Synthesis and biological evaluation of novel neamine-nucleoside conjugates potentially targeting to RNAs

Eighteen novel neamine-nucleoside conjugates with ethylenediamine-lysine or ethylenediamine-arginine as the linker were synthesized and their potential binding to A site of 16S RNA and TAR RNA was evaluated using SPR (surface plasmon resonance). Compared with neamine, compounds 10i and 10q show 6.3 and 4.8 times potential in binding to A site of 16S RNA and eight and six times potential in binding to TAR RNA, respectively. According to the data of SPR, it indicates that amino acid residue and nucleobase moieties of the designed neamine-nucleosides conjugates exhibit the important contributions for the binding to A site of 16S RNA and TAR RNA. The molecular docking study on the interaction between the ligands and A site of 16S RNA is in agreement with the experimental data. The novel type of modification may provide a promising way for the development of neamine derivatives effectively targeting to RNAs.     

Synthesis of neamine-carboline conjugates for RNA binding and their antibacterial activities

Three types of neamine-β-carboline conjugates were synthesized in good yields by the coupling of neamine and β-carboline-3-carboxylic acids using aliphatic diamine as a linker. The binding properties of these conjugates to 16S rRNA and 18S rRNA were evaluated by surface plasmon resonance (SPR), showing that some conjugates had stronger binding affinities than neamine. In vitro antimicrobial activities were also evaluated and the results showed that some synthetic compounds exhibited better antibacterial activities than neamine. The preliminary structure-activity relationship was discussed. The present experimental data demonstrated that synthetic neamine-carboline conjugates might hold the potential as new antibiotics.     

New Fluorescent Conjugates of Uridine Nucleoside and Substituted 1,8-Naphthalimide: Synthesis, Weak Interactions and Solvent Effects on Spectra

Summary.  Novel fluorescent conjugates of uridine nucleoside and 4-dimethylamino-1,8-naphthalimide via linkage with different length, and their precursors were synthesized. Their spectroscopic properties were examined in ten different solvents. It was found that the spectroscopic properties for these conjugates are strongly dependent on polarity and hydrogen bonding ability of solvents. Their fluorescence spectra are also strongly influenced by intramolecular aromatic stacking and hydrogen bonding between the base or sugar moiety of the uridine nucleoside and naphthalimide moiety, which is controlled by the length of the linker. Corresponding author. E-mail: xhqian@dlut.edu.cn; xhqian@ecust.edu.cn Received May 27, 2002; accepted (revised) July 16, 2002     

Nucleic acid secondary structures containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine

Oligodeoxynucleotides containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine were prepared by standard solid phase synthesis. The synthetic building block for incorporating the double-headed moiety was prepared from thymidine, which was stereoselectively converted to a protected 5'(S)-C-hydroxyethyl derivative and used to alkylate the additional thymine by a Mitsunobu reaction. The oligodeoxynucleotides were studied in different nucleic acid secondary structures: duplexes, bulged duplexes, three-way junctions and artificial DNA zipper motifs. The thermal stability of these complexes was studied, demonstrating an almost uniform thermal penalty of incorporating one double-headed nucleoside moiety into a duplex or a bulged duplex, comparable to the effects of the previously reported double-headed nucleoside 5'(S)-C-(thymin-1-yl)methylthymidine. The additional base showed only very small effects when incorporated into DNA or RNA three-way junctions. The various DNA zipper arrangements indicated that extending the linker from methylene to ethylene almost completely removed the selective minor groove base-base stacking interactions observed for the methylene linker in a (-3)-zipper, whereas interactions, although somewhat smaller, were observed for the ethylene linker in a (-4)-zipper motif.     

Crucial role of linker portion in acridine-bearing oligonucleotides for highly efficient site-selective RNA scission

Through a series of linkers, 9-amino-2-methoxy-6-nitroacridine and 9-amino-6-chloro-2-methoxyacridine were tethered to the middle of oligonucleotide, and the abilities of these conjugates for site-selective activation of RNA (inducing site-selective scission by Lu(III)) were compared. The RNA-activating ability was strongly dependent on the structures of both acridine and linker. By tethering 9-amino-2-methoxy-6-nitroacridine with a rigid and chiral linker, derived from l-threoninol, quite fast site-selective RNA scission was accomplished.     

