Application of 2-amino-6-vinylpurine as an efficient agent for conjugation of oligonucleotides

Attempts have been made to conjugate a variety of molecules with oligonucleotides to achieve useful functions. In this study, we have established a new efficient method for post-synthetic conjugation of oligonucleotides with the use of the 2-amino-6-vinylpurine nucleoside. Amino nucleophiles form the corresponding conjugates under acidic conditions, whereas thiol nucleophiles reacted efficiently under alkaline conditions. Thus, glutathione and HS-Cys-(Arg)8 without protecting groups were efficiently conjugated to the 2-amino-6-vinylpurine-bearing ODN under alkaline conditions. The use of 2-amino-6-vinylpurine as an agent for conjugation is advantageous in that it is stable during the reaction and may be applied to conjugation of ODNs with multiple functional molecules.     

Alteration of cross-linking selectivity with the 2′-OMe analogue of 2-amino-6-vinylpurine and evaluation of antisense effects

We previously reported that oligodeoxynucleotides containing 2-amino-6-vinylpurine (2-AVP: 1) exhibit efficient selective cross-linking to cytosine. In this study, the 2′-OMe nucleoside analogue (2) of 2-AVP was designed in order to increase its affinity to RNA and enhance metabolic stability. It has been demonstrated that 2′-OMe oligonucleotides bearing 2 achieve highly selective cross-linking to the thymine base in DNA and show higher antisense effect on luciferase production in cell lysate.     

The alkyl-connected 2-amino-6-vinylpurine (AVP) crosslinking agent for improved selectivity to the cytosine base in RNA

We have previously reported that the 2-amino-6-vinylpurine (AVP) nucleoside exhibits a highly efficient and selective crosslinking reaction toward cytosine and displayed an improved antisense inhibition in cultured cells. In this study, we further investigated the alkyl-connected AVP nucleoside analogs for more efficient crosslinking to the cytosine base (rC) of the target RNA. We synthesized three AVP analogs which connect the 2-amino-6-vinylpurine unit to the 2′-deoxyribose through a methylene, an ethylene, or a butylene linker. The ODN incorporating the AVP analog with the methylene or the butylene linker showed a slightly higher crosslinking to the target rC of RNA than the original AVP with no linker. In contrast, the AVP with the ethylene linker formed a selective and efficient crosslink to the rC of the target RNA.     

Efficient cross-linking to cytidine using substituted phenylsulfide derivatives of 2-amino-6-vinylpurine nucleoside via synchronous activation within duplex.

We have previously described that oligonucleotides containing phenylsulfoxide derivative of 2-amino-6-vinyulpurine nucleoside analog (1) are activated within duplex to form cross-link toward cytidine selectively at the target site. The new cross-linking motif with phenylsulfoxide structure (2) is characteristic in that the stable precursor may be transformed automatically within duplex to a reactive species. To search for more stable precursor susceptible for activation, we designed a series of substituted phenylsulfide analogs of 1. It has been demonstrated that introduction of an electron-donating group on the phenyl ring improved the cross-linking reaction. Particularly, 2-carboxyphenyl sulfide derivative exhibited cross-linking as effectively as phenylsulfoxide derivative without chemical oxidation prior to cross-linking.     

Antisense probing of the human U4/U6 snRNP with biotinylated 2'-OMe RNA oligonucleotides

We have used antisense 2'-OMe RNA oligonucleotides carrying four 5'-terminal biotin residues to probe the structure and function of the human U4/U6 snRNP. Nine oligonucleotides, complementary to multiple regions of U4 and U6 snRNAs, bound stably and specifically to U4/U6 snRNP. This allowed for efficient and selective removal of U4/U6 from HeLa cell nuclear extracts. Binding of oligonucleotides to certain snRNA domains inhibited splicing and affected the U4-U6 interaction. Pre-mRNA and splicing products could also be affinity-selected through binding of the oligonucleotides to U4/U6 snRNPs in splicing complexes. The results suggest that U4 snRNP is not released during spliceosome assembly.     

Production rates of CO2 by suspended and immobilized bacteria degrading 6-amino-2-naphthalenesulphonic acid

Summary Production rates of CO₂ were calculated on the basis of kinetic data obtained from 6-amino-2-naphthalenesulphonic acid (6A2NS) degradation with a mixed bacterial culture. A linear correlation between product (CO₂) formation and growth rate was found for submersed growing cultures as well as for bacteria immobilized on sand particles. For immobilized biomass a distinction was made between active cells and bacterial exopolymers using model calculations.Dedicated to Prof. Dr. Fritz Wagner, TU Braunschweig, on the occasion of his 60th birthdayOffprint requests to: D. C. Hempel     

Efficient triple helix formation by oligodeoxyribonucleotides containing alpha- or beta-2-amino-5-(2-deoxy-D-ribofuranosyl) pyridine residues.

