Sequence Effects in Conjugated Donor–Acceptor Trimers and Polymers

To investigate the sequence effect on donor–acceptor conjugated oligomers and polymers, the trimeric isomers PBP and BPP , comprising dialkoxy phenylene vinylene ( P ), benzothiadiazole vinylene ( B ), and alkyl endgroups with terminal olefins, are synthesized. Sequence effects are evident in the optical/electrochemical properties and thermal properties. Absorption maxima for PBP and BPP differ by 41 nm and the electrochemical band gaps by 0.1 V. The molar emission intensity is five times greater in PBP than BPP . Both trimers are crystalline and the melting points differ by 17 °C. The PBP and BPP trimers are used as macromonomers in an acyclic diene metathesis polymerization to give PolyPBP and PolyBPP . The optical and electrochemical properties are similar to those of their trimer precursors—sequence effects are still evident. These results suggest that sequence is a tunable variable for electronic materials and that the polymerization of oligomeric sequences is a useful approach to introducing sequence into polymers.

     

Cationic and Anionic Conjugated Polyelectrolytes: Aggregation‐Mediated Fluorescence Energy Transfer to Dye‐Labeled DNA

An electrostatic complex of water‐soluble conjugated polyelectrolytes (CPs) between anionic poly(9,9‐bis(4′‐sulfonatobutyl)fluorene‐co‐alt‐1,4‐phenylene) disodium salt (a‐PFP) and cationic poly(9,9‐bis((6′‐N,N,N,‐trimethylammonium)hexyl)fluorene‐co‐2,1,3‐bezothiadiazole) dibromide (85:15) (c‐PFB₁₅) was tested as a fluorescence resonance energy transfer (FRET) donor to Texas Red (TR)‐labeled single‐stranded DNA (ssDNA‐TR) via two‐step FRET processes. Electrostatic complexation of a‐PFP and c‐PFB₁₅ in water leads to aggregation of polymer chains, a concomitant reduction of intersegment distances, and energy transfer to the benzothiadiazole (BT) segments. The following complexation with ssDNA‐TR leads to energy transfer from BT to TR via two‐step FRET processes. This detection schematic shows an FRET‐induced signal amplification, which can be achieved by adjusting the charge ratio in the cationic/anionic CP complex and controlling the number density of the binding CPs around the acceptor, resulting in enhanced antenna effects and sensitivity in CP‐based FRET DNA detection assays.

     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

Rational Design and Synthesis of Optimized Glycoclusters for Multivalent Lectin–Carbohydrate Interactions: Influence of the Linker Arm

The design of multivalent glycoclusters requires the conjugation of biologically relevant carbohydrate epitopes functionalized with linker arms to multivalent core scaffolds. The multigram‐scale syntheses of three structurally modified triethyleneglycol analogues that incorporate amide moiety(ies) and/or a phenyl ring offer convenient access to a series of carbohydrate probes with different water solubilities and rigidities. Evaluation of flexibility and determination of preferred conformations were performed by conformational analysis. Conjugation of the azido‐functionalized carbohydrates with tetra‐propargylated core scaffolds afforded a library of 18 tetravalent glycoclusters, in high yields, by Cu^I‐catalyzed azide–alkyne cycloaddition (CuAAC). The compounds were evaluated for their ability to bind to PA‐IL (the LecA lectin from the opportunistic pathogen Pseudomonas aeruginosa). Biochemical evaluation through inhibition of hemagglutination assays (HIA), enzyme‐linked lectin assays (ELLA), surface plasmon resonance (SPR), and isothermal titration microcalorimetry (ITC) revealed improved and unprecedented affinities for one of the monovalent probes (K_d=5.8 μM ) and also for a number of the tetravalent compounds that provide several new nanomolar ligands for this tetrameric lectin.     

