A convenient ‘click chemistry’ approach to perylene diimide-oligonucleotide conjugates

Terminal alkyne-containing phosphoramidite and solid support were prepared and used for the synthesis of 5′- and 3′-alkyne-modified oligonucleotides. The copper-catalyzed Huisgen [3+2] cycloaddition reaction in water-DMSO was used for the efficient preparation of perylene diimide-oligonucleotide conjugates suitable for constructing various types of PDI-modified DNA duplexes.     

Pathway-dependent self-assembly of perylene diimide/peptide conjugates in aqueous medium

Most molecular self-assembly strategies involve equilibrium systems, leading to a single thermodynamic product as a result of weak, reversible non-covalent interactions. Yet, strong non-covalent interactions may result in non-equilibrium self-assembly, in which structural diversity is achieved by forming several kinetic products based on a single covalent building block. We demonstrate that well-defined amphiphilic molecular systems based on perylene diimide/peptide conjugates exhibit kinetically controlled self-assembly in aqueous medium, enabling pathway-dependent assembly sequences, in which different organic nanostructures are evolved in a stepwise manner. The self-assembly process was characterized using UV/Vis circular dichroism (CD) spectroscopy, and cryogenic transmission electron microscopy (cryo-TEM). Our findings show that pathway-controlled self-assembly may significantly broaden the methodology of non-covalent synthesis.     

Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates

BACKGROUND: Pyrrole-imidazole polyamides are synthetic ligands that recognize predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA-binding proteins. As a result of their DNA-binding properties, polyamides could deliver reactive moieties for covalent reaction at specific DNA sequences and thereby inhibit DNA-protein interactions. Site-specific alkylation of DNA could be a useful tool for regulating gene expression. As a minimal first step, we set out to design and synthesize a class of hairpin polyamides equipped with DNA alkylating agents and characterize the specificity and yield of covalent modification. RESULTS: Bis(dichloroethylamino)benzene derivatives of the well-characterized chlorambucil (CHL) were attached to the gamma turn of an eight-ring hairpin polyamide targeted to the HIV-1 promoter. We found that a hairpin polyamide-CHL conjugate binds and selectively alkylates predetermined sites in the HIV promoter at subnanomolar concentrations. Cleavage sites were determined on both strands of a restriction fragment containing the HIV-1 promoter, revealing good specificity and a high yield of alkylation. CONCLUSIONS: The ability of polyamide-CHL conjugates to sequence specifically alkylate double-stranded DNA in high yield and at low concentrations sets the stage for testing their use as regulators of gene expression in cell culture and ultimately in complex organisms.     

Reversible formation of DNA G-quadruplex hairpin dimers from stilbenediether conjugates

Rapid and reversible G-quadruplex hairpin dimer formation is observed for bis(oligonucleotide) conjugates possessing stilbenediether (Sd) linkers connecting two short poly(G) sequences.     

Reliable structures and energetics for two new delocalized pi...pi prototypes: cyanogen dimer and diacetylene dimer

Two new prototype delocalized pi[dot dot dot]pi complexes are introduced: the dimers of cyanogen, (N[triple bond]C-C[triple bond]N)(2), and diacetylene, (HC[triple bond]C-C[triple bond]CH)(2). These dimers have properties similar to larger delocalized pi...pi systems such as benzene dimer but are small enough that they can be probed in far greater detail with high accuracy electronic structure methods. Parallel-slipped and T-shaped structures of both cyanogen dimer and diacetylene dimer have been optimized with 15 different procedures. The effects of basis set size, theoretical method, counterpoise correction, and the rigid monomer approximation on the structure and energetics of each dimer have been examined. MP2 and CCSD(T) optimized geometries for all four dimer structures are reported, as well as estimates of the CCSD(T) complete basis set (CBS) interaction energy for every optimized geometry. The data reported here suggest that future optimizations of delocalized pi[dot dot dot]pi clusters should be carried out with basis sets of triple-zeta quality. Larger basis sets and the expensive counterpoise correction to the molecular geometry are not necessary. The rigid monomer approximation has very little effect on structure and energetics of these dimers and may be used without consequence. Due to a consistent cancellation of errors, optimization with the MP2 method leads to CCSD(T)/CBS interaction energies that are within 0.2 kcal mol(-1) of those for structures optimized with the CCSD(T) method. Future studies that aim to resolve structures separated by a few tenths of a kcal mol(-1) should consider the effects of optimization with the CCSD(T) method.     

