Synthesis and properties of mirror-image DNA.

We have investigated the conformations of the hexadeoxyribonucleotide, L-d(CGCGCG) composed of L-deoxyribose, the mirror image molecule of natural D-deoxyribose. In this paper, we report the synthesis of four L-deoxynucleosides and the L-oligonucleotide-ethidium bromide interactions. The L-deoxyribose synthon 9 was synthesized from L-arabinose with an over all yield of 28.5% via the Barton-McCombie reaction. The L-deoxynucleosides were obtained by a glycosylation of appropriate nucleobase derivatives with the 1-chloro sugar 9. After derivatization to nucleoside phosphoramidites, L-deoxycytidine and L-deoxyguanosine were incorporated into a hexadeoxynucleotide, L-d(CGCGCG) by a solid-phase beta-cyanoethylphosphoramidite method. This L-hexanucleotide was resistant to digestion with nuclease P1. The conformations of L-d(CGCGCG) were an exact mirror image of that of the corresponding natural one as described previously, and the conformations of the L-d(CGCGCG)-ethidium bromide complex were also the mirror images of those of the D-d(CGCGCG)-ethidium bromide complex under both low and high salt conditions. These results suggest that ethidium bromide prefers not a right-handed helical sense, but the base-base stacking geometry of the B-form rather than that of the Z-form. Thus, L-DNA would be a useful tool for studying DNA-drug interactions.     

Synthesis and properties of a mutant type of xanthan

A mutant of Xanthomas campestris produces good yields of an exopolysaccharide. This material differs from the wild-type xanthan from the parent bacteria, in its very low content of acetate and pyruvate and in its molar ratio of D-glucose:D-mannose of 2:1. Analysis of the products from xanthan lyase indicates that most of the side-chains are disaccharides rather than the normal trisaccharides. The polymer has lower viscosity than normal xanthan. The consistency index was 20 mPa.s compared with 78 mPa.s for the product of the parent strain under standard conditions. The polysaccharide could be further modified by prolonged treatment with β-glucuronidase, which removed some of the terminal β-D-glucuronosyl residues. This enzyme-modified product had much higher viscosity than that from the mutant.     

Synthesis and characterization of cobaloxime dendrimer precursors

Reactions of bromobutyl or bromohexyl cobaloxime complexes with 3,5-dihydroxybenzyl alcohol in the presence of potassium carbonate gave, in both cases, mono- and di-cobalt complexes. These complexes were characterized largely by their NMR spectra. In addition, a new dimeric alkylcobaloxime complex was formed in these reactions by HBr elimination from the bromoalkyl complexes. This dimer was fully characterized and its X-ray crystal structure was determined. A zero generation dendrimer containing three cobaloxime groups was obtained by reaction of the bromobutyl cobaloxime with the core molecule 1,1,1-tris(4-hydroxyphenyl)ethane.     

DNA binding properties of a new class of linked anthramycin analogs.

We have investigated the DNA binding properties of the anthramycin analogues 4, 5, and 6 using fluorescence spectroscopy. A considerable fluorescence enhancement occurs when pyrrolo [1,4] benzodiazepines (P[1,4]Bs) are covalently attached to duplex DNA, which was used to show that neither the presence of RNA, single-stranded DNA, or protein had any effect on the degree of fluorescence enhancement resulting from the incubation of 5 and 6 with DNA. The enhancement was found to be dependent on the presence of the imine functionality in each of the compounds. A wavelength of 320 nm was used to excite the chromophore and its emission wavelength maximum was 420 nm. Additionally, we have discovered that the P[1,4]B ring system exhibits exceptionally favorable fluorescence polarization anisotropy (FPA) decay characteristics. For these more detailed fluorescence measurements, we used the structurally simpler analogue 4,. The time resolved maximum FPA for 4 in glycerol at 25 degrees C is 0.28. This result indicates that the P[1,4]B family of antibiotics could serve as sensitive probes of DNA dynamics in the 0.1 to 35 ns time scale.     

Synthesis of new azino fused benzimidazolium salts. a new family of DNA intercalating agents. I

A series of new pyrido[1,2-a]- and pyridazino[1,6-a]benzimidazolium salts have been synthesized from readily available 1,3-disubstituted 2-alkylbenzimidazolium salts. Their affinity to DNA and in vitro cytotoxicity versus HT-29 have been tested. The initial results show that the title compounds are a new family of intercalating agents.     

