from 6.64% to 10.2% (n = 5). This method has the advantages of high probe-density of in-situ synthesis, and off-chip flexibility. Moreover, it does not need any immobilization process to bond oligonucleotides on the substrate.