Synthesis and triplex forming properties of pyrrolidino pseudoisocytidine containing oligodeoxynucleotides

Pyrrolidino pseudo-C-nucleosides are isosteres of natural deoxynucleosides which are protonated at the pyrrolidino ring nitrogen under physiological conditions. As constituents of a triplex forming oligodeoxynucleotide (TFO), the positive charge is expected to stabilise DNA triple helices via electrostatic interactions with the phosphodiester backbone of the target DNA. We describe the synthesis of the pyrrolidino isocytidine pseudonucleoside and the corresponding phosphoramidite building block and its incorporation into TFOs. Such TFOs show substantially increased DNA affinity compared to unmodified oligodeoxynucleotides. The increase in affinity is shown to be due to the positive charge at the pyrrolidino subunit.     

Synthesis and pairing properties of alpha-tricyclo-DNA

We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.     

DNA binding properties of oligodeoxynucleotides containing pyrrolidino C-nucleosides

We have incorporated pyrrolidino-C-nucleosides (pyrrolidino-pseudonucleosides) containing the base uracil and N-1-methyl uracil into oligodeoxynucleotides and compared their thermal duplex and triplex stabilities with unmodified or pseudouridine-containing oligodeoxynucleotides. We find relative destabilizations of triplex formation by ca. -13 to -1 degrees C per modification (relative to thymidine) in a strongly sequence dependent mode. Duplex formation is less destabilizing and more homogeneous with -4 to -2 degrees C per modification.     

Synthesis and characterization of oligodeoxynucleotides containing formamidopyrimidine lesions and nonhydrolyzable analogues

Oligodeoxynucleotides containing formamidopyrimidine lesions and C-nucleoside analogues at defined sites were prepared by solid-phase synthesis and in some cases enzymatic ligation. Formamidopyrimidine lesions were introduced as dinucleotides to prevent rearrangement to their pyranose isomers. Oligodeoxynucleotides containing single diastereomers of C-nucleoside analogues of Fapy.dA were introduced by using the respective phosphoramidites. The formamidopyrimidine lesions reduce the T(M) of dodecamers relative to their unmodified nucleotide counterparts when opposite the nucleotide proper base-pairing partner. However, duplexes containing Fapy.dG-dA mispairs melt significantly higher than those comprised of dG-dA. All duplexes containing Fapy.dA-dX or its C-nucleoside analogue melt lower than the respective complexes containing dA-dX. Studies of the alkaline lability of oligodeoxynucleotides containing formamidopyrimidine lesions indicate that Fapy.dA is readily identified as an alkali-labile lesion with use of piperidine (1.0 M, 90 degrees C, 20 min), but Fapy.dG is less easily identified in this manner.     

Synthesis and properties of 2-azidodeoxyadenosine and its incorporation into oligodeoxynucleotides

2-Azidodeoxyadenosine (7) was conveniently synthesized from deoxyguanosine (2) by use of a combined reagent of TMSN₃–BuONO. The structure of the tautomer of the azido derivative was determined by ¹H NMR. Reaction of 7 with iPr₂NP(OEt)₂ gave an intermediate 10 of the Staudinger reaction. Incorporation of 7 into a DNA 13mer resulted in a significant decrease of the T_m value of the DNA duplex upon hybridization with the complementary strand. The thermal stability was discussed based on the hydrogen bond energy and electrostatic repulsion.     

Synthesis and antitumor activity of new alkylphospholipids containing modifications of the phosphocholine moiety

New antitumor alkylglycerophospholipids, in which primarily the phosphocholine moiety of the platelet activating factor (PAF) molecule was modified, were synthesized from 1-alkyl-2-substituted glycerols by introducing polar head phosphoryl groups having methylene bridges of various lengths (from 2 to 14 carbons). They were tested for PAF agonistic activity and antitumor properties. In a series of 1-octadecyl-2-acetoacetylglycerophospholipids (1a-f), an increase in the length of the methylene bridge separating the phosphate and trimethylammonio group in the polar head side chain at position 3 of the glycerol backbone resulted in a progressive decrease in PAF agonistic activity and a characteristic change in antitumor activity against human promyelocytic leukemia cells (HL-60). Maximal potency was obtained with the compound having a decamethylene bridge (1e, IC50 value = 1.5 microgram/ml). Thus, alkylphospholipids possessing a decamethylene bridge and a variety of substituents at position 2 (1g-n) were synthesized. They showed potent inhibitory activity with IC50 values ranging from 0.4 to 1.9 micrograms/ml, depending on the nature of the 2-substituent in the phospholipid molecule. In in vivo tests of the present series of alkylglycerophospholipids (1a--n), using mice bearing sarcoma 180 and mice with mammary carcinoma MM46 (both cells and compounds were given i.p.), 1-octadecyl-2-acetoacetyl-3-glyceryl omega-trimethylammoniodecyl phosphate (1e) showed the most potent life-prolonging effect. The structure-activity relationships are discussed.     