Self‐Assembly of Conjugated Metallopolymers with Tunable Length and Controlled Regiochemistry

Self‐assembled materials can be designed to express useful optoelectronic properties; however, achieving structural control is a necessary precondition for the optimization of desired properties. Here we report a simple, metal‐templated polymerization process that generates helical metallopolymer strands over 75 repeat units long (28 kDa) from a single bifunctional monomer and Cu^I. The resulting polymer consists of a double helix of two identical conjugated organic strands enclosing a central column of metal ions. The length of this metallopolymer can be controlled by adding monofunctional subcomponents to end‐cap the conjugated ligands. The use of ditopic and bulky monotopic subcomponents, respectively, allows a head‐to‐head or head‐to‐tail double helix to be generated. Spectroscopic measurements of different polymer lengths demonstrate how control over polymer length leads to control over the electronic and luminescent properties of the resulting material, thereby enabling tunable white‐light emission.     

Effects of Side Arm Length and Structure of Para-Substituted Phenyl Derivatives on Their Binding to the Host Cyclobis(paraquat-p-phenylene)

The binding constants with the host cyclobis(paraquat-p-phenylene), 1(4+), have been determined in CH(3)CN by UV-vis spectrophotometry for a series of p-phenylene guests, symmetrically substituted with side arms of varying length and functionality. Semiempirical molecular orbital theory was employed to provide a detailed structural and energetic interpretation of the experimental binding data. In particular, the length of the side arms and the type and position of the heteroatoms on the side arms were systematically varied in order to understand the effects of external interactions on the association constants of the guests with host 1(4+). A large chelate effect involving the ethyleneoxy side arm oxygen atoms and a cooperative effect between the guest aromatic core and the side arms are significant factors which determine the binding with this host. Sequential ethyleneoxy linkages along the side arms markedly increase the binding constant with respect to a compound in which the same number of oxygens along the side arms are separated by longer aliphatic linkages. In addition, a multiplicative rather than additive effect on the binding constant is observed which demonstrates that the oxygen atoms exhibit a strong chelate effect. It was also discovered that while the side arms of these guests contribute most of the driving force for complexation, an aromatic core is necessary for the guest to reside in the cavity of the host. The binding of these guests then is dependent upon cooperation between the arms and the aromatic core. Furthermore, elongation of the central aromatic core with aliphatic side arms containing no heteroatoms leaves the association constant relatively unchanged and replacement of the oxygen atoms with sulfur markedly decreases the observed binding. These effects have been used to rationalize several observations regarding this system in the literature and may serve to improve the design of new supramolecular systems and to better understand the host/guest interaction process.     

Vectorizing Pro-Insecticide: Influence of Linker Length on Insecticidal Activity and Phloem Mobility of New Tralopyril Derivatives

To improve the proinsecticidal activity and phloem mobility of amino acid–tralopyril conjugates further, nine conjugates were designed and synthesized by introducing glutamic acid to tralopyril, and the length of the linker between glutamic acid and tralopyril ranged from 2 atoms to 10 atoms. The results of insecticidal activity against the third-instar larvae of P. xylostella showed that conjugates 42, 43, 44,and 45 (straight-chain containing 2–5 atoms) exhibited good insecticidal activity, and their LC₅₀ values were 0.2397 ± 0.0366, 0.4413 ± 0.0647, 0.4400 ± 0.0624, and 0.4602 ± 0.0655 mM, respectively. The concentrations of conjugates 43–45 were higher than that of conjugate 42 in the phloem sap at 2 h, and conjugate 43 showed the highest concentration. The introduction of glutamic acid can improve phloem mobility. The in vivo metabolism of conjugates 42 and 43 was investigated in P. xylostella, and the parent compound tralopyril was detected at concentrations of 0.5950 and 0.3172 nmol/kg, respectively. According to the above results, conjugates 42 and 43 were potential phloem mobile pro-insecticide candidates.     

Tuning Cooperativity by Controlling the Linker Length of Silica-Supported Amines in Catalysis and CO(2) Capture

Cooperative interactions between aminoalkylsilanes and silanols on a silica surface can be controlled by varying the length of the alkyl linker attaching the amine to the silica surface from C1 (methyl) to C5 (pentyl). The linker length strongly affects the catalytic cooperativity of amines and silanols in aldol condensations as well as the adsorptive cooperativity for CO(2) capture. The catalytic cooperativity increases with the linker length up to propyl (C3), with longer, more flexible linkers (up to C5) providing no additional benefit or hindrance. Short linkers (C1 and C2) limit the beneficial amine-silanol cooperativity in aldol condensations, resulting in lower catalytic rates than with the C3+ linkers. For the same materials, the adsorptive cooperativity exhibits similar trends for CO(2) capture efficiency.     