Structural,photoelectrical and thermol properties of ultra-stable Benzo[ghi]perylene trimide dimer anion

Perylene diimide and its various derivatives tend to form stable anion radicals, which can usually form a variety of aggregates with special properties. Herein, we reported synthesis and properties of the benzo[ghi]perylene trimide and its anion radical π-bonded dimer. The dimer exhibited high stable in solid status and in most organic solvents, but conversion of L-type π-bonded dimer to face to face type π-bonded dimer or π-stacked oligomer occurs in dimethyl formamide solution. The temperature and crystallization influenced the π-bonded length in the dimer and the partial memory can be reserved and probed in solution at room temperature.     

Charge-transfer and spin dynamics in DNA hairpin conjugates with perylenediimide as a base-pair surrogate

A perylenediimide chromophore (P) was incorporated into DNA hairpins as a base-pair surrogate to prevent the self-aggregation of P that is typical when it is used as the hairpin linker. The photoinduced charge-transfer and spin dynamics of these hairpins were studied using femtosecond transient absorption spectroscopy and time-resolved EPR spectroscopy (TREPR). P is a photooxidant that is sufficiently powerful to quantitatively inject holes into adjacent adenine (A) and guanine (G) nucleobases. The charge-transfer dynamics observed following hole injection from P into the A-tract of the DNA hairpins is consistent with formation of a polaron involving an estimated 3-4 A bases. Trapping of the (A 3-4) (+*) polaron by a G base at the opposite end of the A-tract from P is competitive with charge recombination of the polaron and P (-*) only at short P-G distances. In a hairpin having 3 A-T base pairs between P and G ( 4G), the radical ion pair that results from trapping of the hole by G is spin-correlated and displays TREPR spectra at 295 and 85 K that are consistent with its formation from (1*)P by the radical-pair intersystem crossing mechanism. Charge recombination is spin-selective and produces (3*)P, which at 85 K exhibits a spin-polarized TREPR spectrum that is diagnostic of its origin from the spin-correlated radical ion pair. Interestingly, in a hairpin having no G bases ( 0G), TREPR spectra at 85 K revealed a spin-correlated radical pair with a dipolar interaction identical to that of 4G, implying that the A-base in the fourth A-T base pair away from the P chromophore serves as a hole trap. Our data suggest that hole injection and transport in these hairpins is completely dominated by polaron generation and movement to a trap site rather than by superexchange. On the other hand, the barrier for charge injection from G (+*) back onto the A-T base pairs is strongly activated, so charge recombination from G (or even A trap sites at 85 K) most likely proceeds by a superexchange mechanism.     

Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.     

Four-way-branched DNA-porphyrin conjugates for construction of four double-helix-DNA assembled structures

[reaction: see text] DNA-porphyrin conjugates having four DNA strands were designed and synthesized. Four double helices were assembled using two DNA-porphyrin conjugates and their complementary strands, and the formation of the four double-helix assembled structures with the two DNA-porphyrin units was examined by gel electrophoresis and spectroscopic analysis. The interaction between two porphyrin chromophores in the complex was investigated by measurement of fluorescence lifetimes, and the singlet energy transfer between the two different phorphyrin units (Zn-porphyrin and H2-porphyrin) was observed. These results indicate that multiple and different porphyrin chromophores can be integrated into the DNA structures by programming the sequences of the DNA strands.     