Synthesis and properties of new rubomycin derivatives

Condensation of rubomycin (daunorubicin) with respective hydrazides yielded novel substituted hydrazones: 13-cyanoacetyl hydrazone rubomycin, 13-L-phenylalanyl hydrazone rubomycin, 13-BOC-3-(uracilyl-1)-DL-alanyl hydrazone rubomycin and 13-BOC-3-(adenylyl-9)-DL-alanyl hydrazone rubomycin. With successive treatment of rubomycin with hydrazine hydrate and respective ketones novel asymmetric azines were prepared: 13-cyclopentylidene hydrazone rubomycin, 13-alpha,alpha'-dimethyl-cyclopentylidene hydrazone rubomycin and 13-(1-phenylethylidene-1) hydrazone rubomycin. 14-Adenylyl-N9-rubomycin was synthesized by interaction of 14-bromorubomycin with adenine and hydrogenation of its analog, 14-N-imidazolyl rubomycin by sodium borhydrite yielded 13-dihydro-14-N-imidazolyl rubomycin. There was observed correlation between the antimicrobial activity of the derivatives against B. mycoides and their cytostatic effect on the cells of murine leukemia NK/LI. The high in vitro activity of 13-cyclopentylidene hydrazone rubomycin showed satisfactory correlation with the results of the study on the antitumor effect in animals.     

Synthesis and tubulin-binding properties of new allocolchicinoids

Allocolchicinoids with B- and C-ring variations were synthesized using sequential enyne-metathesis/ Diels-Alder reactions (A → AB → ABC approach) and evaluated for their inhibitory effect on tubulin assembly in vitro. (−)-Allocolchicine 11 with methyl ester at C10 and (±)-cyclopropyl allocolchicinoid 32 exhibit similar activity than (−)-colchicine (1), probably derived from a similar flexibility in the biphenyl system. The presence of methyl ester at C10 led to a little loss in potency in comparison with the series with methyl ester at C9. A complete loss of activity was observed for allocolchicine 9 with methyl ester at C11.     

Synthesis and DNA binding properties of DNA-PNA chimeras

A systematic study to evaluate the ability of 5'-DNA-3'-p-(N)-PNA-(C) chimeras to form triple helix structures has been undertaken. Preliminary results carried out on a 16-mer chimera with three PNA monomers at the 3'-end showed the formation of a stable DNA-PNA/DNA/DNA triplex, having similar conformational behaviour to a canonical DNA/DNA/DNA triplex.     

Synthesis and antiproliferative activity of novel steroidal dendrimer conjugates

We describe the synthesis of steroidal dendrimer conjugates of first and second generation with tetramethylene core and 5-hydroxy-isophtalic acid dimethyl ester as branching unit modified to incorporate ethynylestradiol or 17α-estradiol as terminal units. The steroidal dendrimer conjugates, the free drug (steroids) and dendrimer were tested against a panel of cancer cell lines (CEM, MCF7, HeLa) and normal human fibroblast (BJ). The steroidal dendrimer conjugates of first generation exhibited cytotoxic activity and induced apoptosis in chronic leukemia (CEM) as resultant activation of caspase cascade which is mainly provoked in G2/M arrested cells.     

Synthesis and properties of a new cleavable nucleic acid-protein crosslinking reagent

A new compound, dithiobis[9-(2-ethylenecarbamoylethylamino)-2,3-dimethoxy-6-azido-acridine], was synthesized and used in some preliminary experiments to form cleavable complexes between nucleic acids and proteins. In a first step the azidoacridine moiety of the reagent intercalates between the bases of nucleic acids and is then bound by reaction of the azido group. The disulfide group of the reagent is simultaneously converted under reducing conditions into a thiol which, in a second step, can be bound by oxidation to -SH groups of a vicinal protein (additional -SH groups can be inserted in the protein using 2-iminothiolane). The nucleic acid-protein complexes thus formed can be redissociated by reduction. The potential applications of this new cleavable crosslinking reagent could be extended to topographical investigations of any biological structure composed of nucleic acids and proteins.     

Synthesis of a cyclopentane amide DNA analogue and its base pairing properties

cpa-DNA monomers containing the bases adenine and thymine have been synthesized starting from the known compound 1 in 12 steps. Partially and fully modified cpa-thymidine and cpa-adenosine containing oligodeoxynucleotides were synthesized by standard oligonucleotide chemistry. Fully modified homo-cpa-A sequences lead to duplex destabilization by -1.4 degrees C/mod. relative to DNA. As its congener bca-DNA, cpa-DNA prefers left-handed duplex formation where possible.     