Suppression of Delayed-type Hypersensitivity and Hemolysis Induced by Previously Photooxidized Psoralen: Effect of Fluence Rate and Psoralen Concentration

Abstract— The kinetics of the formation of biologically active psoralen photooxidation (POP) products were analyzed by the biological effects produced. Effects of the UV light fluence rate and psoralen concentration during the preir-radiation were investigated to assess the yield of POP products, which were active in vivo (inducing suppression of delayed-type hypersensitivity [DTH] reaction to sheep red blood cells) and in vitro (altering the human erythrocyte membrane permeability). It was shown that the reciprocity law of the irradiation fluence rate and time was not valid in the case of POP-induced hemolysis and DTH suppression. Immunosuppressive POP products were more efficiently formed at low fluence rate (20.8 W/m²), whereas POP hemolysins were more efficiently produced at a high fluence rate (180 W/m²) of UV light. The yield of immunosuppressive POP products was enhanced in dilute psoralen solutions, while the POP hemolysins yield increased with increasing psoralen concentration. A kinetic scheme for psoralen photoproduct formation was proposed. Kinetic analysis showed that a labile intermediate was produced as the result of excitation of psoralen. This intermediate was either converted to a stable immunosuppressive POP product, or two intermediates combined to form a POP hemolysin. It is proposed that PUVA therapy conditions are more favorable for the formation of immunosuppressive rather than membrane-damaging psoralen photooxidation products.     

Guanidinylated Amphiphilic Polycarbonates with Enhanced Antimicrobial Activity by Extending the Length of the Spacer Arm and Micelle Self‐Assembly

Nine guanidinylated amphiphilic polycarbonates are rationally designed and synthesized. Each polymer has the same biodegradable backbone but different side groups. The influence of the hydrophobic/hydrophilic effect on antimicrobial activities and cytotoxicity is systematically investigated. The results verify that tuning the length of the spacer arm between the cationic guanidine group and the polycarbonate backbone is an efficient design strategy to alter the hydrophobic/hydrophilic balance without changing the cationic charge density. A spacer arm of six methylene units (CH₂)₆ shows the best antimicrobial activity (minimum inhibitory concentration, MIC = 40 µg mL^?1 against Escherichia coli, MIC = 20 µg mL^?1 against Staphylococcus aureus, MIC = 40 µg mL^?1 against Candida albicans) with low hemolytic activity (HC₅₀ > 2560 µg mL^?1). Furthermore, the guanidinylated polycarbonates exhibit the ability to self‐assemble and present micelle‐like nanostructure due to their intrinsic amphiphilic macromolecular structure. Transmission electron microscopy and dynamic light scattering measurements confirm polymer micelle formation in aqueous solution with sizes ranging from 82 to 288 nm.     

Photoreaction of New Psoralen Analogs with DNA: Sequence and Mutation Specificity in the Escherichia coli lacZ Gene

New thio- and seleno-analogs of psoralen were synthesized and analyzed for their photoreactivity toward DNA. Using oligonucleotides of denned sequence, we first showed that these derivatives predominantly generated interstrand crosslinks at 5′-TpA sites. We also observed a surprisingly high reactivity of 7H-thiopyrano[3,2-f][l]benzofuran-7-one (PSO[0-S]) with the BamHl and PstI oligomers, giving rise to the formation of crosslinks at 5′-ApT sites and of the thymidine-psoralen-cytosine type. Next, the sequence specificity in the photochemical binding of all the compounds was investigated in two DNA fragments encompassing the lacZ gene of Escherichia coli, using the T₄ DNA polymerase sequencing methodology. Resulting maps demonstrated that thio-and seleno-analogs of psoralen preferentially photoreact-ed with thymine and cytosine residues. The AT-rich sequences proved to be particularly reactive sites as did adjacent thymines, especially at C-surrounding residues. Likewise, photoaddition at cytosines in CA/AC context was observed. It was highly significant that all of the derivatives exhibited similar sequence specificities with only minor differences. However, PSO(O-S) differed from the other heteropsoralens. Photoadducts occurred with a higher frequency at AC and CA dinucleotides, and new sites were detected. A comparison with 8-methoxypsor-alen photobinding is also reported. Finally, the mutagenic consequences of photoadducts induced in M13mp19 DNA by PSO(O-S) were determined in a forward system that detects all classes of mutagenic events. The high phototoxicity exhibited by PSO(O-S) could be attributed to crosslinks, and the comparison of the observed mutational specificity with the photoadduct distribution within the same gene showed that mutations were targeted at potential monoadduct sites where photolesions were detected in our footprinting experiments     

