Synthesis and properties of DNA oligomers containing 2'-deoxynucleoside N-oxide derivatives

Cytosine and adenine N-oxide derivatives have long been known as products resulting from the oxidative damage of DNA by peroxides such as hydrogen peroxide. Although the synthesis and properties of 2'-deoxynucleoside N-oxide derivatives have been well described, little has been reported about the chemical and biochemical behavior of initially formed DNA oligomers containing these N-oxide bases. In this study, we established a convenient method for the solid-phase synthesis of oligodeoxynucleotides incorporating 2'-deoxycytidine N-oxide (dC O) or 2'-deoxyadenosine N-oxide (dA O) by using the postsynthetic oxidation of N-protected DNA oligomers except for the target dC or dA site with m-CPBA in MeOH in a highly selective manner. In this strategy, the benzoyl, phthaloyl, and (4-isopropylphenoxy)acetyl groups proved to serve as base protecting groups to avoid oxidation of adenine, cytosine, and guanine, respectively, at the unmodified sites.     

Monofunctionally trans-diammine platinum(II)-modified peptide nucleic acid oligomers: a new generation of potential antisense drugs

A solid-phase approach is described that provides facile access to monofunctionally trans-PtII-modified PNA oligomers of arbitrary sequence for potential use both in antigene and antisense strategies. The approach includes the synthesis of a platinated building block 1 and its subsequent incorporation into three different PNA oligomers 5-7 by solid-phase synthesis. In a model cross-linking reaction one of the latter is found to recognize sequence-specifically a target oligonucleotide 8 and to cross-link to it. The resulting structure is the trans-PtII-cross-linked PNA/DNA duplex 9 as revealed by mass spectrometry in combination with a Maxam-Gilbert sequencing experiment.     

Facile synthesis of @-tide beta-strand peptidomimetics: improved assembly in solution and on solid phase

The synthesis of @-tide beta-strand peptidomimetics has been improved such that oligomers now can be obtained from solution- and solid-phase synthesis protocols approaching the efficiency and flexibility of peptide chemistry. These methods enable the synthesis of @-tide oligomers with a variety of amino acids and with lengths up to 13 units. [reaction: see text]     

Solid-phase synthesis of peptide ribonucleic acids (PRNA)

The range of available peptide ribonucleic acid (PRNA) monomers was fully expanded for the use in solid-phase synthesis of PRNA oligomers, which were designed to reversibly control the recognition and complexation behavior of the complementary DNA/RNA by external factors. A couple of PRNA 12-mers with desired purine-pyrimidine mixed sequences were prepared indeed in high yields by the solid-phase synthesis.     

Synthesis of mixed sequence borane phosphonate DNA

A novel solid-phase phosphoramidite-based method has been developed for the synthesis of borane phosphonate DNA. Keys to this new approach are replacement of the common 5'-dimethoxytrityl blocking group with a 5'-silyl ether and the use of new protecting groups on the bases (adenine, N6-dimethoxytrityl; cytosine, N4-trimethoxytrityl; guanine, N2-[9-fluorenylmethoxycarbonyl]; thymine, N3-anisoyl). Because of these developments, it is now possible for the first time to synthesize oligodeoxynucleotides having any combination of the four 2'-deoxynucleosides and both phosphate and borane phosphonate internucleotide linkages (including oligomers having exclusively borane phosphonate linkages).     

From solid-phase synthesis of pi-conjugated oligomers to combinatorial library construction and screening

A feature article describing concepts for the solid-phase synthesis of pi-conjugated oligomers as material-related structures and the translation of the synthetic routes into combinatorial protocols.     