Solid-phase synthesis and evaluation of TAR RNA targeted beta-carboline-nucleoside conjugates

Four types of beta-carboline-nucleoside conjugates were synthesized. The binding affinities of these beta-carboline-nucleoside conjugates , and to TAR RNA were evaluated by affinity capillary electrophoresis. The data of binding affinities to TAR RNA show that conjugates and are stronger binders than the parent compound . Computer modeling indicates that the beta-carboline-nucleoside conjugate can fit to the UCU three-nucleotide bulge region of TAR RNA.     

Syntheses of 5′‐Nucleoside Monophosphate Derivatives with Unique Aminal,Hemiaminal, and Hemithioaminal Functionalities: A New Class of 5′‐Peptidyl Nucleotides

A number of synthetically useful transformations have been developed to generate novel 5′‐peptidyl nucleoside monophosphate analogues that incorporate sensitive phosphoaminal, ‐hemiaminal or ‐hemithioaminal functionalities. The strategies adopted entailed the coupling between dipeptides, which enclose a reactive Cα‐functionalized glycine residue and phosphate or phosphorothioate moieties. These developments led to potentially powerful and general methodologies for the preparation of α‐phosphorylated pseudopeptides as well as nucleoside monophosphate mimics. The resulting conjugates are of interest for a variety of important applications, which range from drug development to synthetic biology, as pronucleotides or artificial building blocks for the enzymatic synthesis of xenobiotic information systems. The potential of all dipeptide‐TMP conjugates as pyrophosphate mimics in the DNA polymerization reaction was tested, and the influence of the nature of the linker was evaluated by in vitro chain elongation assay in the presence of wild‐type microbial DNA polymerases.     

Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach

To explore the relationship between the assembly of the 30S ribosomal subunit and interactions among the constituent components, 16S RNA and proteins, relative binding free energies of the T. thermophilus 30S proteins to the 16S RNA were studied based on an implicit solvent model of electrostatic, nonpolar, and entropic contributions. The late binding proteins in our assembly map were found not to bind to the naked 16S RNA. The 5' domain early kinetic class proteins, on average, carry the highest positive charge, get buried the most upon binding to 16S RNA, and show the most favorable binding. Some proteins (S10/S14, S6/S18, S13/S19) have more stabilizing interactions while binding as dimers. Our computed assembly map resembles that of E. coli; however, the central domain path is more similar to that of A. aeolicus, a hyperthermophilic bacteria.     

Photosensitizer–Antibiotic Conjugates: A Novel Class of Antibacterial Molecules

Bacterial resistance to a variety of antibiotics has led to intensive research into the effect of photosensitizers as a cytotoxic agent against bacterial cells. In this study, we synthesized the following conjugates with or without a linker: rose bengal-penicillanic acid (RBPA), rose bengal-linker-penicillanic acid (RBLPA) and rose bengal-linker-kanamycin (RBLKAN). The antibacterial activity of these conjugates was examined on Staphylococcus aureus and Escherichia coli. Exposure of the cultures to 100 J cm⁻² showed that the minimum inhibitory concentration (MIC) of RBPA, RBLPA and RBLKAN on S. aureus was 0.195, 0.156 and 0.004 μm, respectively. The MIC of RBPA, RBLPA and RBLKAN on E. coli was 1.56, 2.5 and 0.156 μm, respectively. In dark control experiments, the MIC of these conjugates was not detected until a concentration that was 16-fold that of the MIC found in the light experiments. RBPA and RBLPA as well as RBLKAN are bactericidal for both bacterial cells. Total eradication of S. aureus and E. coli was observed with RBLKAN (0.078 and 20 μm 16 J cm⁻², respectively). Under these conditions, scanning electron microscopic analysis showed significant damage to these bacteria. However, the photosensitizer and antibiotics individually were not effective.     

Novel designed polymer–acyclovir conjugates with linker‐controlled drug release and hepatoma cell targeting

To develop designed polymer–drug conjugates, where the rate of drug liberation and hepatoma cell targeting function could be rationally and widely controlled, we facilely synthesized a series of novel, galactose‐functionalized polymer–acyclovir conjugates with different linkers and first reported the effect of the linker structure including the type of acyclovir‐linked bond (an ester bond or an amide bond) and relative length of the linker between acyclovir and the polymer main chain on release rate and targeting ability of conjugates. In vitro release studies showed that the cumulative released acyclovir from these polymer–acyclovir conjugates was between 24 and 65% in pH 1.2 glycine solution after 7 days. The ester bond more easily underwent hydrolysis than the amide bond. The longer the relative linker length was, the faster the acyclovir was released. The cell recognition experiments visualized using confocal laser scanning microscopy exhibited that the resultant galactose‐functionalized polymer–acyclovir conjugates had evident targeting to hepG2 cells, and targeting ability was also in connection with the relative length of linker. By choosing appropriate linker, cellular internalization of acyclovir could be well achieved. We consider these results to be helpful for the design of multifunctional polymeric prodrugs, in which the required release rate and targeting ability could be rationally controlled by predetermined molecular architecture. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 117–126, 2008     

