Synthesis of oligonucleotide derivatives using ChemMatrix supports

Oligonucleotide-peptide conjugates: solid-phase synthesis under acidic conditions and use in ELISA assays

Here we used solid-phase methods to prepare oligonucleotides carrying fibrin/ filaggrin citrullinated peptides. Post-synthetic conjugation protocols were successfully applied for the synthesis of oligonucleotides carrying small peptides. A stepwise protocol using acid treatment for the final deprotection allowed the preparation of polypyrimidine oligonucleotides carrying longer and arginine-rich peptides. An ELISA-based test using the oligonucleotide-citrullinated peptide conjugates was developed for the detection of anti-citrullinated protein/peptide antibodies in human serum from rheumatoid arthritis patients.

ChemMatrix(®) for complex peptides and combinatorial chemistry

CM resin is a totally PEG-based resin, made exclusively from primary ether bonds and therefore highly chemically stable. Compared to other PEG resins, it exhibits good loading and is user friendly because of its free-flowing form upon drying. It shows improved performance over PS resins for the preparation of hydrophobic, highly structured poly-Arg peptides. In combination with ψPros, it allows the synthesis of small proteins such as the chemokine RANTES. Like other PEG-based resins, CM resin swells well in biocompatible solvents such as water, thereby allowing on-bead screening. Furthermore, the high loading of this resin permits the use of a tiny quarter of a bead as a microreactor for HPLC and MALDI-TOF analysis, thus further extending its applications in the field of combinatorial chemistry.

Synthesis of oligonucleotides carrying amino lipid groups at the 3'-end for RNA interference studies

Novel lipid derivatives carrying amino and triazolyl groups were efficiently synthesized and covalently anchored at the 3'-termini of oligonucleotides. The desired amino-lipid conjugates were fully characterized by reversed-phase HPLC and MALDI-TOF mass spectrometry. The methodology was applied to the synthesis of lipid-siRNA designed to inhibit tumor necrosis factor (TNF-α) in order to obtain siRNAs with anti-inflammatory properties. The siRNA duplex carrying amino-lipids at the 3'-end of the passenger strand has inhibitory properties similar to those of unmodified RNA duplexes in HeLa cells, indicating that the new lipid derivatives are compatible with the RNA interference machinery.

Click chemistry with DNA

The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne-azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbones. In this critical review we describe some of the pioneering work that has been carried out in this area (78 references).