Synthesis of DNA/RNA and Their Analogs via Phosphoramidite and H-Phosphonate Chemistries

Abstract

Abstract:The chemical synthesis of DNA and RNA is universally carried out using nucleoside phosphoramidites or H-phosphonates as synthons. This review focuses on the phosphorus chemistry behind these synthons and how it has been developed to generate procedures whereby yields per condensation approach 100% with very few side products. Additionally the synthesis and properties of certain DNA and RNA analogs that are modified at phosphorus will also be discussed. These analogs include boranephosphonates, metallophosphonates, and alkylboranephosphines.

The Risk of the Preparation of Artificial DNAs via an Interrupted Automated Solid-Phase Triester Method

“…An elaborate description is given under Mechanistic View, see Schemes 1 and 2. The group of Van Boeckel (Kuijpers et al [1] ) published the synthesis of well-defined, short phosphatemethylated DNA fragments according to the step-wise phosphoramidite procedure with one Fmoc-protected A nucleotide, according to Koole et al, [12][13][14] indicated as solution-phase synthesis. Meanwhile, Van Boeckel's group confirmed the backbone methylation in Koole's study.…”

“…This chemistry was described in a recent review by Roy and Caruthers. [12] Attention was also given to modified DNAs. Letsinger et al were the first chemists who synthesized natural DNA strands using phosphite triesters as intermediates.…”

“…Letsinger et al were the first chemists who synthesized natural DNA strands using phosphite triesters as intermediates. For a historical view see Roy and Caruthers [12] . The synthesis of phosphatemethylated DNA has been introduced by Miller et al with the view of studying the duplex formation with RNA.…”

Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores

“…Subsequently, the phosphoramidites 10a–f were isolated in excellent yields (83–98%) by following a standard phosphitylation procedure. 42 The presented strategy allows for late-stage incorporation of the respective dyes minimizing losses that typically accumulate over the course of multi-step syntheses. This is particularly crucial if the fluorophores are not readily available.…”

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

“…Within 7 years of this work, the first reported synthetic gene encoding the 14-amino-acid hormone, somatostatin, was expressed in recombinant Escherichia coli (Itakura et al 1977). Subsequent improvements to oligonucleotide synthesis chemistries and techniques in the early 1980s (reviewed in Caruthers 2011; Roy and Caruthers 2013) led to the development of solid-phase phosphoramidite chemistries whose robustness and fidelity allowed for automated methods to be developed to enable scalable oligonucleotide synthesis that is used to this day for the commercial synthesis of oligonucleotides. Synthetic oligonucleotides for gene synthesis applications are generally synthesized using variations of the phosphoramidite chemistry methods either on traditional column-based synthesizers or microarray-based synthesizers that will be discussed in the following sections.…”