TFA-Pentylaminolinker Phosphoramidite is a specialized reagent used in the synthesis of oligonucleotides, particularly for introducing functional groups or linkers during automated DNA or RNA synthesis.
Reference Reading
1. Synthesis of Aminotroponyl-/Difluoroboronyl Aminotroponyl Deoxyuridine Phosphoramidites
Bibhuti Bhusana Palai, Subhashree S Panda, Nagendra K Sharma. Curr Protoc. 2022 Dec;2(12):e609. doi: 10.1002/cpz1.609.
This report describes the chemical synthesis of aminotroponyl-conjugated deoxyuridine analog (at-dU) and its difluoroboron complex (dfbat-dU) and their phosphoramidites by using the versatile phosphorylating reagent 2-Cyanoethyl N,N-diisopropylchlorophosphoramidite. Tropolone is a non-benzenoid aromatic bioactive natural fluorescent molecule, possessing intramolecular charge transfer and metal chelating properties with transition metal ions such as Cu2+/ Zn2+/ Ni2+ . Its synthetic derivatives, 2-aminotropones also exhibit unique bioactivities and are considered potential therapeutic drug candidate. Recently, the fluorescence properties of aminotropone has improved by complexing with difluoroboron residue that generates aminotroponyl-BODIPY analog. These could be employed for the synthesis of at-dU/dfbat-dU containing DNA oligonucleotides for designing the 11 B/19 F-NMR/fluorescence-based DNA probes. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of N-propargyl-2-aminotropone (2) and difluoroboronyl N-propargyl-2-aminotropone (3) molecules. Basic Protocol 2: Synthesis of N-propargyl-2-aminotroponyl deoxyuridinyl (at-dU) phosphoramidites (7). Basic Protocol 3: Synthesis of difluoroboronyl N-propargyl-2-aminotroponyl deoxyuridinyl (dfbat-dU) phosphoramidites (10).
2. On-demand synthesis of phosphoramidites
Alexander F Sandahl, Thuy J D Nguyen, Rikke A Hansen, Martin B Johansen, Troels Skrydstrup, Kurt V Gothelf. Nat Commun. 2021 May 12;12(1):2760. doi: 10.1038/s41467-021-22945-z.
Automated chemical synthesis of oligonucleotides is of fundamental importance for the production of primers for the polymerase chain reaction (PCR), for oligonucleotide-based drugs, and for numerous other medical and biotechnological applications. The highly optimised automised chemical oligonucleotide synthesis relies upon phosphoramidites as the phosphate precursors and one of the drawbacks of this technology is the poor bench stability of phosphoramidites. Here, we report on the development of an on-demand flow synthesis of phosphoramidites from their corresponding alcohols, which is accomplished with short reaction times, near-quantitative yields and without the need of purification before being submitted directly to automated oligonucleotide synthesis. Sterically hindered as well as redox unstable phosphoramidites are synthesised using this methodology and the subsequent couplings are near-quantitative for all substrates. The vision for this technology is direct integration into DNA synthesisers thereby omitting manual synthesis and storage of phosphoramidites.
3. Carbohydrate-oligonucleotide conjugates
Gwladys Pourceau, Albert Meyer, Jean-Jacques Vasseur, François Morvan. Curr Protoc Nucleic Acid Chem. 2009 Dec;Chapter 4:Unit4.38. doi: 10.1002/0471142700.nc0438s39.
This unit describes a strategy for attaching two mannose and two galactose residues to an oligonucleotide. This conjugation can be performed at the 5'-end of the oligonucleotide sequence, using modified phosphoramidites. First, the oligonucleotide scaffold is synthesized on solid support using a DNA synthesizer, with commercially available and modified phosphoramidites. After the first "click" reaction with a galactosylated azide derivative on solid support, the bromine atoms are replaced with azides and a second click reaction is performed with propargylated mannose either on solid support or in solution. Additionally, using a monoalkynated solid support, the conjugation with carbohydrate residues can be performed at the 3'-end of the oligonucleotide according to a similar protocol.
