Oligonucleotide Synthesis and Modification

Standard phosphoramidites for oligonucleotide synthesis (DNA, RNA, 2'-O-methyl RNA), 6-FAM phosphoramidite and C6-aminolinker were purchased from Glen Research. Phosphoramidites of LNA, LNA 2,6-diaminopurine riboside and 2'-O-methyl-2,6-diaminopurine riboside were synthesized according to published procedures [43 (link)]. Dimethyl sulfate (DMS) was from Aldrich and N-methylisatoic anhydride (NMIA) was from Molecular Probes. Reverse transcriptase SuperScript III was from Invitrogen. AmpliScribe T7 Transcription Kit and RNase H were from Epicenter. Pfu polymerase and dNTP were from Fermentas. Roche was provider of ddNTP. Restriction enzymes: EcoRI and PstI were from Promega. DH5α competent cells, agarose and HybriSlip hybridization cover were bought from Invitrogen. T4 polynucleotide kinase was product of EURx. Silanized slides were purchased from Sigma.