Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout.

By using (S)-2-amino-1,3-propanediol as a linker, thiazole orange (TO) was incorporated in a dimeric form into DNA. The green fluorescence (λ=530 nm) of the intrastrand TO dimer is quenched, whereas the interstrand TO dimer shows a characteristic redshifted orange emission (λ=585 nm). Steady-state optical spectroscopic methods reveal that the TO dimer fluorescence is independent of the sequential base contexts.

Subnanosecond, mid-IR, 0.5 kHz periodically poled stoichiometric LiTaO3 optical parametric oscillator with over 1 W average power.

We report a subnanosecond mid-IR tunable optical parametric oscillator based on periodically poled stoichiometric lithium tantalate (PPSLT), pumped by an amplified single frequency microchip laser at 1064 nm at a repetition rate of 0.5 kHz. Using a 20 mm long PPSLT crystal polled with three different domain periods (30.

Broadband femtosecond circular dichroism spectrometer with white-light polarization control.

A broadband, femtosecond transient circular dichroism (TRCD) spectrometer has been developed and tested in the wavelength range from 350 to 700 nm. The spectrometer uses a femtosecond probe white light with well-defined circular polarization. The latter is modulated by the polarization of a narrowband seed pulse.

Dynamics and efficiency of electron injection and transport in DNA using pyrenecarboxamide as an electron donor and 5-bromouracil as an electron acceptor.

The photophysical and photochemical behavior of a series of hairpin-forming DNA conjugates possessing a 5'-tethered pyrenecarboxamide chromophore and one or two bromouracil bases has been investigated. Quenching of the pyrene fluorescence and transient absorption spectra characteristic of the pyrene cation radical are observed only when bromouracil is located at the first or second base pair position nearest to the point of pyrene attachment. These observations are consistent with an intercalated structure for these conjugates in which pyrene is adjacent to the second base pair.

Structure and photoinduced electron transfer in DNA hairpin conjugates possessing a tethered 5'-pyrenecarboxamide.

The structure, spectroscopy, and photophysical behavior of a series of hairpin-forming conjugates possessing a 5'-tethered N-alkylpyrenecarboxamide chromophore have been investigated. Comparison of the NMR spectra of the conjugates and analogs lacking the tethered pyrene indicates that the pyrene does not behave as an end-capping group but rather is intercalated between the two terminal hairpin base pairs. An intercalated structure is also consistent with the thermodynamic parameters for hairpin formation and the steady state and transient spectral properties of the conjugates.

Photoinduced charge separation in pyrenedicarboxamide-linked DNA hairpins.

The synthesis and photophysical properties of the dihydroxypropylamide derivative of pyrene-1,6-dicaboxamide, its aniline dyad, and DNA conjugates are reported. The dicarboxamide serves as a hairpin linker for bis(oligonucleotide) conjugates having short base pair stems. The dihydroxypropyl derivative has a large fluorescence quantum yield and long singlet decay time, as determined by fluorescence and time-resolved broad band pump-probe spectroscopy.

Getting to guanine: mechanism and dynamics of charge separation and charge recombination in DNA revisited.

The mechanism and dynamics of charge separation and charge recombination in synthetic DNA hairpins possessing a stilbenedicarboxamide linker and a single guanine-cytosine base pair have been reinvestigated. The combination of femtosecond broad-band pump probe spectroscopy, nanosecond transient absorption experiments, and picosecond fluorescence decay measurements permits analysis of the formation and decay of the stilbene anion radical. Reversible hole injection resulting in the formation of the stilbene-adenine contact radical ion pair is found to occur on the picosecond time scale.

Reversible bridge-mediated excited-state symmetry breaking in stilbene-linked DNA dumbbells.

The excited-state behavior of synthetic DNA dumbbells possessing stilbenedicarboxamide (Sa) linkers separated by short A-tracts or alternating A-T base-pair sequences has been investigated by means of fluorescence and transient absorption spectroscopy. Electronic excitation of the Sa chromophores results in conversion of a locally excited state to a charge-separated state in which one Sa is reduced and the other is oxidized. This symmetry-breaking process occurs exclusively via a multistep mechanism-hole injection followed by hole transport and hole trapping-even at short distances.

Ultrafast energy delocalization and electron transfer dynamics in 2-aminopurine-containing trinucleotides.

The fate of electronically excited states in DNA base stacks is of tremendous importance for subsequent photochemical damage reactions in the genome. In this study we present a femtosecond broadband pump-probe study on the adenine isomer 2-aminopurine (Ap) incorporated into trinucleotides. After selective excitation of Ap we can monitor energy delocalization between neighboring Ap moieties as well as excited state electron transfer, depending on the sequence of the trinucleotide.

Toward an understanding of white-light generation in cubic media - polarization properties across the entire spectral range.