促性腺激素释放激素类似物-紫杉醇靶向抗肿瘤缀合物的合成及评价

以促性腺激素释放激素类似物(GnRHa)为靶向配体, 以紫杉醇为抗癌因子, 分别以硫醚键和二硫键为连接臂, 设计合成了2个靶向抗肿瘤缀合物. 研究了缀合物的肿瘤细胞增殖抑制活性和GnRH受体结合活性, 结果表明, 2个缀合物均具有较强的抗肿瘤活性和GnRH受体亲和力; 另外, 血浆稳定性实验结果显示, 以硫醚键偶联的缀合物1在血浆中孵育24 h, 原型保留仍在50%以上, 具有较高的稳定性.     

Tuning urea-phenanthridinium conjugates for DNA/RNA and base pair recognition

A series of novel urea-phenanthridine conjugates was prepared. The variation of linker length connecting two urea-phenanthridinium conjugates regulated their binding mode toward double stranded polynucleotides, consequently controlling selectivity of compounds toward ds-RNA over ds-DNA stabilization as well as selective fluorescence response toward addition of G-C base pair and A-U(T) base pair containing polynucleotides.     

Quenched auto-ligating DNAs: multicolor identification of nucleic acids at single nucleotide resolution

We describe the synthesis and study of multicolor quenched autoligating (QUAL) probes for identification and discrimination of closely related RNA and DNA sequences in solution and in bacteria. In these probes, a dabsyl quencher doubles as an activator in the oligonucleotide-joining reaction. The oligonucleotides remain dark until they bind at adjacent sites, and "light up" on nucleophilic displacement of the dabsyl probe by the phosphorothioate probe. Four fluorescent dye conjugates were prepared and tested with probes and targets that differ by one nucleotide. Experiments on polymer beads show clear color-based discrimination of DNAs added in solution. Two-color quenched probe pairs were then tested in the discrimination of 16S rRNA sequences in Escherichia coli. Single nucleotide resolution was achieved in the cells with green/red QUAL probes, allowing identification of a one-base sequencing error in the 16S rRNA database. Finally, QUAL probes were successfully applied in live bacterial cells. The method requires only incubation followed by fluorescence imaging, and requires no enzymes, added reagents, cross-linking, fixing, or washes. Because probes must bind side-by-side to generate signal, there is little or no interference from unintended protein binding, which can occur with other probe types. The results suggest that QUAL probes may be of general use in the detection and identification of sequences in solution, on microarrays, and in microorganisms.     

Synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having stilbenedicarboxamide linkers

The synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having A-tract base pair domains connected by rod-like stilbenedicarboxamide linkers are reported. The nicked dumbbells have one to eight dA-dT base pairs and are missing a sugar-phosphate bond either between the linker and a thymine nucleoside residue or between two thymine residues. Chemical ligation of all of the nicked dumbbells with cyanogen bromide affords the dumbbell conjugates in good yield, providing the smallest mini-dumbbells prepared to date. The dumbbells have exceptionally high thermal stability, whereas the nicked dumbbells are only marginally more stable than the hairpin structures on either side of the nick. The structures of the nicked dumbbells and dumbbells have been investigated using a combination of circular dichroism spectroscopy and molecular modeling. The base pair domains are found to adopt normal B'-DNA geometry and thus provide a helical ruler for studies of the distance and angular dependence of electronic interactions between the chromophore linkers.     

Stabilisation of a nucleic acid three-way junction by an oligonucleotide containing a single 2'-C to 3'-O-phosphate butylene linkage prepared by a tandem RCM-hydrogenation method

A cyclic dinucleotide with a butylene linker between the upper 2'-C position and the 3'-O-phosphate linkage was synthesised from simple nucleoside building blocks via a tandem ring-closing metathesis and hydrogenation procedure. The major of two phosphorus epimers was incorporated into an oligodeoxynucleotide, as well as into an LNA-DNA mixmer oligonucleotide. These were evaluated as parts in three different secondary structures, a duplex, a bulged duplex and a three-way junction, with both DNA and RNA complements. In the DNA:RNA hybrid molecule, the oligodeoxynucleotide containing this single 2'-C to 3'-O-phosphate butylene linkage was found to stabilise a three-way junction.     

