Reactions of acyl phosphonates with organoaluminum reagents: a new method for the synthesis of secondary and tertiary α-hydroxy phosphonates

The reactions of organoaluminum reagents (trimethylaluminum, triethylaluminum, etc.) with aryl and alkyl acyl phosphonates, which lead to the formation of α-hydroxy phosphonates in moderate to good yields, are reported. This method provides easy access to secondary and tertiary α-hydroxy phosphonates depending on the reaction conditions. The reactions of triethylaluminum with a series of acyl phosphonates at 0 °C gave the secondary α-hydroxy phosphonates, while at −100 °C they afford the tertiary α-hydroxy phosphonates.     

Automated analytical microarrays: a critical review

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications. Figure MCR 3: A fully automated chemiluminescence microarray reader for analytical microarrays     

Bifunctional DNA Architectonics: Three‐Way Junctions with Sticky Perylene Bisimide Caps and a Central Metal Lock

A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris‐bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe³⁺, Ni²⁺ and Zn²⁺ by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5′‐terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady‐state fluorescence. The PDI‐mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal‐ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher‐ordered structures as the result of DNA assemblies mediated by the PDI interactions.     

Toward the Rational Design of Galactosylated Glycoclusters That Target Pseudomonas aeruginosa Lectin A (LecA): Influence of Linker Arms That Lead to Low‐Nanomolar Multivalent Ligands

Anti‐infectious strategies against pathogen infections can be achieved through antiadhesive strategies by using multivalent ligands of bacterial virulence factors. LecA and LecB are lectins of Pseudomonas aeruginosa implicated in biofilm formation. A series of 27 LecA‐targeting glycoclusters have been synthesized. Nine aromatic galactose aglycons were investigated with three different linker arms that connect the central mannopyranoside core. A low‐nanomolar (K_d=19 nm , microarray) ligand with a tyrosine‐based linker arm could be identified in a structure–activity relationship study. Molecular modeling of the glycoclusters bound to the lectin tetramer was also used to rationalize the binding properties observed.     

A modular approach to DNA-programmed self-assembly of macromolecular nanostructures

DNA-programmed organic reactions are new and powerful tools for assembling chemical compounds into predetermined complex structures and a brief review of their use is given. This approach is particular efficient for the selection and covalent coupling of multiple components. DNA-templated synthesis is used for polymerization of PNA tetramers and for copying of the connectivity information in DNA. Direct DNA-programmed multicomponent coupling of custom designed organic modules is described. The macromolecular structures obtained are highly conjugated potentially conducting nanoscaffolds. Some future developments in this area are discussed.     

PNA encoding (PNA=peptide nucleic acid): from solution-based libraries to organized microarrays

Microarray-based technologies have attracted attention in chemical biology by virtue of their miniaturized format, which is well suited to probe ligand-protein interactions or investigate enzymatic activity in complex biological mixtures. A number of research groups have reported the preparation of surfaces on microarrays with specific functional groups to chemoselectively attach small molecules from libraries. We have developed an alternative method whereby libraries are encoded with peptide nucleic acid (PNA), such that libraries which exist as mixtures in solution self-assemble into an organized microarray through hybridization to produce readily available DNA arrays. This allows libraries synthesized by split and mix methods to be decoded in a single step. An asset of this method compared to direct spotting is that libraries can be used in solution for bioassays prior to self-assembly into the microarray format.     

A novel approach to oligonucleotide synthesis using an imidazolium ion tag as a soluble support

The synthesis of oligonucleotides in solution using a soluble, ionic liquid based support is described. Short oligomers of varying base composition were synthesized using this method in high yields and high purity, requiring no chromatography for purification prior to cleavage from the support. The solution-phase-synthesized oligomers were compared to the same sequences prepared using standard gene machine techniques by LCMS. This methodology may provide a cheaper route for the large-scale synthesis of oligonucleotides.     

Iodocyclization of trifluoromethylallenic phosphonates: an efficient approach to trifluoromethylated oxaphospholenes

α-Trifluoromethylallenic phosphonates were prepared by the reaction of diethyl chlorophosphite (DECP) and 4,4,4-trifluorobut-2-yn-1-ols in the presence of Et₃N. The iodocyclization of these fluorine-containing allenic phosphonates was achieved with iodine under mild conditions to give the corresponding trifluoromethylated oxaphospholenes in moderate to good yields.     

Metal alkoxides as versatile precursors for group 4 phosphonates: synthesis and X-ray structure of a novel organosoluble zirconium phosphonate

Reactions of Ph2P(O)(OH) and t-BuP(O)(OSiMe3)(OH) with Ti(O-i-Pr)4 in equimolar ratios gave titanium phosphonates of the type [(O-i-Pr)3Ti(mu-O)2PR1R2]2 (1, R1 = R2 = Ph; 2, R1 = t-Bu, R2 = OSiMe3) as colorless crystalline solids in moderate yields. Reactions of Ph2P(O)(OH) and the isopropoxides of zirconium and hafnium resulted in products of the composition [(O-i-Pr)3M(mu-O-i-Pr)2(mu-OPOPh2)M(O-i-Pr)2]Ph2P(O)(OH) (M = Zr (3), Hf (4)) in high yields. The compounds were characterized by 1H, 31P, and 29Si NMR, infrared (IR), and mass spectroscopic (MS) techniques. The molecular structures of 2 and 3 were confirmed by X-ray crystallography.     

