Bacterial initiators form dynamic filaments on single-stranded DNA monomer by monomer.

DNA replication initiation is mediated across all domains of life by initiator proteins oligomerizing at replication origins. Recently, it was shown that initiators can directly bind single-stranded DNA (ssDNA) and thus might enhance origin melting. In this study, we used single-molecule fluorescence assays to probe the ssDNA binding mechanism of the replication initiator DnaA. Our experiments revealed that DnaA forms a dynamic filament on ssDNA in 3' to 5' directionality in the presence of ATP and analogs. After nucleation with a three-monomer seed, monomers dynamically assemble and disassemble one monomer at a time at the 5' end, each monomer binding three nucleotides of ssDNA. The addition of adjacent double-stranded DnaA binding sites stabilized the DnaA filament on ssDNA. Our results extend the current models of origin melting via DnaA ssDNA interaction.

Enzymatic oxygen scavenging for photostability without pH drop in single-molecule experiments.

Over the past years, bottom-up bionanotechnology has been developed as a promising tool for future technological applications. Many of these biomolecule-based assemblies are characterized using various single-molecule techniques that require strict anaerobic conditions. The most common oxygen scavengers for single-molecule experiments are glucose oxidase and catalase (GOC) or protocatechuate dioxygenase (PCD). One of the pitfalls of these systems, however, is the production of carboxylic acids. These acids can result in a significant pH drop over the course of experiments and must thus be compensated by an increased buffer strength. Here, we present pyranose oxidase and catalase (POC) as a novel enzymatic system to perform single-molecule experiments in pH-stable conditions at arbitrary buffer strength. We show that POC keeps the pH stable over hours, while GOC and PCD cause an increasing acidity of the buffer system. We further verify in single-molecule fluorescence experiments that POC performs as good as the common oxygen-scavenging systems, but offers long-term pH stability and more freedom in buffer conditions. This enhanced stability allows the observation of bionanotechnological assemblies in aqueous environments under well-defined conditions for an extended time.

Measurements of 13C multiple-quantum coherences in amyloid fibrils under magic-angle spinning.

The excitation and detection of high-order multiple quantum coherences among (13)C nuclear spins are demonstrated in the samples of [1-(13)C]-L-alanine and (13)C labeled amyloid fibrils at a spinning frequency of 20 kHz. The technique is based on the double-quantum average Hamiltonian prepared by the DRAMA-XY4 pulse sequence. Empirically, we find that multiple supercycles are required to suppress the higher-order effects for real applications. Measurements for the fibril samples formed by the polypeptides of PrP(113-127) provide the first solid-state NMR evidence for the stacking of multiple ß-sheet layers at the structural core of amyloid fibrils.

Steric zipper formed by hydrophobic peptide fragment of Syrian hamster prion protein.

Steric zippers, where the residues of two neighboring ß-sheet layers are tightly interdigitated, have been proposed as fundamental structural units of amyloid fibrils by Eisenberg and co-workers. The steric zipper formed by polypeptides containing the palindromic sequence AGAAAAGA has a distinctive feature that the distance between two interdigitated ß-sheet layers is comparable to the interstrand distance of the individual ß-sheet. This structural motif is of great interest in the study of prion disease because the AGAAAAGA sequence is highly conserved in prion proteins of different species. In this work, the amyloid fibrils formed by the polypeptides of PrP(113-127), viz. Ac-AGAAAAGAVVGGLGG-NH(2), are taken as the model compound to investigate the biophysical principles governing the steric zipper formation. The target fibrils adopt the structural motif of class 7 steric zipper, which is formed by stacking of antiparallel ß-sheet layers with residue 117 + k forming backbone hydrogen bonds to residue 120 - k. Implication of our results in the infectivity of scrapie prion is briefly discussed.

Molecular structure of amyloid fibrils formed by residues 127 to 147 of the human prion protein.

Amyloid fibrils are filamentous and insoluble forms of peptides or proteins. Proline has long been considered to be incompatible with the cross-beta structural motif of amyloid fibrils. On the basis of solid-state NMR spectroscopy data, we present a structural model of an in-register parallel beta sheet for the amyloid fibrils formed from a human prion protein fragment, huPrP(127-47). We have developed a simple solid-state NMR spectroscopy technique to identify solvent-protected backbone amide protons in a H/D exchange experiment without disaggregating the amyloid fibrils, from which we find that proline residue P(137) does not disrupt the beta-sheet structure from G(127) to G(142). We suggest that the resultant kink at P(137) generates a twist between adjacent peptide strands to maintain hydrogen bonding in the beta-sheet regions flanking the P(137) residue. Although proline can be well integrated into the cross-beta structure of amyloid fibrils, the kink formed at the position of the proline residue will considerably weaken the hydrogen bonding between the neighboring strands, especially when the mutation site is near the central region of a beta sheet.

Pt- and Au-catalyzed oxidative cyclization of 2-ethenyl-1-(prop-2'-yn-1'-ol)benzenes to naphthyl aldehydes and ketones: catalytic oxidation of metal-alkylidene intermediates using H2O and H2O2.

2-Ethenyl-1-(prop-2'-yn-1'-ol)benzenes was cyclized through catalytic oxidation with PtCl(2)/CO/H(2)O and PEt(3)AuCl/H(2)O(2); the metal-naphthylidene intermediates were identified and oxygenated with water and H(2)O(2), respectively; for the efficiency of cyclization, the Au catalytic system is superior to that of the PtCl(2)-catalysis because of its compatibility toward diverse alcohol substrates including both internal alkynes and terminal alkynes.

Computational studies on stable triplet states of heteroacetylenes and the effects of halogen substituents.

This paper describes theoretical studies of halogen-substituted heteroacetylenes (XCMY, M = Si and Ge; X, Y = H, Cl and F) performed at the QCISD(T)/6-311G//QCISD/6-31G level of theory. The electronegative halogen substituents destabilize the singlet state such that the triplet state tends to become favorable. The triplet state has the bifunctional electronic structure of a triplet carbene joined to a heavy singlet carbene. We found that the substituents effectively reduce the energy of the donor-acceptor interactions (E(D-A)) between the two in-plane lone pairs of electrons of the singlet state; therefore, the remaining pi bond is less favorable energetically than the triplet state with a sigma bond. A related phenomenon occurs for the homonuclear heavy acetylenes in singlets in which the lead compound RPbPbR switches to a Pb-Pb sigma bond from the pi bonds observed for the lighter acetylenes.

Metal-catalyzed chemoselective cycloisomerization of cis-2,4-dien-1-als to 3-cyclopentenones and 4-alkylidene-3,4-dihydro-2H-pyrans.

[reaction: see text] PtCl(2) (5 mol %) catalyst effected cycloisomerization of cis-2,4-dien-1-al (1) to 3-cyclopentenone (3) efficiently in hot toluene. In the presence of p-TSA, this PtCl(2) catalysis gave 2-cyclopentenone (5) exclusively because of the secondary isomerization reaction. Although the 1-2 equilibrium state greatly favors aldehyde (1), PdCl(2)(PhCN)(2) (5 mol %) catalyzed cycloisomerization of aldehyde (1) to 4,6,7,8-tetrahydro-3H-isochromene (4) smoothly in hot toluene. A plausible mechanism is proposed on the basis of reaction observation and isotope-labeled experiment.