Beyond exciton theory: a time-dependent DFT and Franck-Condon study of perylene diimide and its chromophoric dimer

The diimide perylene motif exhibits a dramatic intensity reversal between the 0 --> 0 and 0 --> 1 vibronic bands upon pi-pi stacking; this distinct spectral property has previously been used to measure folding dynamics in covalently bound oligomers and synthetic biological hybrid foldamers. It is also used as a tool to assess organization of the pi-stacking, indicating the presence of H- or J-aggregation. The zeroth-order exciton model, often used to describe the optical properties of chromophoric aggregates, is solely a transition dipole coupling scheme, which ignores the explicit electronic structure of the system as well as vibrational coupling to the electronic transition. We have therefore examined the optical properties of gas-phase perylene tetracarboxylic diimide (PTCDI) and its chromophoric dimer as a function of conformation to relate the excited-state distributions predicted by exciton theory with that of time-dependent density functional theory (TDDFT). Using ground- and excited-state geometries, the Franck-Condon (FC) factors for the lowest energy molecular nature electronic transition have been calculated and the origin of the intensity reversal of 0 --> 0 and 0 --> 1 vibronic bands has been proposed.     

Novel fluorescent dyes with fused perylene tetracarboxlic diimide and BODIPY analogue structures

Two novel fluorescent dyes based on perylene tetracarboxylic diimides and BODIPY were designed and synthesized. Significant features, such as longer wavelength absorption and emission, high fluorescence quantum yields, and strong electron accepting abilities, are observed for these compounds.     

Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates

The thermal stability and conformational dynamics of DNA hairpin and dumbbell conjugates having short A-tract base pair domains connected by tri- or hexa(ethylene glycol) linkers is reported. The formation of stable base-paired A-tract hairpins having oligo(ethylene glycol) linkers requires a minimum of four or five A-T base pairs. The formation of base-paired dumbbells having oligo(ethylene glycol) linkers by means of chemical ligation of nicked dumbbells requires a minimum of two A-T base pairs on either side of the nick. Molecular modeling indicates that the hexa(ethylene glycol) linker is sufficiently long to permit formation of strain-free loop regions and B-DNA base pair domains. In contrast, the tri(ethylene glycol) is too short to permit Watson-Crick base pairing between the bases attached to the linker. The shorter linker distorts the duplex, resulting in fluxional behavior in which the base pairs adjacent to the linker and at the open end of the hairpin dissociate on the nanosecond time scale. The loss of interstrand binding energy caused by these fluctuations leads to a difference of approximately 5 degrees C in melting temperature between EG3 and EG6 hairpins. An analysis of the fluxional behavior of the EG3 adjacent base-pair has been used to study the pathways for base flipping and base stacking, including the identification of rotated base (partially flipped) intermediates that have not been described previously for A-T base pairs.     

New cyanine-oligonucleotide conjugates: relationships between chemical structures and properties

Because the influence of the chemical structure of monomethine cyanine-oligo-2'-deoxyribonucleotide (ODN) conjugates on their binding and fluorescence properties has remained largely undetermined, we synthesized and studied a wide range of conjugates with various structural patterns. Different cyanine dyes such as thiocyanine, quinocyanine, and thiazole orange isomers were obtained. In the case of unsymmetrical cyanines, the linker was attached to either the quinoline or the benzothiazole nucleus. The influence of the ODN counterpart was evaluated by linking the cyanines to the 5'-end or to an internucleotidic phosphate. In the first case, the influence of neighboring nucleic bases was studied, whereas in the second, the stereochemical configuration at the phosphorus atom bearing the cyanine was investigated. We report here on relationships between the structures of the dyes and conjugates and some of their properties, such as the stability and fluorescence changes observed on their hybridization with the target sequence. This study provides useful information towards the design of ODN-cyanine conjugates.     

Naphthalene and perylene diimides for organic transistors

The development of ambient stable organic n-channel semiconductor molecules for thin-film transistors has experienced a tremendous impetus in the last decade to close the gap in performance in comparison to that of their p-channel counterparts. Especially naphthalene and perylene tetracarboxylic diimides (NDI and PDI) have shown to be the most valuable building blocks to achieve this challenging goal and to gain insight into the molecular structure-transistor performance relationship. Remaining challenges and new emerging research fields for these n-type semiconductors are the optimization of their deposition on flexible substrates, the control of their long term ambient stability and their implementation in complementary transistor circuits, display and sensor devices.     