The influence of cytosine methylation on the chemoselectivity of benzo[a]pyrene diol epoxide‐oligonucleotide adducts determined using nanoLC/MS/MS

Benzo[a]pyrene is a major carcinogen implicated in human lung cancer. Almost 60% of human lung cancers have a mutation in the p53 tumor suppressor gene at several specific codons. An on‐line nanoLC/MS/MS method using a monolithic nanocolumn was applied to investigate the chemoselectivity of the carcinogenic diol epoxide metabolite, ( ± )‐(7R,8S,9S,10R)‐benzo[a]pyrene 7,8‐diol 9,10‐epoxide [( ± )‐anti‐benzo[a]pyrene diol epoxide (BPDE)], which was reacted in vitro with a synthesized 14‐mer double stranded oligonucleotide (5′‐ACCCG₅CG₇TCCG₁₁CG₁₃C‐3′/5′‐GCGCGGGCGCGGGT‐3′) derived from the p53 gene. This sequence contained codons 157 and 158, which are considered mutational ‘hot spots’ and have also been reported as chemical ‘hot spots’ for the formation of BPDE‐DNA adducts. In evaluating the effect of cytosine methylation on BPDE‐DNA adduct binding, it was found that codon 156, containing the nucleobase G₅ instead of the mutational hot spot codons 157 (G₇) and 158 (G₁₁), was the preferential chemoselective binding site for BPDE. In all permethylated cases studied, the relative ratio for adduction was found to be G₅? G₁₁ > G₁₃ > G₇. Permethylation of CpG dinucleotide sites on either the nontranscribed or complementary strand did not change the order of sequence preference but did enhance the relative adduction level of the G₁₁ CpG site (codon 158) approximately two‐fold versus the unmethylated oligomer. Permethylation of all CpG dinucleotide sites on the duplex changed the order of relative adduction to G₅? G₇ > G₁₁ > G₁₃. The three‐ to four‐fold increase in adduction at the mutational hot spot codon 157 (G₇) relative to the unmethylated or single‐stranded permethylated cases suggests a possible relationship between the state of methylation and adduct formation for a particular mutation site in the p53 gene. Using this method, only 125 ng (30 pmol) of adducted oligonucleotide was analyzed with minimal sample cleanup and high chromatographic resolution of positional isomers in a single chromatographic run. Copyright © 2009 John Wiley & Sons, Ltd.     

A novel strategy for in situ maskless synthesis of biochips： Self-driving micro-fluid porous type printing （SMPTP）

A novel maskless technique,self-driving micro-fluid porous type printing(SMPTP),was reported to in situ synthesize oligonucleotide arrays on glass slide,which has the merits of low cost,high quality and simple craft.In SMPTP for fabricating gene- chips,porous fiber tubes with a number of nanometric or micron channels functioned as“active letters”and were assembled in designed patterns,which are identical to the distribution of monomers in each layer of the array,and four patterns were needed for each layer.By means of capillarity,the synthesis solution was automatically taken into porous tubes assembled in a printing plate and reached the surface.An oligonucleotide array of 160 features with four different 15-mer probes was in situ synthesized using this technique.The four specific oligonucleotide probes,including the matched and the mismatched by the fluorescent target sequence,gave obviously different hybridization fluorescent signals.     

How to Make a DNA Chip

Microarrays are one of the hottest areas in biological research today. Microarrays have been mostly applied to nucleic acid analysis, specifically to the assessment of which genes are being expressed and at what level. Early microarrays were prepared by using photolithographic methods, which were more commonly used for integrated circuit (“computer chip”) production. Hence the colloquial term “DNA chip” came into being. The completion of the sequencing of the human genome and that of many other organisms makes the determination of gene function an important next step in understanding the role of DNA in the processes of life. DNA microarrays are an excellent tool to address this question because their numerous probe sites enable the analysis of many genes simultaneously. With good experience in this initial use, many further applications of microarrays are being developed, including genotyping in research and genetic diagnosis in medicine. DNA microarrays have made abundantly clear the power of vast parallelism in biological analysis, which is raising interest in other types of microarrays (small‐molecule, protein). Many applications for DNA microarrays have been developed and clearly many more will emerge through the creativity of the scientists who use them. In early studies, users produced their own microarrays. The apparent power of microarrays has demanded improvements in production methods, and technologies from physical sciences and engineering are now being applied to DNA chips. Many branches of chemistry can contribute to improved methods: from synthetic chemistry (to attach or prepare DNA), to the physical chemistry of surfaces, to analytical chemistry (to assess surface reactions).