Optimization of the double pump-probe technique: decoupling the triplet yield and cross section

The double pump-probe technique (DPP), first introduced by Swatton et al. [Appl. Phys. Lett. 1997, 71, 10], is a variant of the standard pump-probe method but uses two pumps instead of one to create two sets of initial conditions for solving the rate equations, allowing a unique determination of singlet- and triplet-state absorption parameters and transition rates. We investigate the advantages and limitations of the DPP theoretically and experimentally and determine the influence of several experimental parameters on its accuracy. The accuracy with which the DPP determines the triplet-state parameters improves when the fraction of the population in the triplet state relative to the ground state is increased. To simplify the analysis of the DPP, an analytical model is presented, which is applicable to both the reverse saturable and the saturable absorption regimes. We show that the DPP is optimized by working in the saturable absorption regime. Although increased accuracy is in principle achievable by increasing the pump fluence in the reverse saturable absorption range, this can cause photoinduced decomposition in photochemically unstable molecules. Alternatively, we can tune the excitation wavelength to the spectral region of larger ground-state absorption, to achieve similar accuracy. This results in an accurate separation of triplet yield and excited-state absorption cross section. If the cross section at another wavelength is then desired, a second pump-probe experiment at that wavelength can be utilized given the previously measured triplet yield under the usually valid assumption that the triplet yield is independent of excitation wavelength.     

Protein detection by nanopores equipped with aptamers

Protein nanopores have been used as stochastic sensors for the detection of analytes that range from small molecules to proteins. In this approach, individual analyte molecules modulate the ionic current flowing through a single nanopore. Here, a new type of stochastic sensor based on an αHL pore modified with an aptamer is described. The aptamer is bound to the pore by hybridization to an oligonucleotide that is attached covalently through a disulfide bond to a single cysteine residue near a mouth of the pore. We show that the binding of thrombin to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex, alters the ionic current through the pore. The approach allows the quantification of nanomolar concentrations of thrombin, and provides association and dissociation rate constants and equilibrium dissociation constants for thrombin·aptamer interactions. Aptamer-based nanopores have the potential to be integrated into arrays for the parallel detection of multiple analytes.     

Continuous stochastic detection of amino Acid enantiomers with a protein nanopore

A stochastic sensing method: Discrimination between enantiomeric amino acids is achieved when the amino acids bind to a Cu(II) complex within a protein nanopore sensor, which provides a chiral environment. The potential of the method is demonstrated by real-time observation of the increase in enantiomeric excess during an enzymatic kinetic resolution.     

S-nitrosothiol chemistry at the single-molecule level

SNO patrol: S-Nitrosothiols (RSNO) are important molecules involved in cell signaling, which control physiological processes such as vasodilation and bronchodilation. By using the protein pore α-hemolysin as a nanoreactor, the biological chemistry of RSNO has been investigated at the single-molecule level.     

Mechanisms of kinetic trapping in self-assembly and phase transformation

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions.     

Establishing Drug Resistance in Microorganisms by Mass Spectrometry

A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and ¹³C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.

Stochastic sensing of nanomolar inositol 1,4,5-trisphosphate with an engineered pore

The introduction of a ring of arginine residues near the constriction in the transmembrane beta barrel of the staphylococcal alpha-hemolysin heptamer yielded a pore that could be almost completely blocked by phosphate anions at pH 7.5. Block did not occur with other oxyanions, including nitrate, sulfate, perchlorate, and citrate. Based on this finding, additional pores were engineered with high affinities for important cell signaling molecules, such as the Ca(2+)-mobilizing second messenger inositol 1,4,5-trisphosphate (IP(3)), that contain phosphate groups. One of these engineered pores, P(RR-2), provides a ring of fourteen arginines that project into the lumen of the transmembrane barrel. Remarkably, P(RR-2) bound IP(3) with low nanomolar affinity while failing to bind another second messenger, adenosine 3', 5'-cyclic monophosphate (cAMP). The engineered alpha-hemolysin pores may be useful as components of stochastic sensors for cell signaling molecules.