Synthesis of cyclopentane amide DNA (cpa-DNA) and its pairing properties

We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degrees C/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra.     

Synthesis and properties of polyesters containing naphthalenetetracarboxylic imide

Poly(ethylene naphthalates) containing small contents of N, N'-bis(ω-hydroxypropyl)naphthalene-1, 4, 5, 8-tetracarboxylic imide(HPNTI) unit as the photostabilizing component, which are stable to ultraviolet lights, were synthesized from dimethyl naphthalate, ethylene glycol, and HPNTI. The polyesters obtained were characterized by fluorescence spectroscopy and measurements of molecular weights and thermal properties.     

Synthesis and properties of polysulfonamides containing thiophene links

In order to study the synthesis and properties of polysulfonamides containing thiophene links, 2,2-bis(5-chlorosulfonyl-2-thienyl)propane [BCTP], 2,2-bis(5-chlorosulfonyl-2-thienyl)butane [BCTB], 1,1-bis(5-chlorosulfonyl-2-thienyl)cyclohexane [BCTC], and 2,4-dichlorosulfonyl thiophene [DCST] were prepared and interfacial polycondensations with various aliphatic diamines were carried out. The resulting polymers had inherent viscosities in the range of 0.13–0.41 dL/g and showed high extent of moisture absorptions. Most of the polysulfonamides were soluble in electron-donating solvents such as pyridine, DMF, DMSO, NMP, etc. These polysulfonamides exhibited relatively good thermal stabilities. The TGA data revealed 5% weight losses at 275–405°C and residual weights at 500°C were 13–40% under nitrogen. It was also found that dithienyldisulfonyl chlorides produced more thermally stable polymers than DCST, which were comparable to common polysulfonamides from aromatic disulfonyl chlorides.     

New base pairing motifs. The synthesis and thermal stability of oligodeoxynucleotides containing imidazopyridopyrimidine nucleosides with the ability to form four hydrogen bonds

The synthesis and thermal stability of oligodeoxynucleotides (ODNs) containing imidazo[5',4':4,5]pyrido[2,3-d]pyrimidine nucleosides 1-4 (N(N), O(O), N(O), and O(N), respectively) with the aim of developing two sets of new base pairing motifs consisting of four hydrogen bonds (H-bonds) is described. The proposed four tricyclic nucleosides 1-4 were synthesized through the Stille coupling reaction of a 5-iodoimidazole nucleoside with an appropriate 5-stannylpyrimidine derivative, followed by an intramolecular cyclization. These nucleosides were incorporated into ODNs to investigate the H-bonding ability. When one molecule of the tricyclic nucleosides was incorporated into the center of each ODN (ODN I and II, each 17mer), no apparent specificity of base pairing was observed, and all duplexes were less stable than the duplexes containing natural G:C and A:T pairs. On the other hand, when three molecules of the tricyclic nucleosides were consecutively incorporated into the center of each ODN (ODN III and IV, each 17mer), thermal and thermodynamic stabilization of the duplexes due to the specific base pairings was observed. The melting temperature (T(m)) of the duplex containing the N(O):O(N) pairs showed the highest T(m) of 84.0 degrees C, which was 18.2 and 23.5 degrees C higher than that of the duplexes containing G:C and A:T pairs, respectively. This result implies that N(O)and O(N) form base pairs with four H-bonds when they are incorporated into ODNs. The duplex containing N(O):O(N) pairs was markedly stabilized by the assistance of the stacking ability of the imidazopyridopyrimidine bases. Thus, we developed a thermally stable new base pairing motif, which should be useful for the stabilization and regulation of a variety of DNA structures.     

Synthesis and catalytic properties of tetraorganodistannoxanes containing silicon

Three tetraorganodistannoxanes containing silicon were synthesized and their catalytic properties in esterification and acetalization were observed via the reactions of acetic acid with isoamyl alcohol and butyraldehyde with glycol. The factors affecting the reaction, such as the catalyst dosage, reaction time and solvent, etc. were discussed. The results show that the three tetraorganodistannoxanes displayed similar good catalytic activities compared to dichlorotetrabutyldistannoxane in esterification and acetalization. When the dosage of [ClBu₂SnOSn-(CH₂SiMe₃)₂Cl]₂ was 1.5% based on the mass of reactant, the yield of isoamyl acetate was 91.8% and the yield of butyraldehyde glycol acetal 94.2%. The different alkyl and bridging groups on Sn sites in the structure of tetraorganodistannoxanes showed some influence on the catalytic activities of these compounds. __________ Translated from Chinese Journal of Applied Chemistry, 2007, 24 (11): 1265–1272     