Nucleosides and nucleotides. 183. Synthesis of 4'alpha-branched thymidines as a new type of antiviral agent

A series of 4'alpha-branched thymidines was synthesized and evaluated as potential antiviral agents. 4'-Ethylthymidine (3), 4'-ethenylthymidine (5), and 4'-ethynylthymidine (6) exhibited potent anti-HSV-1 and anti-HIV-1 activities with no significant cytotoxicity.     

Optimization of transfection properties of DNA-lysine dendrimer complexes

We studied the possibility of optimizing the DNA transfection properties of carriers based on lysine dendrimers of the third and the fifth generation, including those containing a chloroacetyl or a lipophilic palmitoyl moiety at C-end. The use of lysosome-destroying antibiotic chloroquine and an amphipathic polycationic nonadecapeptide JTS-1 was found to enhance the DNA transfecting properties of the lysine dendrimers. The triple complex including DNA, a lysine dendrimer of the third generation modified with lipophylic moieties of palmitic acid at its C-end, and JTS-1 was shown to be comparable in its transfecting activity to a complex containing Escort, a commercial cationic liposome carrier.     

Optimization of transfection properties of DNA-lysine dendrimer complexes

We studied the possibility of optimizing the DNA transfection properties of carriers based on lysine dendrimers of the third and the fifth generation, including those containing a chloroacetyl or a lipophilic palmitoyl moiety at the C-end. The use of the lysosome-destroying antibiotic chloroquine and the amphipathic polycationic nonadecapeptide JTS-1 was found to enhance the DNA-transfecting properties of the lysine dendrimers. A triple complex including DNA, a lysine dendrimer of the third generation modified with lipophilic moieties of palmitic acid at its C-end, and JTS-1 was shown to be comparable in its transfecting activity to a complex containing Escort, a commercial cationic liposome carrier.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 2, 2005, pp. 167–174.Original Russian Text Copyright © 2005 by Vlasov, Lesina, Korolkov, Guryanov, Bayanova, Baranov, Kiselev, Baranov.     

Synthesis of a new analog of thymidine for in vivo non-radioactive labeling of DNA.

The introduction of 6-(p-bromobenzoylamino)caproyl radical in the methyl group of 2'-O-deoxythymidine is described. In vivo incorporation of this nucleoside to DNA was determined using a monoclonal antibody that recognized the radical.     

DNA recognition by a new family of type I restriction enzymes: a unique relationship between two different DNA specificities.

The DNA sequences recognized by the allelic type I restriction enzymes EcoR124 and EcoR124/3 were determined. EcoR124 recognizes 5'-GAA(N6)RTCG-3' and EcoR124/3 recognizes 5'-GAA(N7)RTCG-3'. These are typical of sequences recognized by type I recognition enzymes in that they consist of two specific domains separated by a non-specific spacer sequence. For these two enzymes, the specific sequences are identical but the length of the non-specific spacer is different. The specific domains of EcoR124/3 are thus 3.4 A further apart than those of EcoR124 and rotated with respect to each other through a further 36 degrees.     

Synthesis of beta-D-galactofuranosyl nucleoside analogues. A new type of beta-D-galactofuranosidase inhibitor.

The development of beta-D-galactofuranosidase inhibitors provides a good chemotherapeutic target for treatment of major human diseases, because beta-D-galactofuranose is a constituent of important pathogen microorganisms but is absent in mammals. With this purpose we have prepared beta-D-galactofuranosyl nucleoside analogues, derived by the addition of nucleophiles to perbenzoylated beta-D-galactofuranosyl isothiocyanate, a compound previously prepared in this laboratory. N-beta-D-Galactofuranosyl-O-ethylthiourethane, N-beta-D-galactofuranosyl-4-oxoimidazolidine-2-thione, N-beta-D-galactofuranosyl-4-imidazoline-2-thione, and N-beta-D-galactofuranosyl-4-methoxyimidazolidine-2-thione, were prepared. The biological assays showed that imidazoline and imidazolidine-2-thione derivatives act as a new type of exo beta-D-galactofuranosidase inhibitor.     

Synthesis and DNA binding properties of dioxime-peptide nucleic acids

Peptide nucleic acids (PNAs) C- or N-modified with dioxime ligands were prepared by solid-phase synthesis using iron(II)-clathrochelates as protected dioxime building blocks. These PNA bind complementary DNA sequence specifically, though with much reduced affinity in comparison with nonmodified PNA. The dioxime-PNA conjugates bind Cu2+ and Ni2+ at microM concentration.