Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Stainless steel capillary columns for high temperature gas chromatography

A layer of elemental silicon has been deposited on the surface of stainless steel tubing by means of chemical vapor deposition (CVD). Two kinds of capillary column were prepared from the deactivated tubing: cross-linked, silanol-terminated polydime-thylsiloxane wall coated open tubular (WCOT) columns and molecular sieve 13X porous layer open tubular (PLOT) columns. Unlike fused silica capillary columns, stainless steel WCOT and PLOT columns can be operated at temperatures in excess of 400°C. High temperature simulated distillation has been performed successfully with a macro bore WCOT column and rapid PNA (paraffin, naphthene, and aromatic) analysis with a multidimensional gas solid chromatographic (GSC) system using PLOT columns.     

Synthesis and polymerisation of lipophilic peptide nucleic acids derived from stearic acid and pentacosa-10,12-diynoic acid

The adenine, cytosine and thymine peptide nucleic acid (PNA) monomers and PNA T₁₀ oligomers bearing either a diacetylenic or stearoyl moiety at the N- or C-terminus have been successfully prepared. The resulting thymine monomeric and T₁₀-mer derivatives have been subsequently incorporated into polydiacetylene-containing liposomes.     

Analysis of polynuclear aromatic hydrocarbons by glass capillary gas chromatography using simultaneous flame ionization and electron capture detection

The possibility of simultaneous application of an electron capture (ECD) and a flame ionization detector (FID) connected to a glass capillary column for analyzing polynuclear aromatic hydrocarbons (PNA) has been investigated. The ECD/FID ratio is determined for 46 PNA compounds. The ratios vary from 0.02 to 117 with relative standard deviations better than 20 percent determined from 10 replicate analyses. The results suggest that the method may be used for obtaining additional evidence in identifying PNA in environmental samples. Impurities and transformation products in the standard were identified by computerized glass capillary gas chromatography/mass spectrometry. Quinones and diones are responsible for the high EC-response determined in some trace components in the standard. An application of the method is shown for PNA from particulates in urban atmospheres.     

The binding of single-stranded DNA and PNA to single-walled carbon nanotubes probed by flow linear dichroism

The binding of single-stranded DNAs and a neutral DNA analogue (peptide nucleic acid, PNA) to single-walled carbon nanotubes in solution phase has been probed by absorbance spectroscopy and linear dichroism. The nanotubes are solubilised by aqueous sodium dodecyl sulfate, in which the nucleic acids also dissolve. The linear dichroism (LD) of the nanotubes, when subtracted from that due to the nanotubes/nucleic acid samples, gives the LD of the bound nucleic acid. The binding of the single-stranded DNA to the single-walled nanotubes is quite different from that previously observed for double-stranded DNA. It is likely that the nucleic acid bases lie flat on the nanotube surface with the backbone wrapping round the nanotube at an oblique angle in the region of 45 degrees . The net effect is like beads on a string. The base orientation with the single-stranded PNA is inverted with respect to that of the single-stranded DNA, as shown by their oppositely signed LD signals.     

Saccharide-branched Cyclodextrins as Targeting Drug Carriers

A synthetic series of heptakis-galactose-branched cyclodextrins (termed CDs) having a longer spacer arm using two amino-caproic acids as an enlarging unit were prepared. Starting with heptakis-amino-β-CD or heptakis-amino-caproic-amide-β-CD, treated with galactosyl-glucono-amide-caproic acid, the new compounds heptakis (Gal-cap1)-CD (4) or heptakis (Gal-cap2)-CD (5) were obtained. The longer galactose spacer arm extremely favors the PNA association. The effect of branch length on K with PNA was enhanced up to 138-fold 3 as well as with DXR enhanced up to 81-fold. Hexakis (Gal-cap2)-CD (6) was prepared and the association constants with rat liver cells were observed to be 2.5 × 10¹⁰ M⁻¹. A multi-high mannose type oligosaccharide branched CD (7) showed a large association constant with DXR up to 1.1 × 10⁹ M⁻¹. The two-dimensional map for the association constants of newly synthesized oligosaccharide-branched CDs toward lectin or liver cells versus the association constants toward a drug (doxorubicin) suggested a method of finding a better targeting drug carrier. The structural effect of the oligosaccharide-CDs showed that the number and length of the branch were dominant factors in designing for enhanced dual recognition.     

Synthesis of Potential Antimicrobial Agents from Maltose. III. Introduction of an Amino Group Into the 3′-Position of 1,6-Anhydro-Disaccharides

Abstract

Regioselective cleavage of 1,6-anhydro-maltose (1) with periodate and the subsequent recyclization with nitromethane gave 1,6-anhydro-3′-deoxy-3′-nitro-disaccharides (3). Three diastereomers, prepared by benzylidenation of 3, were separated by column chromatography. Each of 4′,6′-O-benzylidene derivatives successively underwent debenzylidenation, reduction of the nitro group, and peracetylation to give 3′-acetamido-3′-deoxy-disaccharide derivatives (7, 8, and 9). The configurations of the 3-amino sugar moietres in 7 (D-gluco), 8 (D-manno) and 9 (D-galacto) were determined on the basis of the ¹H NMR data. The main product (7) was further modified to the 6-deoxy-6-nitro derivative.     

Dynamic Cooperative Glycan Assembly Blocks the Binding of Bacterial Lectins to Epithelial Cells

Pathogens frequently rely on lectins for adhesion and cellular entry into the host. Since these interactions typically result from multimeric binding of lectins to cell‐surface glycans, novel therapeutic strategies are being developed with the use of glycomimetics as competitors of such interactions. Herein we study the benefit of nucleic acid based oligomeric assemblies with PNA–fucose conjugates. We demonstrate that the interactions of a lectin with epithelial cells can be inhibited with conjugates that do not form stable assemblies in solution but benefit from cooperativity between ligand–protein interactions and PNA hybridization to achieve high affinity. A dynamic dimeric assembly fully blocked the binding of the fucose‐binding lectin BambL of Burkholderia ambifaria , a pathogenic bacterium, to epithelial cells with an efficiency of more than 700‐fold compared to l ‐fucose.     

Base dependent pyrrolidine ring pucker in aep-PNA monomers: NMR and PSEUROT analysis

The aep-PNA is a chiral and cyclic PNA analogue, which has a stronger and base dependent binding affinity with complementary DNA. To understand the base dependent properties at monomer level, the structural studies of aep-PNA-(T/C/A) monomers have been carried out focussing on the conformational analysis of pyrrolidine ring pucker in aep-PNA by ¹H NMR and the coupling constant data fitted into PSEUROT software. The results indicate that the type of pyrrolidine pucker depends on the electronic nature of substituent, implying the effect of pyrimidine or purine substituents in determining the ring pucker in monomers. This may consequently influence the aep-PNA oligomer conformation. Since pyrrolidine nucleic acids have emerged as an important class of PNA analogues, present results may have importance for their future development.     

Use of Micelles in the TLC Separation of Polynuclear Aromatic Compounds and Amino Acids

Abstract

The polynuclear aromatic compounds (PNA): anthracene, napthalene, phenanthrene, pyrene, pyrenecarboxaldehyde, benzo (a) pyrene, benzo (e) pyrene, perylene and fluorene can be chromatographed on polyamide TLC sheets using an aqueous micellar solution cf sodium dodecylsulfate (SDS) as the mobile phase. Reversed micellar solutions (of sodium dioctylsulfosuccinate) were used in a reverse phase chromatographic separation of amino acids. Some amino acids tended to streak slightly rather than move as discrete spots. Conditions could be adjusted, however, so that most of the amino acids and all PNA's would move as spots.