Enzyme-free interrogation of RNA sites via primers and oligonucleotides 3'-linked to gold surfaces.

The synthesis of a phosphoramidite is described that was used for the preparation of oligonucleotides with a 3'-terminal thiol, linked to the DNA via a SAM-forming undecyl chain and a nonadsorptive tetraethylene glycol unit. A gold surface featuring oligonucleotide probes allowed for label-free in situ mass spectrometric determination of a nucleotide in subpicomole quantities of an RNA transcript.