[Show abstract][Hide abstract] ABSTRACT: The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template-primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd's range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.
Nucleic Acids Research 05/2014; · 8.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Several difurylperfluorocyclobutenes showing reversible photochromism were synthesized. In comparison to their cyclopentene homologues they show enhanced quantum yields for ring opening but reduced quantum yields for ring closure. X-ray structure analysis and quantum chemical calculations provide a conclusive explanation for such a behaviour.
Chemical Communications 10/2012; 48(92):11355-7. · 6.38 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We report on the experimental analysis of the charge transport through single-molecule junctions of the open and closed isomers of photoswitching molecules. Sulfur-free diarylethene molecules are developed and studied via electrical and optical measurements as well as density functional theory calculations. The single-molecule conductance and the current-voltage characteristics are measured in a mechanically controlled break-junction system at low temperatures. Comparing the results with the single-level transport model, we find an unexpected behavior of the current-dominating molecular orbital upon isomerization. We show that both the side chains and end groups of the molecules are crucial to understand the charge transport mechanism of photoswitching molecular junctions.
[Show abstract][Hide abstract] ABSTRACT: The yield of chemical reactions involving intermediate radical pairs is
influenced by magnetic fields well beyond the levels expected from energy
considerations. This dependence can be traced back to the microscopic dynamics
of electron spins and constitutes the basis of the chemical compass. Here we
propose a new experimental approach based on molecular photoswitches to achieve
additional control on the chemical reaction and to allow short-time resolution
of the spin dynamics. Our proposal enables experiments to test some of the
standard assumptions of the radical pair model and improves the sensitivity of
chemical magnetometers by two orders of magnitude.
[Show abstract][Hide abstract] ABSTRACT: In theories of spin-dependent radical pair reactions, the time evolution of the radical pair, including the effect of the chemical kinetics, is described by a master equation in the Liouville formalism. For the description of the chemical kinetics, a number of possible reaction operators have been formulated in the literature. In this work, we present a framework that allows for a unified description of the various proposed mechanisms and the forms of reaction operators for the spin-selective recombination processes. On the basis of the concept that master equations can be derived from a microscopic description of the spin system interacting with external degrees of freedom, it is possible to gain insight into the underlying microscopic processes and develop a systematic approach toward determining the specific form of the reaction operator in concrete scenarios.
The Journal of Physical Chemistry A 03/2012; 116(16):4020-8. · 2.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Recently, photoswitchable molecules, i.e. diarylethene, gained
significant interest due to their applicability in data storage media,
as optical switches, and in novel logic circuits .
Diarylethene-derivative molecules are the most promising candidates to
design electronic functional elements, because of their excellent
thermal stability, high fatigue resistance, and negligible change upon
switching . Here, we present the preferential conductance of
specifically designed sulfur-free diarylethene molecules  bridging
the mechanically controlled break-junctions at low temperatures . The
molecular energy levels and electrode couplings are obtained by
evaluating the current-voltage characteristics using the single-level
model . The charge transport mechanism of different types of
diarylethene molecules is investigated, and the results are discussed
within the framework of novel theoretical predictions. [4pt]  M. Del
Valle etal., Nat Nanotechnol 2, 176 (2007) S. J. van der Molen etal.,
Nano. Lett. 9, 76 (2009).[0pt]  D. Sysoiev etal., Chem. Eur. J. 17,
6663 (2011).[0pt]  Y. Kim etal., Phys. Rev. Lett. 106, 196804
(2011).[0pt]  Y. Kim etal., Nano Lett. 11, 3734 (2011). L. Zotti
etal., Small 6, 1529 (2010).
[Show abstract][Hide abstract] ABSTRACT: The kinetic rate equation for the photosensitized cleavage reaction of surface-bound photolabile chromophores with free diffusion of sensitizer molecules from the bulk of a solution to the surface is derived by determining the stationary solution of a diffusion equation with suitable boundary conditions. The relation between the phenomenological rate constant for the photosensitized reaction at the surface and in the bulk is established. Applying the result to the analysis of an experimental example, the origin of the quasi zeroth-order kinetics of the sensitized reaction is revealed. A theoretical comparison of intramolecular sensitization in photocleavable protecting groups with a molecular antenna and sensitization with the freely diffusing sensitizer shows that in a typical case sensitization with free diffusion is more effective than intramolecular sensitization for sensitizer concentrations higher than 5 mM.
