Characterization of superlighting polymer-DNA aggregates: a fluorescence and light scattering study

The massive amplification of fluorescence signal observed upon hybridization of as few as five DNA molecules into self-assembled structures formed between a cationic polymer and DNA oligonucleotides is investigated. These superlighting polymer-DNA aggregates were studied by fluorescence spectroscopy, static and dynamic light scattering, and zeta potential measurements in order to characterize the aggregation behavior and to understand the processes involved during DNA detection. Multi-angle laser light scattering was also used to obtain the weight-average aggregate mass (AM), the aggregation number (Nagg), the radius of gyration (Rg), and the dissymmetry ratio (z). These results have been used, together with TEM imaging, to propose a suitable physical model for the aggregates.

Optical and Photophysical Properties of Indolocarbazole Derivatives

We present a study of the optical and photophysical properties of five ladder indolo[3,2-b]carbazoles, namely, M1, M2, M3, M4, and M5. The ground-state optimized structures were obtained by B3LYP/6-31G* density functional theory (DFT) calculations, whereas the optimization (relaxation) of the first singlet excited electronic state (S1) was performed using the restricted configuration interaction (singles) (RCIS/6-31G*) approach. The excitation to the S1 state does not cause important changes in the geometrical parameters of the compounds, as corroborated by the small Stokes shifts. The excitation and emission energies have been obtained by employing the time-dependent density functional theory (TDDFT). For all the compounds, excitation to the S1 state is weakly allowed, whereas the S2 <-- S0 electronic transition of each oligomer possesses a much larger oscillator strength. The absorption and fluorescence spectra of the compounds have been recorded in chloroform. A reasonable agreement is obtained between TDDFT vertical transition energies and the (0,0) absorption and fluorescence bands. On one hand, the pattern of the aliphatic side chains does not affect the absorption and fluorescence maxima of the compounds. On the other hand, the replacement of aliphatic chains by phenyl or thiophene rings induces hypsochromic shifts in the absorption and fluorescence spectra. Finally, the fluorescence quantum yield and lifetime of the compounds in chloroform have been obtained. From these data, the radiative and nonradiative rate constants of the deactivation of the S1 state have been determined.

Reagentless Ultrasensitive Specific DNA Array Detection Based on Responsive Polymeric Biochips

Self-assembled molecular structures immobilized on solid substrates and composed of fluorophore-tagged oligonucleotide probes and an optical polymeric transducer were investigated for the trace level detection of DNA target molecules. Rapid and efficient energy transfer between the polymeric transducer and fluorophores within the molecular aggregates leads to a massive intrinsic amplification of the fluorescence signal and to the label-free detection of as little as 300 DNA molecules, with the specificity required for the detection of single-nucleotide mismatches. This capacity for attomolar detection levels while the sensing structures are attached onto solid supports could lead to the development of biochip platforms for fast and simple PCR-free multitarget DNA detection.

Optical sensors based on hybrid DNA/conjugated polymer complexes

Single-stranded DNA (ss-DNA) can specifically bind to various targets, including a complementary ss-DNA, ions, proteins, drugs, and so forth. When binding takes place, the oligonucleotide probe often undergoes a conformational transition. This conformational change of the negatively charged ss-DNA can be detected by using a water-soluble, cationic polythiophene derivative, which transduces the complex formation into an optical (colorimetric or fluorometric) signal without any labeling of the probe or the target. This simple and rapid methodology has enabled the specific and sensitive detection of nucleic acids and human thrombin. This new biophotonic tool can easily be applied to the detection of various other biomolecules and is also useful in the high-throughput screening of new drugs.

Investigation of a Fluorescence Signal Amplification Mechanism Used for the Direct Molecular Detection of Nucleic Acids

A fluorescence signal amplification mechanism allowing detection limits for DNA in the zeptomolar range was investigated. Photophysical properties of the molecular system were studied in order to better explain the signal amplification that is observed. We show that the confinement of a fluorescent DNA hybridization transducer in aggregates improves its quantum yield and photostability. Furthermore, we show that the combination of the resonance energy transfer occurring within the aggregates with the use of a conjugated polymer as the hybridization transducer and donor allows ultrafast and efficient energy coupling to the aggregates and can lead to the excitation of a large number of acceptors by only one donor.

Direct molecular detection of nucleic acids by fluorescence signal amplification

An integrated PCR-free DNA sensor, which combines a sequence-specific receptor, an optical polymeric transducer, and an intrinsic fluorescence amplification mechanism, is reported. This sensor is based on the different conformations adopted by a cationic polythiophene when electrostatically bound to ss-DNA or ds-DNA, and on the efficient and fast energy transfer between the resulting fluorescent polythiophene/ds-DNA complex and neighboring fluorophores attached to ss-DNA probes. This molecular system allows the detection of only five molecules in 3 mL of an aqueous solution, or 3 zM, in 5 min. Moreover, this work demonstrates, for the first time, the direct detection of single nucleotide polymorphisms (SNPs) from clinical samples in only a few minutes, without the need for nucleic acid amplification.

