Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires

A systematic study of the amplified optical detection of DNA by Mg(2+)-dependent DNAzyme subunits is described. The use of two DNAzyme subunits and the respective fluorophore/quencher-modified substrate allows the detection of the target DNA with a sensitivity corresponding to 1 × 10(-9) M. The use of two functional hairpin structures that include the DNAzyme subunits in a caged, inactive configuration leads, in the presence of the target DNA, to the opening of one of the hairpins and to the activation of an autonomous cross-opening process of the two hairpins, which affords polymer DNA wires consisting of the Mg(2+)-dependent DNAzyme subunits. This amplification paradigm leads to the analysis of the target DNA with a sensitivity corresponding to 1 × 10(-14) M. The amplification mixture composed of the two hairpins can be implemented as a versatile sensing platform for analyzing any gene in the presence of the appropriate hairpin probe. This is exemplified with the detection of the BRCA1 oncogene.     

Tuning of switching properties and excited-state dynamics of fulgides by structural modifications

The ultrafast photo-induced dynamics of the E-isomers of four selected photochromic fulgides with distinct structural motifs have been elucidated by femtosecond broadband transient absorption spectroscopy in n-hexane as solvent. E→C and E→Z isomerisations, respectively, with time constants of ～0.12 ± 0.02 ps and ～0.34 ± 0.03 ps taking place in parallel were found for derivatives with a methyl substituent at the central hexatriene (HT) unit. In contrast, fulgides with increased steric constraints by an iso-propyl substituent or by intramolecular bridging displayed virtually zero E→Z isomerisation, but instead a desired accelerated and more efficient ring closure in a reaction time of only ～50 ± 10 fs. Both photoisomerisations appear to follow excited-state pathways with distinctive conical intersections. For the ring closure, direct barrierless pathways with steep downhill gradients are likely. Furthermore, the results indicate conformer-specific reactions, with ring closure exclusively by the E(α) conformer and E→Z isomerisation predominantly by the E(β) conformer, because the E(α)→Z channel is unfavoured by the faster and kinetically more competitive E(α)→C reaction. DFT calculations of the equilibrium structures showed that the sterically demanding groups at the HT unit shift the conformer equilibria towards the E(α) conformers. At the same time, they appear to cause a favourable pre-orientation of the furyl unit that accelerates the conrotatory ring closure in the E(α)→C reaction. Benzo-annulation of the furyl unit has little effect on the observed dynamics. Overall, the results demonstrate how the excited-state dynamics and thereby the photoswitching properties of fulgides can be successfully tuned and improved by structural modifications at the chromophores.     

Electronic and steric effects on the photo-induced C→E ring-opening of structurally modified furylfulgides

The ultrafast C→E ring-opening reactions of four selectively modified furylfulgides have been studied by means of ultrafast broadband transient absorption spectroscopy after femtosecond laser excitation at λ = 500 nm. A large difference in the dynamics was found in the case of benzannulation at the furyl moiety as an example for an electronic effect by extension of the conjugated π-electron system compared to furylfulgides carrying sterically different alkyl substituents at the central cyclohexadiene (CHD) ring. The measured very similar spectro-temporal absorption maps for the furylfulgides with a methyl or isopropyl group at the CHD ring or an intramolecular alkyl bridge from the CHD to the furyl moiety showed two distinctive excited-state absorptions with slightly different decay times. The first time constant (τ(1) = 0.39-0.57 ps) was assigned to the rapid departure of the excited wavepacket from the Franck-Condon region. The slightly longer second decay time of τ(2) = 0.66-0.92 ps, depending on the compound, was attributed to the electronic deactivation and ring-opening through a conical intersection to the S(0) state. In contrast, the benzannulation at the furyl moiety was found to lead to a bi-phasic excited-state decay with τ(2) = 4.7 ps and a much slower additional contribution of τ(3) = 17.4 ps, ≈25 times longer compared to the normal furylfulgides. The drastic change is attributed to a trapping of excited molecules in a local potential energy minimum en route to the conical intersection.     

Superior Z→E and E→Z photoswitching dynamics of dihydrodibenzodiazocine, a bridged azobenzene, by S1(nπ*) excitation at λ = 387 and 490 nm

The ultrafast Z→E and E→Z photoisomerisation dynamics of 5,6-dihydrodibenzo[c,g][1,2]diazocine (1), the parent compound of a class of bridged azobenzene-based photochromic molecular switches with a severely constrained eight-membered heterocyclic ring as central unit, have been studied by femtosecond time-resolved spectroscopy in n-hexane as solvent and by quantum chemical calculations. The diazocine contrasts with azobenzene (AB) in that its Z rather than E isomer is the energetically more stable form. Moreover, it stands out compared to AB for the spectrally well separated S(1)(nπ*) absorption bands of its two isomers. The Z isomer absorbs at around λ = 404 nm, the E form has its absorption maximum around λ = 490 nm. The observed transient spectra following S(1)(nπ*) photoexcitation show ultrafast excited-state decays with time constants τ(1) = 70 fs for the Z and <50 fs for the E isomer reflecting very fast departures of the excited wave packets from the S(1) Franck-Condon regions and τ(2) = 270 fs (320 fs) related to the Z→E (resp. E→Z) isomerisations. Slower transient absorption changes on the time scale of τ(3) = 5 ps are due to vibrational cooling of the reaction products. The results show that the unique steric constraints in the diazocine do not hinder, but accelerate the molecular isomerisation dynamics and increase the photoswitching efficiencies, contrary to chemical intuition. The observed isomerisation times and quantum yields are rationalised on the basis of CASPT2//CASSCF calculations by a S(1)/S(0) conical intersection seam at a CNNC dihedral angle of ≈96° involving twisting and torsion of the central CNNC moiety. With improved photochromism, high quantum yields, short reaction times and good photostability, diazocine 1 and its derivatives constitute outstanding candidates for photoswitchable molecular tweezers and other applications.     

q-Blossoming for analytic functions

Numerical Algorithms - We construct a q-analog of the blossom for analytic functions, the analytic q-blossom. This q-analog also extends the notion of q-blossoming from polynomials to analytic...     

Studies of Hindered Rotation and Magnetic Anisotropy by 1H, 13C and 19F NMR. The Diels-Alder Adduct of N- Pentafluorophenylmaleimide and Phencyclone: A Model for Drugs.

The potent Diels-Alder diene, phencyclone, 1, reacts with N-pentafluorophenylmaleimide, 2, to form an adduct, 3, characterized by ¹H, ¹³C, and ¹⁹F NMR at 300, 75 and 282 MHz, respectively. The one-dimensional (1D) and two-dimensional (2D) ¹H and ¹³C NMR spectra of 3 at ambient temperatures imply a slow exchange limit (SEL) regime with respect to rotation of the unsubstituted bridgehead phenyl groups about severely hindered C(sp²)-C(sp³) bonds. Major non-bonded interactions are expected between the ortho protons of the C₆H₅ groups and H-1, 8 of the phenanthrenoid moiety of 3. ¹⁹F 1D and 2D (COSY) NMR spectra show that the SEL regime also obtains for rotation about the N-C₆F₅ bond of 3, with five separate fluorine signals seen, consistent with a preferred conformation in which the C₆F₅ may lie roughly perpendicular to the plane of the pyrrolidinedione moiety, and may be in the mirror symmetry plane of 3. The results are considered relevant to hindered aryl rotations in numerous Pharmaceuticals. Selected spectral data for 2 and precursors are also presented.