Advances in light-directed synthesis of high-density microarrays and extension to RNA and 2'F-ANA chemistries

This chapter reviews the results of the author's attempts at improving quality, speed, and throughput in the fabrication of high-density deoxyribonucleic acid (DNA) microarrays by photolithography. While the phosphoramidite approach is simple to design and a mere adaptation of the in situ DNA synthesis, the enzymatic approach profits from the robustness of DNA synthesis to potentially obtain longer transcripts. The chapter then discusses ribonucleic acid (RNA) synthesis on microarrays. While the phosphoramidite approach may be useful in designing and preparing short RNA probes, the enzymatic approach may be necessary for the synthesis of structurally and functionally diverse RNA sequences. The chapter further presents the recent work toward the diffusion of in situ array synthesis to nonnatural nucleic acids, poorly covered in photolithography. It finally focuses on 2'-deoxy-2'- fluoroarabinonucleic acid (2'F-ANA), a biologically relevant and DNA-like nucleic acid analogue displaying unusual electronic properties, particularly in the context of G-quadruplexes, i-motifs, and duplex structures.