A Theoretical, Spectroscopic, and Photophysical Study of 2,7-Carbazolenevinylene-Based Conjugated Derivatives

A combined theoretical and experimental study of the structure, optical, and photophysical properties of four 2,7-carbazolenevinylene-based derivatives in solution is presented. Geometry optimizations of the ground states of PCP, PCP-CN, TCT, and TCT-CN were carried out using the density functional theory (DFT/B3LYP/6-31G*). It is found that PCP and TCT are nearly planar in their ground electronic states (S0), whereas the cyano derivatives are more twisted. The nature and the energy of the first singlet-singlet electronic transitions have been obtained from time-dependent density functional theory (TDDFT) calculations performed on the optimized geometries. For all the compounds, excitation to the S1 state corresponds mainly to the promotion of one electron from the highest-occupied molecular orbital to the lowest-unoccupied molecular orbital, and the S1 <-- S0 electronic transition is strongly allowed and polarized along the long axis of the molecular frame. The optimization (relaxation) of the first singlet excited electronic state (S1) has been done using the restricted configuration interaction (singles) (RCIS/6-31G*) approach. It is observed that all four investigated compounds become more planar in their S1 relaxed excited state. Electronic transition energies from the relaxed excited states have been obtained from TDDFT calculations performed on the S1-optimized geometries. The absorption and fluorescence spectra of the carbazolenevinylenes have been recorded in chloroform. A good agreement is obtained between TDDFT vertical transitions energies and the (0,0) absorption and fluorescence bands. The change from phenylene to thiophene rings as well as the incorporation of cyano substituents induce bathochromic shifts in the absorption and fluorescence spectra. From the analysis of the energy of the frontier molecular orbitals, it is believed that thiophene rings and CN substituents induce some charge-transfer character to the first electronic transition, which is responsible for the red shifts observed. Finally, the fluorescence quantum yield and the lifetime of the compounds in chloroform have been obtained. In sharp contrast with many oligothiophenes, it is observed that TCT possesses a high fluorescence quantum yield. On the other hand, the CN-containing derivatives exhibit much lower fluorescence quantum yields, probably due to the combined influence of steric effects and charge-transfer interactions caused by the cyano groups.

Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support

Background

Nucleic acids detection using microarrays requires labelling of target nucleic acids with fluorophores or other reporter molecules prior to hybridization.

Results

Using surface-bound peptide nucleic acids (PNA) probes and soluble fluorescent cationic polythiophenes, we show a simple and sensitive electrostatic approach to detect and identify unlabelled target nucleic acid on microarray.

Conclusion

This simple methodology opens exciting possibilities for applied genetic analysis for the diagnosis of infections, identification of genetic mutations, and forensic inquiries. This electrostatic strategy could also be used with other nucleic acid detection methods such as electrochemistry, silver staining, metallization, quantum dots, or electrochemical dyes.

A first principles calculations and experimental study of the ground- and excited-state properties of ladder oligo(p-aniline)s

The molecular structure of three ladder oligo(p-aniline)s, 5,11-diethyl-6,12-dimethylindolo[3,2-b]carbazole (DIMER 2P), 14-ethyl-5,8-dihydro-diindolo[3,2-b:2',3'-h]carbazole (TRIMER 2P), and 5,8,14-triethyl-diindolo[3,2-b:2',3'-h]carbazole (TRIMER 3P) were investigated by first principles calculations at the Hartree-Fock (HF6-31G*) and density functional theory (DFTB3LYP6-31G*) levels. It is found that the agreement between theoretical and x-ray geometrical parameters is good and rather similar for both theoretical methods. The nature and the energy of the first two singlet-singlet electronic transitions have been obtained by Zerner intermediate neglect of differential overlap/spectroscopy semiempirical calculations performed on the HF6-31G* and DFTB3LYP6-31G* optimized geometries, as well as time-dependent density functional theory (TDDFT) calculations performed on the DFTB3LYP6-31G* optimized structures. For all the compounds and for all the theoretical approaches, it is observed that the S(1)<--S(0) electronic transition (pipi*) is weakly allowed and polarized along the short axis (y) of the molecule. On the other hand, the S(2)<--S(0) electronic transition of each oligomer possesses a much larger oscillator strength and is polarized along the long (x) molecular axis. It is found that TDDFT calculations provide the best overall agreement between the energies and the corresponding optical transitions obtained from the absorption bands (0-0 peaks) measured in dichloromethane as well as providing a good evaluation of the bathochromic shifts caused by the increase in the conjugation length or by the presence of extra alkyl chains on the nitrogen atoms in TRIMER 3P compared to TRIMER 2P.