Triple helices containing C+xGxC triplets are destabilised at physiological pH due to the requirement for base protonation of 2'-deoxycytidine (dC), which has a pKa of 4.3. The C nucleoside 2-amino-5-(2'-deoxy-beta-D-ribofuranosyl)pyridine (beta-AP) is structurally analogous to dC but is considerably more basic, with a pKa of 5.93. We have synthesised 5'-psoralen linked oligodeoxyribonucleotides (ODNs) containing thymidine (dT) and either beta-AP or its alpha-anomer (alpha-AP) and have assessed their ability to form triplexes with a double-stranded target derived from standard deoxynucleotides (i.e. beta-anomers). Third strand ODNs derived from dT and beta-AP were found to have considerably higher binding affinities for the target than the corresponding ODNs derived from dT and either dC or 5-methyl-2'-deoxycytidine (5-Me-dC). ODNs containing dT and alpha-AP also showed enhanced triplex formation with the duplex target and, in addition are more stable in serum-containing medium than standard oligopyrimidine-derived ODNs or ODNs derived from dT and beta-AP. Molecular modelling studies showed that an alpha-anomeric AP nucleotide can be accommodated within an otherwise beta-anomeric triplex with only minor perturbation of the triplex structure. Molecular dynamics (MD) simulations on triplexes containing either the alpha- or beta-anomer of (N1-protonated) AP showed that in both cases the base retained two standard hydrogen bonds to its associated guanine when the 'A-type' model of the triplex was used as the start-point for the simulation, but that bifurcated hydrogen bonds resulted when the alternative 'B-type' triplex model was used. The lack of a differential stability between alpha-AP- and beta-AP-containing triplexes at pH >7, predicted from the behaviour of the B-type models, suggests that the A-type models are more appropriate.     

Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2'-deoxyuridine or 5-bromo-2'-deoxycytidine

The replacement of thymidine with 5-bromo-2′-deoxyuridine (^BrdU) is well-known to sensitize cells to ionizing radiation and photoirradiation. We reported here the sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex oligodeoxynucleotides harboring a ^BrdU or its closely related 5-bromo-2′-deoxycytidine (^BrdC). Our results showed that two types of crosslink products could be induced from d(^BrCG), d(^BrUG), d(G^BrU), or d(A^BrU); the C(5) of cytosine or uracil could be covalently bonded to the N(2) or C(8) of its neighboring guanine, and the C(5) of uracil could couple with the C(2) or C(8) of its neighboring adenine. By using those crosslink product-bearing dinucleoside monophosphates as standards, we demonstrated, by using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), that all the crosslink products described above except d(G[N(2)-5]U) and d(G[N(2)-5]C) could form in duplex DNA. In addition, LC-MS/MS quantification results revealed that both the nature of the halogenated pyrimidine base and its 5′ flanking nucleoside affected markedly the generation of intrastrand crosslink products. The yields of crosslink products were much higher while the 5′ neighboring nucleoside was a dG than while it was a dA, and ^BrdC induced the formation of crosslink products much more efficiently than ^BrdU. The formation of intrastrand crosslink products from these halopyrimidines in duplex DNA may account for the photosensitizing effects of these nucleosides.     

Inhibition of germ tube formation, filamentation and ergosterol biosynthesis inCandida albicans treated with 6-amino-2-n-pentylthiobenzothiazole

Three representativeCandida albicans strains were selected out of 26 clinical isolates and strains from culture collections on the basis of their high level of conversion to germ tubes and mycelial form at mycelium-promoting culture conditions, and on their different sensitivity to 6-amino-2-n-pentylthiobenzothiazole (APB). When these strains were treated with APB at mycelium-promoting culture conditions, a concentration-dependent decrease in the proportion of germ tubes and hyphae was observed, while the proportion of the yeast form increased. When non-saponifiable lipids were extracted from these cultures and analyzed, a concentration-dependent decrease in ergosterol and an increase in 4-methylated sterols was observed. However, the sensitivity of sterol biosynthesis did not directly relate to the sensitivity of the morphological conversion, and was exhibited at higher concentrations of APB. On the basis of these results it is suggested that the inhibition of germ tube formation and filamentation is not a consequence of inhibition of ergosterol biosynthesis in APB-treatedC. albicans.     

