Rewriting the Story of Excimer Formation in Liquid Benzene.

Formation of benzene excimer following UV excitation of the neat liquid is monitored with femtosecond spectroscopy. A prompt rise component in excimer transient absorption, which contradicts the classical scenario of gradual reorientation and pairing of the excited monomers, is observed. Three-pulse experiments in which the population of evolving excimers is depleted by a secondary dump pulse demonstrate that the excimer absorption band is polarized along the interfragment axis. The experiments furthermore prove that the subsequent 4-fold increase in excimer absorption over ∼50 ps is primarily due to an increase in the transition dipole of pairs which are formed early on, and not to excited monomers forming excimers in a delayed fashion due to unfavorable initial geometry. Results are analyzed in light of recent studies of local structure in the liquid benzene combined with advanced electronic structure calculations. The prompt absorption rise is ascribed to excited states delocalized over nearby benzene molecules, which are sufficiently close and nearly parallel in the pure liquid. Such low-symmetry structures, which differ considerably from the optimized structures of isolated benzene dimer and solid benzene, are sufficiently abundant in liquid benzene. Electronic structure calculations confirm the orientation of transition dipoles of the excimers along the interparticle axis and demonstrate how slow refinement of the intermolecular geometry leads to a significant increase in the excimer absorption strength.

Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold.

A series of logic gates, "AND", "OR", and "XOR", are designed using a DNA scaffold that includes four "footholds" on which the logic operations are activated. Two of the footholds represent input-recognition strands, and these are blocked by complementary nucleic acids, whereas the other two footholds are blocked by nucleic acids that include the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The logic gates are activated by either nucleic acid inputs that hybridize to the respective "footholds", or by low-molecular-weight inputs (adenosine monophosphate or cocaine) that yield the respective aptamer-substrate complexes. This results in the respective translocation of the blocking nucleic acids to the footholds carrying the HRP-mimicking DNAzyme sequence, and the concomitant release of the respective DNAzyme. The released product-strands then self-assemble into the hemin/G-quadruplex-HRP-mimicking DNAzyme that biocatalyzes the formation of a colored product and provides an output signal for the different logic gates. The principle of the logic operation is, then, implemented as a possible paradigm for future nanomedicine. The nucleic acid inputs that bind to the blocked footholds result in the translocation of the blocking nucleic acids to the respective footholds carrying the antithrombin aptamer. The released aptamer inhibits, then, the hydrolytic activity of thrombin. The system demonstrates the regulation of a biocatalytic reaction by a translator system activated on a DNA scaffold.

Magneto-mechanical detection of nucleic acids and telomerase activity in cancer cells.

The ultra-sensitive magneto-mechanical detection of DNA, single-base-mismatches in nucleic acids, and the assay of telomerase activity are accomplished by monitoring the magnetically induced deflection of a cantilever functionalized with magnetic beads associated with the biosensing interface. The analyzed M13phi DNA hybridized with the nucleic acid-functionalized magnetic beads is replicated in the presence of dNTPs that include biotin-labeled dUTP. The resulting beads are attached to an avidin-coated cantilever, and the modified cantilever is deflected by an external magnetic field. Similarly, telomerization of nucleic acid-modified magnetic beads in the presence of dNTPs, biotin-labeled dUTP, and telomerase from cancer cell extracts and the subsequent association of the magnetic beads to the cantilever surface results in the lever deflection by an external magnetic field. M13phi DNA is sensed with a sensitivity limit of 7.1 x 10(-20) M by the magneto-mechanical detection method.