Synthesis of Diindolocarbazoles by Ullmann Reaction: A Rapid Route to Ladder Oligo(p-aniline)s

[structure: see text] New and facile synthesis of symmetric diindolocarbazoles was developed using the copper-catalyzed Ullmann reaction. The key step is a double-intramolecular cyclization reaction realized on N-alkyl-3,6-dibromo-2,7-bis(2'aminophenyl)carbazole derivatives which offers the desired symmetric ladder oligo(p-aniline)s. Depending upon the nature of the side- and/or end-groups, well-defined thin films and/or semiladder polymers could be obtained. These electroactive ladder oligomers may have great potential in organic electronics.

Spectroscopic and photophysical properties of carbazole-based triads

A study of the spectroscopy and photophysics of four carbazole-based triads, namely, 1,4-bis(N-octylcarbazol-2-yl)phenylene (CPC), 2,5-bis(N-octylcarbazol-2-yl)thiophene (CTC), 2,7-bis(N-octylcarbazol-2-yl)-9,9-dihexylfluorene (CFC), and 2,7-bis(N-octylcarbazol-2-yl)-N-octylcarbazole (CCC) are reported. From ZINDO/S calculations performed on the optimized ground state geometries (HF/6-31G*), the S1 ← S0 and S2 ← S0 electronic transitions of CPC, CFC, and CCC are weakly allowed, whereas the S3 ← S0 electronic transition is dipole-allowed (x axis) and possesses a high value of the oscillator strength. On the other hand, for CTC, the dipole-allowed electronic transition is S1 ← S0. For the four derivatives, the dipole-allowed transition corresponds mainly to the promotion of an electron from the HOMO to the LUMO. The first absorption band of each derivative can be assigned to the dipole-allowed transition. The geometry optimization of the excited states has been done with RCIS/6-31G* ab initio calculations. For CPC, CFC, and CCC, S3 is much more stabilized than S1 and S2, causing a crossing of the singlet excited states (S3 becomes lower in energy than S1 and S2). Emission energies from the first relaxed excited states (S1 → S0) have been obtained from ZINDO/S calculations performed on the optimized S1 geometries (RCIS/6-31G*). It is found that these energies are in very good agreement with those determined from the fluorescence spectra. Going from CPC to CTC, the replacement of a phenylene ring by a thiophene unit induces a red shift in the absorption and fluorescence spectra. This behavior is interpreted in terms of the electron donor properties of the thiophene ring. The increase of the oligomer chain (CFC and CCC compared to CPC) also induces bathochromic shifts in the spectra because of a longer electronic delocalization along the molecular frame. From fluorescence data, it is observed that a more planar conformation is favored in the relaxed excited states. RCIS/6-31G* ab initio calculations performed on the S1 relaxed excited states confirm this statement. Finally, the photophysical properties of CTC are mainly governed by nonradiative processes (knr), whereas the variation in the photophysics of CPC, CFC, and CCC mainly involves radiative processes (kF).Key words: electronic spectroscopy, fluorescence, photophysics, ab initio calculations, excited states.

Synthesis of Diindolocarbazoles by Cadogan Reaction: Route to Ladder Oligo(p-aniline)s

Symmetric and nonsymmetric diindolocarbazoles were successfully synthesized for the first time by a Cadogan ring closure using N-alkyl-2,7-disubstituted carbazole precursors. Cyclization reaction on N-alkyl-2,7-di(2'-nitrophenyl) carbazole derivatives is not regioselective and produced a separable mixture of symmetric and nonsymmetric diindolocarbazoles. A carbazole derivative with methyl protective groups at the 1- and 8-positions was therefore used to obtain a symmetric ladder oligo(p-aniline) (compound 22). Optical and electrochemical properties of compound 22 indicate that its neutral semiconducting form is stable in air. This novel class of electroactive ladder oligomers should create new opportunities in micro- and nanoelectronics.

Fluorescent Polymeric Transducer for the Rapid, Simple, and Specific Detection of Nucleic Acids at the Zeptomole Level

We report the specific detection of a few hundred molecules of genetic material using a fluorescent polythiophene biosensor. Such recognition is based on simple electrostatic interactions between a cationic polymeric optical transducer and the negatively charged nucleic acid target and can be done in less than 1 h, simply and affordably, and without any chemical reaction. This simple system is versatile enough to detect nucleic acids of various lengths, including a segment from the RNA genome of the Influenza virus.

Optical Sensors Based on Hybrid Aptamer/Conjugated Polymer Complexes

Single-stranded DNA (aptamer) can specifically bind potassium ions or human alpha-thrombin. When binding takes place, the aptamer undergoes a conformational transition from an unfolded to a folded structure. This conformational change of the negatively charged oligonucleotide can be detected by adding a water-soluble, cationic polythiophene derivative, which transduces the new complex formation into an optical (colorimetric or fluorometric) signal without any labeling of the probe or of the target. This simple and rapid methodology has enabled the detection of human thrombin in the femtomole range. This new biophotonic tool can easily be applied to the detection of various other proteins as well as being useful in the high-throughput screening of new drugs.