Structure and dynamics of photogenerated triplet radical ion pairs in DNA hairpin conjugates with anthraquinone end caps

A series of DNA hairpins (AqGn) possessing a tethered anthraquinone (Aq) end-capping group were synthesized in which the distance between the Aq and a guanine-cytosine (G-C) base pair was systematically varied by changing the number (n - 1) of adenine-thymine (A-T) base pairs between them. The photophysics and photochemistry of these hairpins were investigated using nanosecond transient absorption and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. Upon photoexcitation, (1*)Aq undergoes rapid intersystem crossing to yield (3*)Aq, which is capable of oxidizing purine nucleobases resulting in the formation of (3)(Aq(-?)Gn(+?)). All (3)(Aq(-?)Gn(+?)) radical ion pairs exhibit asymmetric TREPR spectra with an electron spin polarization phase pattern of absorption and enhanced emission (A/E) due to their different triplet spin sublevel populations, which are derived from the corresponding non-Boltzmann spin sublevel populations of the (3*)Aq precursor. The TREPR spectra of the (3)(Aq(-?)Gn(+?)) radical ion pairs depend strongly on their spin-spin dipolar interaction and weakly on their spin-spin exchange coupling. The anisotropy of (3)(Aq(-?)Gn(+?)) makes it possible to determine that the π systems of Aq(-?) and G(+?) within the radical ion pair are parallel to one another. Charge recombination of the long-lived (3)(Aq(-?)Gn(+?)) radical ion pair displays an unusual bimodal distance dependence that results from a change in the rate-determining step for charge recombination from radical pair intersystem crossing for n < 4 to coherent superexchange for n > 4.     

Electronic structures and stabilities of sodium clusters: jellium-sphere dimer calculation

Bonding properties of sodium-cluster dimers, (X ₄)₂ and (X ₈)₂, whereX _n is a jellium sphere corresponding to a cluster ofn atoms, were investigated by the linear-combination-of-jellium-orbitals method with local-spin-density-functional approximation. The stability ofn=8 clusters, observed in the experiment, is discussed in relation to the binding properties of dimers. We have found that (1) the (X ₄)₂ bonding has a covalent character, which makes theX ₈ formation favorable, and (2)X ₈ has an inert property because the force between jellium spheres in (X ₈)₂ is due to a weak dispersion force.     

Supramolecularly engineered perylene bisimide assemblies exhibiting thermal transition from columnar to multilamellar structures

Perylene 3,4:9,10-tetracarboxylic acid bisimide (PBI) was functionalized with ditopic cyanuric acid to organize it into complex columnar architectures through the formation of hydrogen-bonded supermacrocycles (rosette) by complexing with ditopic melamines possessing solubilizing alkoxyphenyl substituents. The aggregation study in solution using UV-vis and NMR spectroscopies showed the formation of extended aggregates through hydrogen-bonding and π-π stacking interactions. The cylindrical fibrillar nanostructures were visualized by microscopic techniques (AFM, TEM), and the formation of lyotropic mesophase was confirmed by polarized optical microscopy and SEM. X-ray diffraction study revealed that a well-defined hexagonal columnar (Col(h)) structure was formed by solution-casting of fibrillar assemblies. All of these results are consistent with the formation of hydrogen-bonded PBI rosettes that spontaneously organize into the Col(h) structure. Upon heating the Col(h) structure in the bulk state, a structural transition to a highly ordered lamellar (Lam) structure was observed by variable-temperature X-ray diffraction, differential scanning calorimetry, and AFM studies. IR study showed that the rearrangement of the hydrogen-bonding motifs occurs during the structural transition. These results suggest that such a striking structural transition is aided by the reorganization in the lowest level of self-organization, i.e., the rearrangement of hydrogen-bonded motifs from rosette to linear tape. A remarkable increase in the transient photoconductivity was observed by the flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements upon converting the Col(h) structure to the Lam structure. Transient absorption spectroscopy revealed that electron transfer from electron-donating alkoxyphenyl groups of melamine components to electron-deficient PBI moieties takes place, resulting in a higher probability of charge carrier generation in the Lam structure compared to the Col(h) structure.