Selective recognition of CG interruption by 2′,4′-BNA having 1-isoquinolone as a nucleobase in a pyrimidine motif triplex formation

To develop a novel nucleoside analogue for the effective recognition of CG interruption in a homopurine-homopyrimidine tract of double-stranded DNA (dsDNA), we succeeded in the synthesis of a triplex-forming oligonucleotide (TFO) containing a novel 2′,4′-BNA (Q^B) bearing 1-isoquinolone as a nucleobase, and the triplex-forming ability and sequence-selectivity of the TFO (TFO-Q^B) were examined. On melting temperature (T_m) measurements, it was found that the TFO-Q^B formed a stable triplex DNA in a highly sequence-selective manner under near physiological conditions.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

Stable oligonucleotide-directed triplex formation at target sites with CG interruptions: strong sequence-specific recognition by 2',4'-bridged nucleic-acid-containing 2-pyridones under physiological conditions

A sequence of double-stranded DNA (dsDNA) which can be recognized by a triplex-forming oligonucleotide (TFO) is limited to a homopurine-homopyrimidine sequence. To develop novel nucleoside analogues which recognize CG interruption in homopurine-homopyrimidine dsDNA, we synthesized a novel 2'-O,4'-C-methyleneribonucleic acid (2'-O,4'-C-methylene bridged nucleic acid; 2',4'-BNA) that bears the unnatural nucleobases, 2-pyridone (PB) or its 5-methyl congener (mPB); these analogues were introduced into pyrimidine TFOs using a DNA synthesizer. A TFO with a 2'-deoxy-beta-D-ribofuranosyl-2-pyridone (P) or 2',4'-BNA abasic monomer (HB) was also synthesized. The triplex-forming ability of various synthesized 15-mer TFOs and the corresponding homopurine-homopyrimidine dsDNA, which contained a single pyrimidine-purine (PyPu) interruption, was examined in UV melting experiments. It was found that PB and mPB in the TFOs successfully recognized CG interruption under physiological conditions (7 mM sodium phosphate, 140 mM KCl, 5 mM spermine, pH 7.0). Furthermore, triplex formation between the dsDNA target which contained three CG interruptions and the TFO with three PB units was also confirmed. Additional four-point 2',4'-BNA modifications of the TFO containing three PB units significantly enhanced its triplex-forming ability towards the dsDNA and had a Tm value of 43 degrees C under physiological conditions. These results indicate that a critical inherent problem of TFOs, namely, the sequence limitation of the dsDNA target, may be overcome to a large extent and this should promote antigene applications of TFOs in vitro and in vivo.     

Design, synthesis, and evaluation of a novel bridged nucleic acid, 2′,5′-BNA, with S-type sugar conformation fixed by N-O linkage

We designed a novel 2′-O,5′-N bridged nucleic acid, 2′,5′-BNA^ON, whose sugar puckering was fixed to S-type conformation by an N-O linkage. A dimer unit formed from 2′,5′-BNA^ON-U and thymidine was synthesized via a coupling reaction between a protected 2′,5′-BNA^ON-U monomer and a thymidine derivative. Introduction of 2′,5′-BNA^ON-U into DNA was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. The hybridization abilities of 2′,5′-BNA^ON-U-modified oligonucleotides against DNA or RNA complement were evaluated.     

Thermodynamics of the effects of substituent,degree of substitution,and pH on complex formation of hydroxypropyl-α- and hydroxypropyl-β-cyclodextrins with ascorbic acid

The interaction of ascorbic acid with hydroxypropyl-α- and hydroxypropyl-β-cyclodextrins of different degree of substitution was studied at 298.15 K and different pH using solution calorimetry. In an aqueous solution, only hydroxypropyl-β-cyclodextrins form weak molecular complexes with the nonionized form of ascorbic acid. The thermodynamic functions of complex formation and stability constants of the complexes were calculated. The systems with weak intermolecular interaction without complex formation were characterized by enthalpic virial coefficients. On the basis of the obtained thermodynamic characteristics it was shown that the selectivity of complex formation of hydroxypropyl-α- and hydroxypropyl-β-cyclodextrins with ascorbic acid is determined by the size of the macrocyclic cavity, the presence of the hydroxypropyl substituent, and the medium acidity. The degree of substitution of hydroxypropyl-β-cyclodextrins exerts no substantial effect on the thermodynamic parameters of interaction with ascorbic acid. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1828–1831, August, 2005.     

Influence of support on resistance to carbon-deposition of catalyst for CH4, CO2 with O2 to synthesis gas

In the reaction of catalytic oxidation of CH4,CO2 with O2 to synthesis gas, carbon-deposition is an important factor for deactivation. By adding different oxides to Ni/AI2O3 catalyst, its resistance to carbon-deposition was improved. The experimental results indicate that the order of resistance to carbon-deposition is as follows: Ni/CaO-AI2O3>Ni/MgO-AI2O3>Ni/ TiO2-AI2O3>Ni/CeO2-AI2O3>Ni/La2O3-AI2O3>Ni/Y2O3-AI2O3>Ni/Fe2O3-AI2O3>Ni/AI2O3. The catalysts were characterized by CO2-TPD, O2-TPD and XPS methods. Here the relation between the order of resistance to carbon-deposition and performance of catalyst is discussed.     

A study of the reaction of Se(IV) with 3,4-diaminobenzoic acid and 4-bromo-1, 2-phenylenediamine

The condensation reactions of Se(IV) with 3,4-diaminobenzoic acid and 4-bromo-1,2-phenylenediamine have been studied by means of UV spectra and kinetic investigations. A mechanism for the formation of 2,1,3-benzoselenadiazole in acidic medium is proposed. The influence of substitution at C(4) in 1,2-phenylenediamine on the reactivity of the system is discussed.     

Influence of support on resistance to carbon-deposition of catalyst for CH4, CO2 with O2 to synthesis gas

In the reaction of catalytic oxidation of CH₄, CO₂ with O₂ to synthesis gas, carbon-deposition is an important factor for deactivation. By adding different oxides to Ni/Al₂O₃ catalyst, its resistance to carbon-deposition was improved. The experimental results indicate that the order of resistance to carbon-deposition is as follows: Ni/CaO-Al₂O₃>Ni/MgO-Al₂O₃>Ni/ TiO₂-Al₂O₃ > Ni/CeO₂-Al₂O₃>Ni/La₂O₃-Al₂O₃>Ni/Y₂O₃-Al₂O₃>Ni/Fe₂O₃-Al₂O₃>Ni/Al₂O₃. The catalysts were characterized by CO₂-TPD, O₂-TPD and XPS methods. Here the relation between the order of resistance to carbon-deposition and performance of catalyst is discussed.     

DNA-, RNA- and self-pairing properties of a pyrrolidinyl peptide nucleic acid with a (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone

A new pyrrolidinyl peptide nucleic acid (PNA) comprising of an alternate sequence of 4′-nucleobase-modified proline with (2′R,4′S) configuration and a (1S,2S)-2-aminocyclopentanecarboxylic acid [(2′R,4′S)-acpcPNA] backbone was synthesized and its DNA-, RNA- and self-pairing properties studied. T_m and CD studies suggested that the (2′R,4′S)-acpcPNA forms antiparallel hybrids to DNA and RNA with high sequence and direction specificity. The stability of these hybrids is comparable to those of the (2′R,4′R)-acpcPNA hybrids previously reported by our group. On the other hand, experiments with a self-complementary sequence indicated that the new (2′R,4′S)-acpcPNA forms a more stable antiparallel self-hybrid than (2′R,4′R)-acpcPNA.