Sequence-specific single-molecule analysis of 8-oxo-7,8-dihydroguanine lesions in DNA based on unzipping kinetics of complementary probes in ion channel recordings

Translocation measurements of intact DNA strands with the ion channel α-hemolysin (α-HL) are limited to single-stranded DNA (ssDNA) experiments as the dimensions of the channel prevent double-stranded DNA (dsDNA) translocation; however, if a short oligodeoxynucleotide is used to interrogate a longer ssDNA strand, it is possible to unzip the duplex region when it is captured in the α-HL vestibule, allowing the longer strand to translocate through the α-HL channel. This unzipping process has a characteristic duration based on the stability of the duplex. Here, ion channel recordings are used to detect the presence and relative location of the oxidized damage site 8-oxo-7,8-dihydroguanine (OG) in a sequence-specific manner. OG engages in base pairing to C or A with unique stabilities relative to native base Watson-Crick pairings, and this phenomenon is used here to engineer probe sequences (10-15mers) that, when base-paired with a 65mer sequence of interest, containing either G or OG at a single site, produce characteristic unzipping times that correspond well with the duplex melting temperature (T(m)). Unzipping times also depend on the direction from which the duplex enters the vestibule if the stabilities of leading base pairs at the ends of the duplex are significantly different. It is shown here that the presence of a single DNA lesion can be distinguished from an undamaged sequence and that the relative location of the damage site can be determined based on the duration of duplex unzipping.     

8-Oxoguanosine switches modulate the activity of alkylated siRNAs by controlling steric effects in the major versus minor grooves

Small interfering double-stranded RNAs have been synthesized bearing one or more base modifications at nucleotide positions 4, 11, and/or 16 in the guide strand. The chemically modified base is an N(2)-alkyl-8-oxo-7,8-dihydroguanine (alkyl = propyl, benzyl) that can alternatively pair in a Watson-Crick sense opposite cytosine (C) or as a Hoogsteen pair opposite adenine (A). Cellular delivery with C opposite led to effective targeting of A-containing but not C-containing mRNA sequences in a dual luciferase assay with RNA interference levels that were generally as good as or better than unmodified sequences. The higher activity is ascribed to an inhibitory effect of the alkyl group projecting into the minor groove of double-stranded RNA preventing off-target binding to proteins such as PKR (RNA-activated protein kinase).     

On the flocculation and re-dissolution of trivalent lanthanide metal ions by sodium dodecyl sulfate in aqueous solutions

The interaction between aqueous solutions of trivalent lanthanide ions (M(3+): La(III) and Gd(III) and Tb (III)) at fixed (1mM) concentrations and various concentrations of sodium dodecyl sulfate (SDS), ranging from pre- to post-micellar, has been investigated by ICP-AES (La(III) and Gd(III)), luminescence spectra (Gd(III)) and lifetimes (Tb(III)) and (139)La NMR spectroscopy. It has been found that at concentration ratios, r=[SDS]/[M(3+)], around the charge neutralization value (ca. 3), dodecyl sulfate (DS(-)) anion interacts with the metal ions to form insoluble aggregates. The metal ion-DS(-) complexes remain flocculated for r values below 5-6 (Gd(III) and La(III), respectively), while at higher r values, re-dissolution takes place. The flocculated aggregates have been characterized by X-ray powder diffraction, and show a lamellar structure. Job plot method indicates that a complex with a 1:3 (M(3+):DS(-)) stoichiometry is formed. From ICP-AES analysis, a model based on a three-step mechanism has been developed and association constants calculated. For all systems the interaction between DS(-) and metal ions follows an associative process with K values ranging between K(1)=10 and K(3)=10(4). These data are discussed on the basis of the physical-chemical characteristics of the metal ions. Re-dissolution with increasing surfactant concentration is attributed to formation of mixed lanthanide/sodium dodecyl sulfate aggregates, with the relative lanthanide fraction in these species decreasing with increasing SDS concentration.     

Dynamics and gravitational wave signature of collapsar formation

We perform 3+1 general relativistic simulations of rotating core collapse in the context of the collapsar model for long gamma-ray bursts. We employ a realistic progenitor, rotation based on results of stellar evolution calculations, and a simplified equation of state. Our simulations track self-consistently collapse, bounce, the postbounce phase, black hole formation, and the subsequent early hyperaccretion phase. We extract gravitational waves from the spacetime curvature and identify a unique gravitational wave signature associated with the early phase of collapsar formation.     

Jet reconstruction and jet properties at HERA

We discuss jet reconstruction methods with respect to their suitability forep collisions at HERA and study the expected properties of such jets. The results are based on complete event simulation using current models of jet evolution and hadronization in combination with experimentally tested jet algorithms. The effects of calorimeter resolution are illustrated by explicit simulation of the energy profile and fluctuations in a simplified, but realistic detector.     

First symmetry tests in polarized Z0 decays to bbg

We have made the first direct symmetry tests in the decays of polarized Z0 bosons into fully identified bbg states, collected in the SLD experiment at SLAC. We searched for evidence of parity violation at the bbg vertex by studying the asymmetries in the b-quark polar- and azimuthal-angle distributions, and for evidence of T-odd, CP-even or CP-odd, final-state interactions by measuring angular correlations between the three-jet plane and the Z0 polarization. We found results consistent with standard model expectations and set 95% C. limits on anomalous contributions.     

Fast weighting functions for retrievals from limb scattering measurements

The satellite-borne UV-visible-NIR spectrometers SCIAMACHY and OSIRIS perform operational measurements of the Earth's limb radiance with global coverage. The vertically resolved atmospheric composition is retrieved from the measurements. We have computed synthetic limb measurements and weighting functions (WFs) with several orders of scattering and surface reflection. Comparisons reveal the wavelength-dependent contributions of single scattering and the second orders of scattering and surface reflection. We have also performed test retrievals of the and profiles with the program package SCIARAYS. They prove that the single scattering approximation is sufficient for the calculation of the WFs during the retrieval process. We conclude that algorithms for the analysis of limb scattering measurements can be accelerated by neglecting higher orders of scattering in the WF calculations.