Synthesis of some derivatives of 6-amino-1,5-anhydro-6-deoxy-d-glucitol and 2-amino-1,5-anhydro-2-deoxy-d-glucitol

6-Amino-1,5-anhydro-6-deoxy-d-glucitol (11) was prepared from 2,3,4,6-tetra-O-acetyl-α-d-glucopyranosyl bromide (1) in six steps. Reduction of 1 with tributyltin hydride, followed by deacetylation, monomolar tosylation, and reacetylation, afforded 2,3,4-tri-O-acetyl-1,5-anhydro-6-O-toluene-p-sulfonyl-d-glucitol (9). Alternatively, tritylation of 1,5-anhydro-d-glucitol, followed by acetylation, detritylation, and tosylation, gave 9. Mesylation gave 8. Treatment of 8 or 9 with azide anion afforded the azide 10, reduction of which with tributyltin hydride gave 11, which was mesylated or tosylated, and then deacetylated to give the 6-methane-sulfonamido or 6-toluene-p-sulfonamido derivative. Similarly, mesylation or tosylation of 3,4,6-tri-O-acetyl-2-amino-1,5-anhydro-2-deoxy-d-glucitol (20) gave the 2-methanesulfonamido or 2-toluene-p-sulfonamido derivatives. Treatment of 11 and 20 with sulfur trioxide-pyridine afforded the sulfoamino derivatives, deacetylation of which gave sugar analogs of cyclamate-like compounds.     

Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing

Studies on hydration are important for better understanding of structure and function of nucleic acids. We compared the hydration of self-complementary DNA, RNA and 2′-O-methyl (2′-OMe) oligonucleotides GCGAAUUCGC, (UA)₆ and (CG)₃ using the osmotic stressing method. The number of water molecules released upon melting of oligonucleotide duplexes, Δn_W, was calculated from the dependence of melting temperature on water activity and the enthalpy, both measured with UV thermal melting experiments. The water activity was changed by addition of ethylene glycol, glycerol and acetamide as small organic co-solutes. The Δn_W was 3–4 for RNA duplexes and 2–3 for DNA and 2′-OMe duplexes. Thus, the RNA duplexes were hydrated more than the DNA and the 2′-OMe oligonucleotide duplexes by approximately one to two water molecules depending on the sequence. Consistent with previous studies, GC base pairs were hydrated more than AU pairs in RNA, whereas in DNA and 2′-OMe oligonucleotides the difference in hydration between these two base pairs was relatively small. Our data suggest that the better hydration of RNA contributes to the increased enthalpic stability of RNA duplexes compared with DNA duplexes.     

Production of a truncated human c-myc protein which binds to DNA

Two kinds of truncated human c-myc proteins were produced in Escherichia coli. The human c-myc gene is composed of three exons, exons 2 and 3 having coding capacity for a protein of 439 amino acids. 252 N-terminal amino acids are encoded by exon 2, the C-terminal 187 amino acids being encoded by exon 3. One of the proteins (p42) produced in E. coli corresponds to 342 amino acids from the 98th Gln to the C-terminus, plus 21 amino acids derived from the H-ras gene at the N-terminus. The other (p23) corresponds to 155 amino acids from the 98th Gln to the 252nd Ser, plus five amino acids (Gly-Gly-Thr-Arg-Arg) at the C-terminus, plus 21 amino acids from the H-ras gene at the N-terminus. The p23 protein was produced by using cDNA in which a frame shift occurred at the boundary between exons 2 and 3. We investigated the DNA-binding activity in p42 and p23 proteins. DNA-cellulose column chromatography showed that p42 binds to DNA, whereas p23 does not. This DNA-binding activity of p42 was inhibited by antiserum prepared against p42 but not by antiserum against p23. This indicates that the DNA-binding activity of c-myc protein is localized in the portion encoded by exon 3.     

Probing the structure and function of U2 snRNP with antisense oligonucleotides made of 2'-OMe RNA

We have used oligonucleotides made of 2'-OMe RNA to analyze the role of separate domains of U2 snRNA in the splicing process. We show that antisense 2'-OMe RNA oligonucleotides bind efficiently and specifically to U2 snRNP and demonstrate that masking of two separate regions of U2 snRNA can inhibit splicing by affecting different steps in the spliceosome assembly pathway. Masking the 5' terminus of U2 snRNA does not prevent U2 snRNP binding to pre-mRNA but blocks subsequent assembly of a functional spliceosome. By contrast, masking of U2 sequences complementary to the pre-mRNA branch site completely inhibits binding of pre-mRNA. Hybrid formation at the branch site complementary region also triggers a specific change which affects the 5' terminus of U2 snRNA.     