Organic Chemistry on Solid Supports

Until recently, repetitive solid-phase synthesis procedures were used predominantly for the preparation of oligomers such as peptides, oligosaccharides, peptoids, oligocarbamates, peptide vinylogues, oligomers of pyrrolin-4-one, peptide phosphates, and peptide nucleic acids. However, the oligomers thus produced have a limited range of possible backbone structures due to the restricted number of building blocks and synthetic techniques available. Biologically active compounds of this type are generally not suitable as therapeutic agents but can serve as lead structures for optimization. “Combinatorial organic synthesis” has been developed with the aim of obtaining low molecular weight compounds by pathways other than those of oligomer synthesis. This concept was first described in 1971 by Ugi.^[56f,g,59c] Combinatorial synthesis offers new strategies for preparing diverse molecules, which can then be screened to provide lead structures. Combinatorial chemistry is compatible with both solution-phase and solid-phase synthesis. Moreover, this approach is conducive to automation, as proven by recent successes in the synthesis of peptide libraries. These developments have led to a renaissance in solid-phase organic synthesis (SPOS), which has been in use since the 1970s. Fully automated combinatorial chemistry relies not only on the testing and optimization of known chemical reactions on solid supports, but also on the development of highly efficient techniques for simultaneous multiple syntheses. Almost all of the standard reactions in organic chemistry can be carried out using suitable supports, anchors, and protecting groups with all the advantages of solid-phase synthesis, which until now have been exploited only sporadically by synthetic organic chemists. Among the reported organic reactions developed on solid supports are Diels–Alder reactions, 1,3-dipolar cycloadditions, Wittig and Wittig–Horner reactions, Michael additions, oxidations, reductions, and Pd-catalyzed C? C bond formation. In this article we present a comprehensive review of the previously published solid-phase syntheses of nonpeptidic organic compounds.     

Expedient synthesis and design strategies for new peptoid construction

[reaction: see text] A range of peptoids can be prepared efficiently using microwave-assisted solid-phase chemistry in a commercial reactor. This method is most effective for the installation of electronically deactivated benzylic amines. The systematic incorporation of these amines into peptoids can deliver oligomers capable of displaying unique and stable structural motifs-microwave-assisted solid-phase synthesis will enable their future study and application.     

Synthesis of oligomers derived from amide-linked neuraminic acid analogues

N-Fluoren-9-ylmethoxycarbonyl-protected sugar amino acids derived from alpha-O-methoxy- and 2,3-dehydroneuraminic acids have been prepared. Incorporation of these monomer units into solid-phase synthesis led to the efficient synthesis of two series of oligomers varying from one to eight units in length. The (1-->5)-linked amides of 2,3-dehydroneuraminic acid were further subjected to hydrogenation giving a third series of oligomers with a beta-hydrido substituent at the anomeric carbon.     

A Rapid Solid-phase Synthesis to Soluble Oligothiophene Molecular Wires

A novel method for the preparation of oligothiophene molecular wires is described via a bi-directional solid-phase synthesis. Using an alternating sequence of bromination and Stille coupling reactions, oligomers were obtained up to the heptamer in excellent yield and purity.     

Synthesis of alpha-(2-->5)Neu5Gc oligomers

A facile synthesis of the sialic acid oligomers alpha-(2-->5)Neu5Gc (1) is presented. Monosaccharides 2-4 with suitable functionality were used as the building blocks. After selective removal of the paired carboxyl and amine protecting groups, the fully protected oligomers were assembled through consecutive coupling of the building blocks by well established peptide coupling techniques. By this approach, fully protected oligomers as large as an octasaccharide were synthesized. Deprotection of these fully protected oligomers was conducted in two steps (LiCl in refluxing pyridine and 0.1 n NaOH) to afford the desired products in high yield. Enzymatic degradation of the octamer with neuraminidase, monitored by capillary electrophoresis (CE), was also accomplished. The stepwise exo-cleavage adducts were all well separated and identified in the CE spectrum. The strategy described here for solution-phase synthesis also provides the basis for future solid-phase synthesis of poly-alpha-(2-->5)Neu5Gc.     

Solid-phase synthesis of enantio-controlled lactic acid oligomers

A synthetic method for lactic acid oligomers via solid-phase synthesis under mild reaction conditions with up to 99% yield is presented. The fine control of the chirality on each lactic acid unit of the oligomers was easily achieved by the substitution of (R)-THP-protected lactic acid (R)-2 by (S)-2 without alternating the procedure. The overall synthesis of the trimer and tetramer was completed in one and two days, respectively. Intramolecular cyclizations of enantio-controlled lactic acids were also attempted through the Yamaguchi macrolactonization or the Mitsunobu reaction. However, we were unable to isolate single cyclic oligomers but always obtained a mixture of cyclic oligomers.     

Artificial DNAs based on alkynyl C-nucleosides as a superior scaffold for homo- and heteroexcimer emissions

DNA-like fluorescent oligomers composed of alkynyl beta-D-ribofuranosides bearing pyrene, perylene, and anthracene as a fluorophore were synthesized by solid-phase DNA synthesis. The fluorescent oligomers possess the defined number and order of the fluorophores. In these oligomers, the adjacent fluorophores efficiently interact with each other by hydrophobic interactions in their electronic ground states in a face-to-face fashion. The predominant excimer emissions were observed from not only the homooligomers (pyrene-pyrene and perylene-perylene systems) but also the heterooligomers (pyrene-perylene, pyrene-anthracene, and perylene-anthracene systems) in aqueous media.     