Photochemical and Photobiological Sciences 01/2012; 11(3):533-8. · 2.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Oxidation of dihydrorhodamine 123 (DHR) to rhodamine 123 (RH) by oxoperoxonitrite (ONOO(-)), formed through recombination of NO and O(2)(·-) radicals resulting from thermal decomposition of 3-morpholinosydnonimine (SIN-1) in buffered aerated aqueous solution at pH 7.6, represents a kinetic model system of the reactivity of NO and O(2)(·-) in biochemical systems. A magnetic-field effect (MFE) on the yield of RH detected in this system is explored in the full range of fields between 0 and 18 T. It is found to increase in a nearly linear fashion up to a value of 5.5±1.6 % at 18 T and 23 °C (3.1±0.7 % at 40 °C). A theoretical framework to analyze the MFE in terms of the magnetic-field-enhanced recombination rate constant k(rec) of NO and O(2)(·-) due to magnetic mixing of T(0) and S spin states of the radical pair by the Δg mechanism is developed, including estimation of magnetic properties (g tensor and spin relaxation times) of NO and O(2)(·-) in aqueous solution, and calculation of the MFE on k(rec) using the theoretical formalism of Gorelik at al. The factor with which the MFE on k(rec) is translated to the MFE on the yield of ONOO(-) and RH is derived for various kinetic scenarios representing possible sink channels for NO and O(2)(·-). With reasonable assumptions for the values of some unknown kinetic parameters, the theoretical predictions account well for the observed MFE.
[Show abstract][Hide abstract] ABSTRACT: In an attempt to design molecular optoelectronic switches functioning in molecular junctions between two metal tips, we synthesized a set of photochromic compounds by extending the π-system of 1,2-bis-(2-methyl-5-formylfuran-3-yl)perfluorocyclopentene through suitable coupling reactions involving the formyl functions, thereby also introducing terminal groups with a binding capacity to gold. Avoiding the presence of gold-binding sulphur atoms in the photoreactive centre, as they are present in the frequently used analogous thienyl compounds, the newly synthesized compounds should be more suitable for the purpose indicated. The kinetics of reversible photoswitching of the new compounds by UV and visible light was quantitatively investigated in solution. The role of conformational flexibility of the π-system for the width of the UV/Vis spectra was clarified by using quantum chemical calculations with time-dependent (TD)-DFT. As a preliminary test of the potential of the new compounds to serve as optoelectronic molecular switches, monolayer formation and photochemical switching on gold surfaces was observed by using surface plasmon resonance.
Chemistry - A European Journal 06/2011; 17(24):6663-72. · 5.93 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Template-directed synthesis of complementary strands is pivotal for life. Nature employs polymerases for this reaction, leaving the ability of DNA itself to direct the incorporation of individual nucleotides at the end of a growing primer difficult to assess. Using 64 sequences, we now find that any of the four nucleobases, in combination with any neighboring residue, support enzyme-free primer extension when primer and mononucleotide are sufficiently reactive, with >or=93% primer extension for all sequences. Between the 64 possible base triplets, the rate of extension for the poorest template, CAG, with A as templating base, and the most efficient template, TCT, with C as templating base, differs by less than two orders of magnitude. Further, primer extension with a balanced mixture of monomers shows >or=72% of the correct extension product in all cases, and >or=90% incorporation of the correct base for 46 out of 64 triplets in the presence of a downstream-binding strand. A mechanism is proposed with a binding equilibrium for the monomer, deprotonation of the primer, and two chemical steps, the first of which is most strongly modulated by the sequence. Overall, rates show a surprisingly smooth reactivity landscape, with similar incorporation on strongly and weakly templating sequences. These results help to clarify the substrate contribution to copying, as found in polymerase-catalyzed replication, and show an important feature of DNA as genetic material.
Proceedings of the National Academy of Sciences 07/2010; 107(27):12074-9. · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The formation of self-assembled monolayers (SAMs) on gold by 2-(5-iodo-2-nitrophenyl) propoxycarbonyl (I-NPPOC)-protected thymidine with an attached mercaptohexyl succinate linker and the kinetics of photochemical release of the I-NPPOC group were monitored using X-ray photoelectron spectroscopy (XPS) and surface plasmon resonance (SPR) detection. In the XPS spectra, the iodine peaks allowed for specific and accurate monitoring of the presence and loss of I-NPPOC groups on the surface. In the SPR experiment, the overall signal change on photoillumination is in accord with a theoretical estimation of the density of I-NPPOC groups in a dense monolayer. The kinetics roughly follow a biexponential time dependence with two very different time constants, corresponding to photochemical quantum yields of 0.22 and 0.0032, respectively.