Interaction of the adenoviral IVa2 protein with a truncated viral DNA packaging sequence

Adenoviral (Ad) infection typically poses little health risk for immunosufficient individuals. However, for immunocompromised individuals, such as AIDS patients and organ transplant recipients, especially pediatric heart transplant recipients, Ad infection is common and can be lethal. Ad DNA packaging is the process whereby the Ad genome becomes encapsulated by the viral capsid. Specific packaging is dependent upon the packaging sequence (PS), which is composed of seven repeated elements called A repeats. The Ad protein, IVa2, which is required for viral DNA packaging, has been shown to bind specifically to synthetic DNA probes containing A repeats I and II, however, the molecular details of this interaction have not been investigated. In this work we have studied the binding of a truncated form of the IVa2 protein, that has previously been shown to be sufficient for virus viability, to a DNA probe containing A repeats I and II. We find that the IVa2 protein exists as a monomer in solution, and that a single IVa2 monomer binds to this DNA with high affinity (K_d <  10 nM), and moderate specificity, and that the trIVa2 protein interacts in a fundamentally different way with DNA containing A repeats than it does with non-specific DNA. We also find that at elevated IVa2 concentrations, additional binding, beyond the singly ligated complex, is observed. When this reaction is modeled as representing the binding of a second IVa2 monomer to the singly ligated complex, the K_d is 1.4 ± 0.7 µM, implying a large degree of negative cooperativity exists for placing two IVa2 monomers on a DNA with adjacent A repeats.     

Synthesis and biological evaluation of 2-amino-2-deoxy- and 6-amino-6-deoxy-cyclomaltoheptaose polysulfates as synergists for angiogenesis inhibition

2-Amino-2-deoxy-cyclomaltoheptaose was prepared from β-cyclodextrin perbenzoate [heptakis(2,3,6-tri-O-benzoyl)cyclomaltoheptaose] by a series of reactions including selective de-O-benzoylation at C-2 of one of the perbenzoylated -glucopyranosyl moieties, oxidation to the 2-ulose derivative, oxime formation, and reduction to the 2-amino-2-deoxy- -glucose moiety. This compound and 6-amino-6-deoxycyclomaltoheptaose accessible from β-cyclodextrin through the known procedure were sulfated to give polysulfated aminocyclomaltoheptaose derivatives (3, 5). Employing β-cyclodextrin polysulfate as a reference compound, the synergistic effects of 3 and 5 for cortexolone on angiogenesis inhibitory activity were examined by rabbit-corneal micropocket assay system. In contrast to the significant anti-angiogenesis activity of the β-cyclodextrin polysulfate-cortexolone pair, neither 3 nor 5 showed any cooperative activity with cortexolone in the inhibition of basic FGF-induced angiogenesis.     

Inhibition of the microsomal N-hydroxylation of 2-amino-6-nitrotoluene by a metabolite of methimazole

Inhibition studies were used to investigate the identity of the microsomal enzyme(s) responsible for the NADPH-dependent N-hydroxylation of 2-amino-6-nitrotoluene. The N-hydroxylation reaction was inhibited by several cytochrome P-450 inhibitors as well as by methimazole, a substrate for flavin-containing monooxygenase. Heat inactivation of flavin-containing monooxygenase had no effect on the rate of the reaction but abolished the inhibition by methimazole. These results indicate that the flavin-containing monooxygenase-mediated metabolism of methimazole produced an inhibitor of the cytochrome P-450-catalyzed N-hydroxylation reaction. When glutathione was included in the incubation the inhibition by methimazole was abolished, presumably due to the reduction of oxygenated metabolites of methimazole. These results show that methimazole inhibition does not necessarily implicate flavin-containing monooxygenase in microsomal N-hydroxylation reactions.     

Isolation of a trisaccharide containing 2-amino-2-deoxy-D-galacturonic acid from the Bordetella pertussis endotoxin

4-O-(2-Amino-2-deoxy-alpha-D-glucopyranosyl-6-O-(2-amino-2-deoxy-alpha-D-galactopyranuronyl)-D-glucopyranose, a branched-chain trisaccharide, was isolated after hydrolysis of Bordetella pertussis endotoxin with 4 M HCl for 1 h at 100 degrees C. The trisaccharide was present in both polysaccharide moieties of the two constituent lipopolysaccharides of this endotoxin. Its structure was established by analysis of the 400-MHz nuclear magnetic resonance spectrum and by chemical and enzymatic degradation.