Microwave-enhanced solid-phase synthesis of N,N'-linked aliphatic oligoureas and related hybrids

A practical and efficient microwave-assisted solid-phase method for the synthesis of N,N'-linked oligoureas and related amide/urea hybrid oligomers, featuring the use of succinimidyl (2-azido-2-substituted ethyl) carbamate monomers, is reported. The rate enhancement of urea formation under microwave irradiation combined with the mild conditions of the phosphine-based azide reduction makes this approach very effective for routine synthesis of oligoureas and possibly for library production.     

Synthesis of crescent aromatic oligoamides

[structures: see text] This article describes the synthetic procedures for the preparation of crescent (and helical) aromatic oligoamides developed in recent years in our laboratory. The large-scale preparation of a variety of monomers derived from various tetrasubstituted benzenes is presented. Three different strategies for constructing various oligomers consisting of meta- and meta/para-linked benzene residues are discussed. Factors affecting coupling efficiency and yields are analyzed. The developed synthetic methods have provided the basis for the preparation of longer oligomers and for the development of solid-phase synthesis.     

Solid-phase Synthesis of PNA Monomer by Ugi Four-component Condensation Reaction

Peptide nucleic acids (PNA) oligomers were synthesized in most cases by peptide a peptide synthesis from N-protected monomers. In this work a new method of obtaining PNA monomer by Ugi four-component condensation reaction was tested by solid-phase synthesis. The Fmoc protected PNA monomer was build up with thymin-l-yl acetic acid, 3-methylbutyl aldehyde, Fmoc protected aminoethyl isocyanide and Gly-Wang resin.     

Nylon/DNA: Single-stranded DNA with a covalently stitched nylon lining

The synthesis of DNA/nylon ladder oligomers is described. Three stages of the development are addressed: the synthesis of 2'-beta-substituted phosphoramidites, the deprotection/purification protocols of ODNs modified with both amino and carboxyl groups, and amide bond-forming reactions on the ODNs. The established technology and the novel DNA-based ladder oligomer structure opens a pathway to the synthesis of topological molecular objects and networks templated by DNA through versatile DNA nanotechnology. The DNA-based ladder oligomers may find application in the antisense area.     

Solid-phase Pd-catalysed cross-coupling methods for the construction of π-conjugated peptide nanomaterials

We describe the development of two procedures for the synthesis of peptides that are embedded with a variety of π-conjugated semi-conducting oligomers. These procedures utilise solid-phase variants of classical palladium-catalysed cross-couplings commonly used to prepare π-conjugated oligomers. The resulting peptide–π–electron hybrids are soluble in aqueous media and self-assemble to produce 1D nanostructures, simultaneously forming networks of π-stacked conduits. The procedures have allowed for the inclusion of complex chromophores including mixed aryl units, ethynylene linkers and sexithiophenes where the latter peptide's nanostructures demonstrated substantial conductivity when employed as an active layer in a field-effect transistor.     

A convenient synthesis of the cytidyl 3′-terminal monomer for solid-phase synthesis of RNG oligonucleotides

Replacing the phosphodiester backbone of RNA with positively charged guanidinium linkages has been shown to enable RNA oligomers to overcome electrostatic repulsion and bind double-stranded DNA in a triplex with high affinity. Ribonucleotide monomers with the ability to form guanidinium linkages have been synthesized for the generation of ribooligonucleotides with guanidinium linkages (RNGs) through solid-phase synthesis. We report herein an efficient method for the synthesis of N⁴-benzoyl-2′-O-(tert-butyldimethylsilyl)-5′-N-(4-monomethoxytritylamino)-3′-O-succinyl-5′-deoxycytidine, a new monomer required for the solid-phase synthesis of cytidyl RNG oligonucleotides.     

An efficient, scalable synthesis of the molecular transporter octaarginine via a segment doubling strategy

[reaction: see text]. Short oligomers of arginine function as remarkably efficient molecular transporters of drugs and probe molecules into cells and tissue. Currently, these compounds are prepared on resin through a unidirectional solid-phase synthesis. To extend the utility of these compounds for therapeutic and research applications, a scalable solution-phase synthesis of Arg8 (1) has been developed on the basis of a segment doubling strategy that proceeds in 13 steps and 28% overall yield from 4, including a novel one-step perdeprotection-perguanidinylation reaction.