[Show abstract][Hide abstract] ABSTRACT: Novel photolabile protecting groups based on the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group with a covalently linked thioxanthone as an intramolecular triplet sensitizer exhibit significantly enhanced light sensitivity under continuous illumination. Herein we present a detailed study of the photokinetics and photoproducts of nucleosides caged with these new protecting groups. Relative to the parent NPPOC group, the light sensitivity of the new photolabile protecting groups is enhanced by up to a factor of 21 at 366 nm and is still quite high at 405 nm, the wavelength at which the sensitivity of the parent compound is practically zero. A new pathway for deprotection of the NPPOC group proceeding through a nitroso benzylalcohol intermediate has been discovered to complement the main mechanism, which involves beta elimination. Under standard conditions of lithographic DNA-chip synthesis, some of the new compounds, while maintaining the same chip quality, react ten times faster than the unmodified NPPOC-protected nucleosides.
[Show abstract][Hide abstract] ABSTRACT: A spectroscopic study of a variety of covalently linked thioxanthone(TX)-linker-2-(2-nitrophenyl)propoxycarbonyl(NPPOC)-substrate conjugates is presented. Herein, the TX chromophore functions as an intramolecular sensitizer to the NPPOC moiety, a photolabile protecting group used in photolithographic DNA chip synthesis. The rate of electronic energy transfer between TX and NPPOC was quantified by means of stationary fluorescence as well as nanosecond and femtosecond time-resolved laser spectroscopy. A dual mechanism of triplet-triplet energy transfer has been observed comprising a slower mechanism involving the T1(pipi*) state of TX with linker-length-dependent time constants longer than 20 ns and a fast mechanism with linker-length-dependent time constants shorter than 3 ns. Evidence is provided that the latter mechanism is due to energy transfer from the T2(npi*) state which is in fast equilibrium with the fluorescent S1(pipi*) state. In the case of direct linkage between the aromatic rings of TX and NPPOC, the spectroscopic properties are indicative of one united chromophore which, however, still shows the typical NPPOC cleavage reaction triggered by intramolecular hydrogen atom transfer to the nitro group.
Journal of the American Chemical Society 11/2007; 129(40):12148-58. · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Nanosecond time-resolved absorption studies in a magnetic field ranging from 0 to 2.0 T have been performed on a series of covalently linked donor(PXZ)-Ru(bipyridine)3-acceptor(diquat) complexes (D-C2+-A2+). In the PXZ moiety, the heteroatom (X = O (oxygen), T (sulfur), and S (selenium)) is systematically varied to study spin-orbit coupling effects. On the nanosecond time scale, the first detectable photoinduced electron-transfer product after exciting the chromophore C2+ is the charge-separated (CS) state, D+-C2+-A+, where an electron of the PXZ moiety, D, has been transferred to the diquat moiety, A2+. The magnetic-field-dependent kinetic behavior of charge recombination (monoexponential at 0 T progressing to biexponential for all three complexes with increasing field) can be quantitatively modeled by the radical pair relaxation mechanism assuming creation of the CS state with pure triplet spin correlation (3CS). Magnetic-field-independent contributions to the rate constant kr of T+/- --> (T0,S) relaxation are about 4.5 x 10(5) s-1 for DCA-POZ and -PTZ (due to a vibrational mechanism) and 3.5 x 10(6) s-1 for DCA-PSZ (due to spin rotational mechanism). Recombination to the singlet ground state is allowed only from the 1CS spin level; spin-forbidden recombination from 3CS seems negligible even for DCA-PSZ. The field dependence of kr (field-dependent recombination) can be decomposed into the contributions of various relaxation mechanisms. For all compounds, the electron spin dipolar coupling relaxation mechanism dominates the field dependence of tau(slow) at fields up to about 100 mT. Spin relaxation due to the g-tensor anisotropy relaxation mechanism accounts for the field dependence of tau(slow) for DCA-PSZ at high fields. For the underlying stochastic process, a very short correlation time of 2 ps has to be assumed, which is tentatively assigned to a flapping motion of the central, nonplanar ring in PSZ. Finally, it has been confirmed by paramagnetic quenching (here Heisenberg exchange) experiments of the magnetic-field effects with TEMPO that all magnetic-field dependencies observed with the present DCA-PSZ systems are indeed due to the magnetic-field dependence of spin relaxation.
The Journal of Physical Chemistry A 05/2007; 111(18):3485-96. · 2.77 Impact Factor