Chemically modified oligonucleotides with efficient RNase H response.

Ten different chemically modified nucleosides were incorporated into short DNA strands (chimeric oligonucleotides ON3-ON12 and ON15-ON24) and then tested for their capacity to mediate RNAse H cleavage of the complementary RNA strand. The modifications were placed at two central positions directly in the RNase H cleaving region. The RNA strand of duplexes with ON3, ON5 and ON12 were cleaved more efficiently than the RNA strand of the DNA:RNA control duplex.

Identification of natural oak lactone precursors in extracts of american and French oak woods by liquid chromatography-tandem mass spectrometry.

A method for the screening of potential natural oak lactone precursors in oak wood extracts using LC-MS/MS combined with information-dependent acquisition was developed. The method was applied to extracts of American and French oak woods. As a result, cis-3-methyl-4-galloyloxyoctanoic acid (ring-opened cis-oak lactone gallate), (3S,4S)- and (3S,4R)-3-methyl-4-O-beta-D-glucopyranosyloctanoic acid (ring-opened cis- and trans-oak lactone glucoside), and (3S,4S)-3-methyl-4-O-(6'-O-galloyl)-beta-D-glucopyranosyloctanoic acid (ring-opened cis-oak lactone galloylglucoside) were identified as natural oak lactone precursors in the extracts by comparison with the respective synthetic reference compounds.

Synthesis and thermal denaturation studies of novel 2'-O,3'-C-linked bicyclic oligonucleotides with a methoxy or a piperazino group facing the major groove of nucleic acid duplexes.

With the aim of evaluating duplex stabilities of oligonucleotides (ONs) with major groove facing functionalities, two novel 2'-O,3'-C-linked bicyclic nucleoside phosphoramidite building blocks were synthesized by routes involving regioselective O-methylation or piperazine attachment using carbonyldiimidazole coupling chemistry. The novel monomers were incorporated into 9-mer mixed base ONs and the thermal stability toward complementary single stranded DNA and RNA was evaluated by thermal denaturation experiments. O-methylated ONs confirmed the applicability of the functionalized bicylic sugar unit for attachment of groups facing the major groove and satisfactory binding properties towards the RNA complement were observed.

Alkylated sugar amino acids: a new entry toward highly functionalized dipeptide isosters.

[reaction: see text] Novel highly functionalized dipeptide isosters are synthesized via a diastereoselective alkyl/arylation protocol of a glucose-derived (R)-tert-butanesulfinylimine. One of these novel sugar amino acid derivatives, a D-Ala-Ser/Thr isostere, was applied in a peptide synthesis protocol to afford a cyclic tetramer.

N-methylpiperazinocarbonyl-2',3'-BcNA and 4'-C-(N-methylpiperazino)methyl-DNA: introduction of basic functionalities facing the major groove and the minor groove of a DNA:DNA duplex.

Piperazino-functionalized 2',3'-BcNA and 4'-C-hydroxymethyl-DNA are appropriate molecular architectures for the introduction of basic functionalities facing the major groove and the minor groove of nucleic acid duplexes, respectively. 4'-C-(N-Methylpiperazino)methyl-DNA monomers induce significantly increased thermal stability of a DNA:DNA duplex.