Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase

Coupling nucleic acid processing enzymes to nanoscale pores allows controlled movement of individual DNA or RNA strands that is reported as an ionic current/time series. Hundreds of individual enzyme complexes can be examined in single-file order at high bandwidth and spatial resolution. The bacteriophage phi29 DNA polymerase (phi29 DNAP) is an attractive candidate for this technology, due to its remarkable processivity and high affinity for DNA substrates. Here we show that phi29 DNAP-DNA complexes are stable when captured in an electric field across the α-hemolysin nanopore. DNA substrates were activated for replication at the nanopore orifice by exploiting the 3'-5' exonuclease activity of wild-type phi29 DNAP to excise a 3'-H terminal residue, yielding a primer strand 3'-OH. In the presence of deoxynucleoside triphosphates, DNA synthesis was initiated, allowing real-time detection of numerous sequential nucleotide additions that was limited only by DNA template length. Translocation of phi29 DNAP along DNA substrates was observed in real time at ?ngstrom-scale precision as the template strand was drawn through the nanopore lumen during replication.     

A Frustrated Phosphane–Borane Lewis Pair and Hydrogen: A Kinetics Study

The energy profile of a frustrated Lewis pair (FLP) dihydrogen splitting system was determined by a combined experimental kinetic and DFT study. A trimethylene‐bridged phosphane–borane FLP was converted into its endothermic H₂‐cleavage product by sequential H⁺/H^? addition. The system could be handled at low temperature, and the kinetics of the H₂ elimination were determined to give a rate constant of k_HH,exp(299 K)=(2.87±0.1)×10^?4 s^?1 in solution. The primary kinetic isotope effects were determined; for example, (k_HH/k_DD)_exp=3.19. The system was accurately analyzed by DFT calculations.     

Functionalization of Intramolecular Frustrated Lewis Pairs by 1,1‐Carboboration with Conjugated Enynes

The vicinal P/B frustrated Lewis pair (FLP) Mes₂PCH₂CH₂B(C₆F₅)₂ undergoes 1,1‐carboboration reactions with the Me₃Si‐substituted enynes to give ring‐enlarged functionalized C₃‐bridged P/B FLPs. These serve as active FLPs in the activation of dihydrogen to give the respective zwitterionic [P]H⁺/[B]H^? products. One such product shows activity as a metal‐free catalyst for the hydrogenation of enamines or a bulky imine. The ring‐enlarged FLPs contain dienylborane functionalities that undergo “bora‐Nazarov”‐type ring‐closing rearrangements upon photolysis. A DFT study had shown that the dienylborane cyclization of such systems itself is endothermic, but a subsequent C₆F₅ migration is very favorable. Furthermore, substituted 2,5‐dihydroborole products are derived from cyclization and C₆F₅ migration from the photolysis reaction. In the case of the six‐membered annulation product, a subsequent stereoisomerization reaction takes place and the resultant compound undergoes a P/B FLP 1,2‐addition reaction with a terminal alkyne with rearrangement.     

Application of the shape group method to conformational processes: Shape and conjugation changes in the conformers of 2-phenyl pyrimidine

The shape group method (SGM) and the associated (a,b)-parameter maps provide a detailed shape characterization of molecular charge distributions. This method is applied to the study of the variations of shape and conjugation of conformers of 2-phenyl pyrimidine in their electronic ground state. Within the SGM framework, the method of (a,b)-parameter maps provides a concise, nonvisual, algorithmic technique for shape characterization of molecules with fixed nuclear geometries. Moreover, shape codes derived from the (a,b)-parameter maps afford a practical means for efficiently storing the shape properties of molecules in an electronic database. The shape codes of two or more charge distributions can be compared directly, and numerical measures of molecular shape similarity can be computed using a technique that is simple, fast, and inexpensive, especially in relation to direct, pairwise comparisons of electronic charge densities. The quantitative and automated nature of the method suggests applications in the field of computer-aided molecular design. In this study, the method is used for the first time to determine detailed numerical shape codes and shape similarity measures for a nontrivial conformational problem involving changes in energy and in conjugation. Numerical shape similarity measures of eight conformers of 2-phenyl pyrimidine are determined and correlated with variations in conformational energy and conjugation. The competing effects of steric repulsion and conjugation lead to important correlations between conformational energy and shape. © 1995 John Wiley & Sons, Inc.     

Synthesis of functionalised cyclopentanes by intramolecular radical-mediated cyclisations of terminal allenic ketones

Electrolysis of a series of terminal allenic ketones e.g. (7), (10), (17) and (21) is shown to result in intramolecular reductive cyclisation, through the $\text{exo}$-mode, producing five-membered rings, $\text{viz}$ (8), (9), (20) and (22) respectively, incorporating a bridgehead hydroxyl group. The unsaturated alcohols (8), (20) and (22), are also obtained when the allenic ketones (7), (17) and (21) are treated with sodium naphthalenide. By contrast treatment of (10) in the sodium naphthalenide gives a low yield ($\text{ca}$ 7%) of the isomeric indenol (11) by cyclisation through the $\text{endo}$-mode.Reductive cyclisations of the terminal acetylenic ketones (14) and (30) produce the corresponding unsaturated alcohols (26) and (31) respectively. Treatment of the alcohols (26) and (31) with catalytic selenium dioxide then provides the enediols (27) and (32) respectively, which make up the B/C ring systems of the novel marine natural products capnellenediol (1) and isoamijiol (2).     

THE EFFECTS OF AGGREGATION ON THE FLUORESCENCE and THE TRIPLET STATE YIELD OF HEMATOPORPHYRIN

Abstract— The fluorescence and triplet state yields of hematoporphyrin have been measured in wuter/methanol mixtures. There is a closely linked response of these yields to aggregation of the hematoporphyrin molecule. The monomer, which is the principal species present at high methanol content, has a triplet state yield of 0.91 and a fluorescence yield of 0.09. By contrast, hematoporphyrin solutions with a high water content containing aggregates have lower fluorescence and triplet state yields, e.g. 0.018 and 0.56, respectively, in water. Static, singlet state quenching in some of the aggregates is responsible for the reduced fluorescence yield. The results also show that in addition to these aggregates there are other types of aggregates where there is an increased singlet to ground state radiative transition probability, resulting from the interaction between transition dipoles in adjacent molecules.