We report the sequencing of highly modified oligonucleotides containing a mixture of 2'-deoxy, 2'-fluoro, 2'-O-methyl, abasic, and ribonucleotides. The passenger and guide strands each containing 48% and 86% of modified nucleotides, respectively, are representative sequences of synthetic short interfering RNAs (siRNAs). We describe herein the sequence confirmation of both strands using a series of robust chemical reactions, followed by analysis via ESI-TOF and ion trap mass spectrometry (ITMS). The following method enables the rapid sequence confirmation of highly modified oligonucleotides.

We present the combined application of chemical and enzymatic digestions toward de novo sequence determination of a modified oligonucleotide. The unknown of interest, consisting of a random mixture of 2'-deoxy, 2'-fluoro, 2'-O-methyl, abasic and/or ribonucleotides, is a representative oligonucleotide used as a component of synthetic short interfering RNAs (siRNAs). The sequence is initially determined using chemical degradation, electrospray ionization (ESI), time-of-flight (TOF), and tandem (MS/MS) mass spectrometry. A nucleoside composition analysis is then performed via enzymatic digestion of the oligonucleotide to complement the chemical sequencing method. The identity and experimental count of each nucleoside within the oligonucleotide are determined by ultra performance liquid chromatography (UPLC) analysis. This additional analysis allows unambiguous sequence assignment of an unknown chemically modified oligonucleotide.

The discovery of highly potent and selective second generation EP(4) antagonist MK-2894 (34d) is discussed. This compound exhibits favorable pharmacokinetic profile in a number of preclinical species and potent anti-inflammatory activity in several animal models of pain/inflammation. It also shows favorable GI tolerability profile in rats when compared to traditional NSAID indomethacin.

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Havellockate (1) was isolated from the soft coral Sinularia granosa located on the Havellock island in the Indian Ocean. This highly compact and polyoxygenated marine diterpene bears a cis-fused hydrindane core that contains eight stereogenic centers as well as a spiro-lactone. To the best of our knowledge, no syntheses of 1 have been reported yet. Herein, we describe the synthesis of the all-carbon framework of havellockate (1) in 18 chemical operations. Our approach highlights the efficiency and utility of the hydroxy-directed Diels-Alder (HDDA) reaction to quickly access the cis-fused hydrindane core and securing the correct stereochemistry at C6 and C7. Moreover, six of the eight stereogenic centers have been installed in the correct stereochemistry.