Interaction with plasmid DNA of Hoechst-TACN conjugates

ABSTRACT

A new family of conjugates between the Hoechst minor groove binder and the TACN metal ion ligand connected through hydrophobic alkyl or more hydrophilic oxyethyl linkers of different length has been prepared. The linkers are connected to the convex side of the Hoechst skeleton thus forcing the TACN ligand to exit the minor groove and interact with the phosphate backbone of DNA. The conjugates preserve the binding mode of Hoechst with an affinity influenced by the nature of the linker, the more hydrophobic being the more efficient. Coordination of Cu(II) or Zn(II) poorly affect these parameters. Nevertheless, the Zn(II) complex bearing a C6 linear alkyl linker induced a modest but reproducible acceleration of the hydrolytic cleavage of DNA which can be ascribed to the ability of the conjugate to deliver the hydrolytic subunit close to the DNA phosphodiester bonds.     

Adamantyl-substituted ligands of colchicine binding site in tubulin: different effects on microtubule network in cancer cells

Structural Chemistry - Four novel conjugates of adamantane connected at a bridgehead position via four-bond linker to structurally different ligands interacting with colchicine binding site of...     

RNA PROTEIN CROSSLINKS INTRODUCED INTO E. coli RIBOSOMES BY USE OF THE INTRINSIC PROBE 4-THIOURIDINE

Abstract— 70S Ribosome substituted by the uridine photoactivable analogue 4-thiouridine has been prepared by an in vivo method (substitution level 4.5%). The r-proteins crosslinked to 16S and 23S rRNA before and after 366-nm photoactivation were identified. Proteins S2-S7-S9/11-S18 are found linked to 16S RNA in dark-prepared 30S subunits. Illumination increases uniformly their binding by a factor of 2.5. Similarly, proteins L5-L15-L18-L23-L28-L32 are found crosslinked to 23S RNA in dark-prepared 50S subunits. Photoactivation increases their binding but in addition promotes the covalent linking of proteins L1-L3-L4.     

Synthetic dsDNA‐Binding Peptides Using Natural Compounds as Model

We have developed a series of short DNA‐binding peptides containing newly synthesized, unnatural as well as natural amino acid building blocks. By a combinatorial‐library approach, oligopeptides were developed with moderate dsDNA‐binding affinities. Two strategies were used to further enhance the binding affinity of the lead peptides: Ac‐Arg‐Ual‐Sar‐Chi‐Chi‐Chi‐Arg‐NH₂ and Ac‐Arg‐Cbg‐Cha‐Chi‐Chi‐Tal‐Arg‐NH₂. Site‐selective amino acid substitutions increased the binding affinities up to 2 × 10^?5 M . Further enhancement of the binding affinities could be achieved by coupling of an acridine intercalating unit, using linker arms of different length and flexibility. With the introduction of a new lysine‐based acridine unit, different types of oligopeptide–acridine conjugates were designed using known dsDNA‐binding ligands as model compounds. The binding capacities of these new oligopeptide–acridine conjugates have been investigated by a fluorescent intercalator (ethidium bromide) displacement (FID) assay. With the synthesis of the dipeptide–acridine conjugates, binding affinities in the low micromolar range were obtained (6.4 × 10^?6 M ), which is similar to the binding strength of the well‐known DNA binder Hoechst 33258.     

Synthesis of amine- and thiol-modified nucleoside phosphoramidites for site-specific introduction of biophysical probes into RNA

For studies of RNA structure, folding, and catalysis, site-specific modifications are typically introduced by solid-phase synthesis of RNA oligonucleotides using nucleoside phosphoramidites. Here, we report the preparation of two complete series of RNA nucleoside phosphoramidites; each has an appropriately protected amine or thiol functional group. The first series includes each of the four common RNA nucleotides, U, C, A, and G, with a 2'-(2-aminoethoxy)-2'-deoxy substitution (i.e., a primary amino group tethered to the 2'-oxygen by a two-carbon linker). The second series encompasses the four common RNA nucleotides, each with the analogous 2'-(2-mercaptoethoxy)-2'-deoxy substitution (i.e., a tethered 2'-thiol). The amines are useful for acylation and reductive amination reactions, and the thiols participate in displacement and oxidative cross-linking reactions, among other likely applications. The new phosphoramidites will be particularly valuable for enabling site-specific introduction of biophysical probes and constraints into RNA.