Development of Phosphoramidite Reagents for the Synthesis of Base-Labile Oligonucleotides Modified with a Linear Aminoalkyl and Amino-PEG Linker at the 3′-End

Oligonucleotides with an amino linker at the 3′-end are useful for the preparation of conjugated oligonucleotides. However, chemically modified nucleosides, which are unstable under basic conditions, cannot be incorporated into oligonucleotides using the conventional method entailing the preparation of oligonucleotides bearing a 3′-amino linker. Therefore, we designed Fmoc-protected phosphoramidites for the synthesis of base-labile oligonucleotides modified with a 3′-amino linker. The resultant phosphoramidites were then successfully incorporated into oligonucleotides bearing a 3′-amino linker. Various basic solutions were investigated for protecting group removal. All the protecting groups were removed by treating the oligonucleotides with 40% aqueous methylamine at room temperature for 2 h. Thus, the deprotection time and temperature were significantly reduced compared to the conventional conditions (28% NH₃ aq., 55 °C, 17 h). In addition, the oligonucleotide protecting groups could be removed using a mild base (e.g., 50 mM potassium carbonate methanol solution). Furthermore, base-labile oligonucleotides bearing an amino linker at the 3′-end were successfully synthesized using the developed phosphoramidite reagents, highlighting the utility of our strategy.     

Oligonucleotides Functionalized by Fluorescein and Rhodamine Dyes: Michael Addition of Methyl Acrylate to 2′‐Deoxypseudouridine

The 2′‐deoxypseudouridine ( 5 ) was functionalized at N(1) with methyl acrylate by Michael addition. The resulting methyl 2′‐deoxypseudouridine‐1‐propanoate ( 6 ) was converted to the phosphoramidite 8 and to the amino‐functionalized derivative 9 , which was transformed into the fluorescein‐labeled phosphoramidites 14 and 16 . Fluorescent oligonucleotides were synthesized either from these building blocks or by post‐synthetic modification of oligomers containing 2′‐deoxypseudouridine subunits. The stability of oligonucleotide duplexes was determined from the melting profiles, measured by UV‐ or VIS‐light absorbance, as well as from the fluorescence emission spectra. While small spacer residues did not affect the thermal stability of the 2′‐deoxypseudouridine‐containing duplexes, large dye residues led to destabilization.     

Oligonucleotides Containing 7-Deazaadenines: The Influence of the 7-Substituent Chain Length and Charge on the Duplex Stability

Oligonucleotides carrying alkynyl and aminoalkynyl chains at the position 7 of 7-deazaadenine are synthesized, and the chain lengths as well as the bulkiness of the substituents are varied. The corresponding nucleosides 1a – f are prepared from 7-deaza-2′-deoxy-7-iodoadenosine and the particular alkynes by the Pd⁰-catalyzed cross-coupling reaction. The nucleosides are converted to the phosphoramidites 2a – f , which are used in solid-phase oligonucleotide synthesis. The stability of the duplexes is determined by the T_m values and the thermodynamic data. Compared to adenine or the unsubstituted 7-deazaadenine, the incorporation of a 7-ethynyl chain in a 7-deazaadenine moiety increases the duplex stability significantly, while a dodecynyl residue or a bulky steroid moiety leads to a duplex destabilization. A 3-aminoprop-1-ynyl residue (see 1g ) or a 5-aminopent-1-ynyl residue (see 1h ), which are charged under neutral conditions, lead to zwitterionic DNA. A high density of charged residues as found in homomers impairs duplex formation, most probably by counter-ion condensation.