We present an extensive investigation of the polarization properties of a femtosecond-laser-induced white-light (WL) continuum generated in a cubic crystal (CaF(2)). The WL spectrum and threshold energies have been examined for input polarizations with various degrees of ellipticity. For linear input polarization, the WL spectrum shows strong depolarization around the input wavelength, while the preservation of the input polarization is pronounced toward the blue spectral region.

Electronic energy delocalization and dissipation in single- and double-stranded DNA.

The mechanism that nature applies to dissipate excess energy from solar UV light absorption in DNA is fundamental, because its efficiency determines the vulnerability of all genetic material to photodamage and subsequent mutations. Using femtosecond time-resolved broadband spectroscopy, we have traced the electronic excitation in both time and space along the base stack in a series of single-stranded and double-stranded DNA oligonucleotides. The obtained results demonstrate not only the presence of delocalized electronic domains (excitons) as a result of UV light absorption, but also reveal the spatial extent of the excitons.

Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer.

In 1999, Wan et al. [Proc. Natl.

Dynamics and mechanism of bridge-dependent charge separation in pyrenylurea-nitrobenzene pi-stacked protophanes.

Herein are reported the synthesis, structure, and electronic properties of a series of tertiary di- and polyarylureas possessing pyrene and nitrobenzene end groups separated by a variable number of internal phenylenediamine bridging groups. These molecules adopt folded "protophane" structures in which the adjacent arenes are loosely pi-stacked. The behavior of both the pyrene and nitrobenzene singlet states has been investigated by means of femtosecond broadband pump-probe spectroscopy, and the transients have been assigned on the basis of comparison to reference molecules.

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.

Photoinduced charge transfer processes along triarylamine redox cascades.

In this paper, we describe the synthesis and photophysical properties of a series of acridine-triarylamine redox cascades. These cascades were designed in order to promote photoinduced hole transfer from an acridine fluorophore into an adjacent triarylamine. The excited dipolar state then injects a hole into the triarylamine redox cascade.

Ultrafast proton-coupled electron-transfer dynamics in pyrene-modified pyrimidine nucleosides: model studies towards an understanding of reductive electron transport in DNA.

5-(Pyren-1-yl)-2'-deoxyuridine (PydU) and 5-(Pyren-1-yl)-2'-deoxycytidine (PydC) were used as model nucleosides for DNA-mediated reductive electron transport (ET) in steady-state fluorescence and femtosecond time-resolved transient absorption spectroscopy studies. Excitation of the pyrene moiety in PydU and PydC leads to an intramolecular electron transfer that yields the pyrenyl radical cation and the corresponding pyrimidine radical anion (dU.- and dC.

Pyrene as a fluorescent probe for DNA base radicals.

The steady-state emission spectra of 5-(1-pyrenyl)-modified pyrimidine and 8-(1-pyrenyl)-modified purine nucleosides in water at different pH values provide important information about the acidity or basicity of photochemically generated DNA base radicals which are key intermediates in DNA-mediated charge transport processes.

Femtosecond charge transfer dynamics of a modified DNA base: 2-aminopurine in complexes with nucleotides.

As a fluorescent isomer of adenine, 2-aminopurine (Ap) is a powerful probe of DNA dynamics and DNA-mediated charge transfer processes. Here, we report studies with femtosecond resolution of the excited-state dynamics of Ap in various solvents and in bimolecular complexes with nucleotides. Using time-resolved transient absorption and fluorescence up-conversion methods we identify charge transfer as the origin for the quenching of the Ap fluorescence by all four DNA nucleotides.

Electron injection into DNA: synthesis and spectroscopic properties of pyrenyl-modified oligonucleotides.

The nucleoside 5-(1-pyrenyl)-2'-deoxyuridine (1) was prepared by a Suzuki-Miyaura cross-coupling reaction and subsequently used as a DNA building block in order to prepare a range of modified oligonucleotides using phosphoramidite chemistry. The DNA duplexes contain a pyrenyl group covalently attached to the nucleobase uracil. Upon excitation at 340 nm an intramolecular electron transfer from the pyrenyl group to the uracil moiety takes place which represents an injection of an excess electron into the DNA base stack.

Reactivities of methylenetriangulanes and spirocyclopropanated bicyclopropylidenes toward bromine. Relative stabilities of spirocyclopropanated versus methyl-substituted bromonium ions.

The bromine additions to methylenecyclopropane (1), bicyclopropylidene (2), and spirocyclopropanated methylenecyclopropanes and bicyclopropylidenes 3-6 in methanol at 25 degrees C proceed essentially with the same rate as those to the corresponding oligomethyl-substituted ethylenes. An increasing number of spiroannelated three-membered rings enhances the rate of bromination and stabilizes the intermediate cyclopropyl bromonium cations against ring opening in the course of bromine addition. Calculations at the B3LYP/6-311G(d,p) level show that unsymmetrical bromonium ions are the intermediates, and that they are stabilized by the spiroannelation with cyclopropane rings.