Oligonucleotides, post-modification

The formation of an aldehyde group on a macromolecule can produce an extremely useful derivative for subsequent modification or conjugation reactions. In their native state, proteins, peptides, nucleic acids, and oligonucleotides contain no naturally occurring aldehyde residues. There are no aldehydes on amino acid side chains, none introduced by post-translational modifications, and no formyl groups on any of the bases or sugars of DNA and RNA. To create reactive aldehydes at specific locations within these molecules opens the possibility of directing modification reactions toward discrete sites within the macromolecule. 

Capillary electrophoresis (CE) coupled to MS has the advantage of high resolution and soft ionization for biomolecules, which may be used to differentiate post-translational modifications and variants of intact proteins and oligonucleotides. Different modes of CE (capillary zone electrophoresis, capillary isoelectric focusing, capillary electrochromatography, micellar electrokinetic chromatography, nonaqueous capillary electrophoresis) to MS as well as online preconcentration techniques (transient capillary isotachophoresis, solid-phase extraction, membrane preconcentration) are used to compensate for the restricted detection sensitivity of the CE methodology [77, 78]. 

The functionalisation at the N1-position of 2 -deoxy-pseudouridine by Michael addition of methyl acrylate offered access to the phosphoramidites (61). The precursor to (61) was also functionalised as an amine derivative, which was transformed into the fluorescein-labelled phosphoramidites (62a-b). Fluorescent oligonucleotides were synthesised either from these latter building blocks or by post-synthetic modifications of oligomers containing the 2 -deoxy-pseudouridine-1 -propanoate units. ... 

Post-synthesis modification may be used to introduce a number of O - alkylated guanosine derivatives into oligonucleotides. Using a 0 -methoxycar-bonylmethyl-dG phosphoramidite and different oligonucleotide deprotection conditions leads to a number of different alkylated guanosine derivatives. 

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