Synthesis and properties of polyamides containing imidazoline rings

The novel polyamide containing an imidazoline ring(PAI) was synthesized by a two-stage melt polymerization of dimethyl terephthalate (DMT) with diethylenetriamine (DETA) or triethylenetetramine (TETA). The heat resistance of PAI was superior to that of polyamide which was synthesized only in the first-stage reaction and didn't contain imidazoline ring. Their chemical structures were identified by infrared spectroscopy and NMR. The optimum condition for production was studied by varying several reaction factors, including the contents of H₂O and H₃PO₄, the reaction temperature and the reaction time at second-stage reaction under vacuum. According to study of the characteristics of solution behavior of PAI, both the viscosity and the degree of cyclization could be described by equation of in m-cresol at 30°C.     

Synthesis and properties of disulfide-bond containing eight-membered rings

The cyclocystine ring structure (CRS, 3), which results from a disulfide-bond between adjacent cysteine residues, is a rare motif in protein structures and is functionally important to those few proteins that posses it. This letter will focus on the construction of CRS mimics and the determination of their respective redox potentials.     

Synthesis and properties of polyketones containing thiophene links

A series of polyketones containing thiophene links was synthesized by the Friedel-Crafts polymerization of these dithienylalkanes with aromatic diacid chlorides or dicarbonyl chlorides comprising thiophene links with diphenyl compounds. The resulting polymers had inherent viscosities in the range of 0.11–0.27 dL/g and showed poor solubilities to common organic solvents except strong acids. These thiophene-based polyketones exhibited fairly good thermal stabilities. The TGA data revealed 5% weight losses at 375–450°C and residual weights at 500°C were 43–79% under nitorgen. It was found that the thermal stabilities of these polymers were superior to those of polymides or polysulfonamides containing thiophene links and almost comparable to common aromatic polyketones     

Synthesis and characterization of oligodeoxynucleotides containing the major DNA adducts formed by 1,6- and 1,8-dinitropyrene

[reaction: see text] An efficient method for the synthesis of oligonucleotides containing a site-specific DNA adduct formed by the carcinogens 1,6- and 1, 8-dinitropyrene has been developed. Palladium-catalyzed amination provided a straightforward route for the synthesis of aminonitropyrenes which, following separation, were reduced to the nitrosonitropyrenes. The N-hydroxyaminonitropyrene, generated in situ from each nitrosonitropyrene, was used successfully to introduce the dinitropyrene-derived DNA adduct at a defined site in an oligonucleotide.     

Synthesis and characterization of pi-stacked phenothiazine-labeled oligodeoxynucleotides

[reaction: see text] A facile procedure for the incorporation of N-methyl phenothiazine as the terminal nucleoside in oligodeoxynucleotides is reported. The phenothiazine nucleoside analogue is synthesized and then incorporated into DNA using an automated DNA solid-phase synthesizer. Phenothiazine-labeled oligodeoxynucleotides form stable B-form duplexes with higher melting temperatures compared to unlabeled DNA duplexes.     

Synthesis and thermomechanical properties of alternating copolymers containing bisphenol-A

Alternating copolymers containing 4,4-isopropylidene-bisphenol (BPA) and comonomers with various degrees of polarity have been evaluated to find comonomer structures which provide low melt viscosity and good thermal stability. The materials were prepared by pyridine-catalyzed nucleophilic displacement reactions similar to that for the preparation of BPA polycarbonate. The molecular weights of the polycarbonates depend on the concentration and nucleophilicity of the attacking diol and the concentration and stability of a colored pyridine-chloroformate adduct formed during polymerization. The greatest thermal stability occurs for BPA–DMS and BPA–DEG. Thermomechanical flow measurements and T_g measurements were used to evaluate melt viscosity. The shapes and magnitudes of the T_g vs. T^f curves are sensitive to the copolymer chemical structure.     

Synthesis and photochromic properties of polymers containing spirooxazine groups

Two spirooxazine (SO) compounds containing bromobutyl substituents on 1-position (SO1) and 9′- position (SO2) have been synthesized and characterized by 1H-NMR, IR and ESI-MS in this paper. SO1-g-PMMA and SO2-g-PMMA polymer were prepared by grafting SO1 and SO2 onto PMMA through C-Br bonding sites. Also, SOs were doped into PMMA matrix to afford SO1-d-PMMA and SO2-d-PMMA. Photochromic behaviors of these compounds have been studied. Compared with SO1, SO2 exhibited better photoresponse and slower bleaching in dichloromethane solution. Inserted into polymer films, the decoloration process of SOs were significantly retarded and it was found that the fading curves fitted a first-order equation; As regard to four polymers, 1-position grafting (SO2-g-PMMA) can cause a higher reduction degree on the thermal fading rate.