DNA frayed wires: Differential polymerization of d(AnGm) oligonucleotides

Oligodeoxyribonucleotides with terminal runs of contiguous guanines, d(A_nG_m), spontaneously associate into high molecular weight complexes that resolve on polyacrylamide gels as a regular ladder pattern of bands with low mobility. The aggregates, which we call frayed wires, arise from the interaction between the guanine residues of the oligonucleotides; the adenine tracts are single stranded and can take part in Watson–Crick interactions. Oligonucleotides, with different arm‐to‐stem ratios and total length, readily associate in the presence of Mg²⁺ to form aggregates consisting of an integer number of strands. The type of the observed aggregates is determined by the length of the guanine run. Oligonucleotides with six guanines form four‐ and eight‐stranded complexes; there is no further polymerization. An increase in the number of guanine residues to 10 and 15 leads to polymerization resulting in a ladder pattern of up to 9 bands and an intense signal at the top of the gel. The relative population of any given species in a frayed wire sample is governed by the guanine stem length and is not affected to any substantial extent by arms up to 40 bases long. The type and concentration of the cation in the solution affect the degree of aggregation, with Na⁺ and K⁺ promoting the formation of complexes comprised of 2–4 strands and Mg²⁺ being the most effective in facilitating polymerization. The electrophoretic behavior of frayed wires was analyzed in the framework of the Ogston theory. The free mobility of frayed wires in the solution is close to the values reported for single‐stranded DNA, indicating the equivalence of the charge density of the two conformations. The retardation coefficients for frayed wires arising from a single kind of parent strand increase with the introduction of each additional strand. There is no correlation between the retardation coefficient and the type of parent strand; rather, the magnitude of the retardation coefficient is determined by the total molecular weight of the complex. The values of the retardation coefficients are consistently higher than those for double‐stranded DNA and they display much stronger dependence on the total molecular weight. Presumably, the distinct structural and dynamic characteristics of the two conformations account for their different electrophoretic behavior. © 1999 John Wiley & Sons, Inc. Biopoly 49: 287–295, 1999     

Structural and spectroscopic studies of a model for catechol oxidase

A binuclear copper complex, [Cu₂(BPMP)(OAc)₂][ClO₄]·H₂O, has been prepared using the binucleating ligand 2,6-bis[bis(pyridin-2-ylmethylamino)methyl]-4-methylphenol (H-BPMP). The X-ray crystal structure reveals the copper centers to have a five-coordinate square pyramidal geometry, with the acetate ligands bound terminally. The bridging phenolate occupies the apical position of the square-based pyramids and magnetic susceptibility, electron paramagnetic resonance (EPR) and variable-temperature variable-field magnetic circular dichroism (MCD) measurements indicate that the two centers are very weakly antiferromagnetically coupled (J = −0.6 cm⁻¹). Simulation of the dipole–dipole-coupled EPR spectrum showed that in solution the Cu–O–Cu angle was increased from 126° to 160° and that the internuclear distance was larger than that observed crystallographically. The high-resolution spectroscopic information obtained has been correlated with a detailed ligand-field analysis to gain insight into the electronic structure of the complex. Symmetry arguments have been used to demonstrate that the sign of the MCD is characteristic of the tetragonally elongated environment. The complex also displays catecholase activity (k _cat = 15 ± 1.5 min⁻¹, K _M = 6.4 ± 1.8 mM), which is compared with other dicopper catechol oxidase models. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Enamel thickness,microstructure and development in Afropithecus turkanensis

Afropithecus turkanensis, a 17-17.5 million year old large-bodied hominoid from Kenya, has previously been reported to be the oldest known thick-enamelled Miocene ape. Most investigations of enamel thickness in Miocene apes have been limited to opportunistic or destructive studies of small samples. Recently, more comprehensive studies of enamel thickness and microstructure in Proconsul, Lufengpithecus, and Dryopithecus, as well as extant apes and fossil humans, have provided information on rates and patterns of dental development, including crown formation time, and have begun to provide a comparative context for interpretation of the evolution of these characters throughout the past 20 million years of hominoid evolution. In this study, enamel thickness and aspects of the enamel microstructure in two A. turkanensis second molars were quantified and provide insight into rates of enamel apposition, numbers of cells actively secreting enamel, and the time required to form regions of the crown. The average value for relative enamel thickness in the two molars is 21.4, which is a lower value than a previous analysis of this species, but which is still relatively thick compared to extant apes. This value is similar to those of several Miocene hominoids, a fossil hominid, and modern humans. Certain aspects of the enamel microstructure are similar to Proconsul nyanzae, Dryopithecus laietanus, Lufengpithecus lufengensis, Graecopithecus freybergi and Pongo pygmaeus, while other features differ from extant and fossil hominoids. Crown formation times for the two teeth are 2.4-2.6 years and 2.9-3.1 years respectively. These times are similar to a number of extant and fossil hominoids, some of which appear to show additional developmental similarities, including thick enamel. Although thick enamel may be formed through several developmental pathways, most Miocene hominoids and fossil hominids with relatively thick enamel are characterized by a relatively long period of cuspal enamel formation and a rapid rate of enamel secretion throughout the whole cusp, but a shorter total crown formation time than thinner-enamelled extant apes.     

Relationships among foliar chemistry, foliar polyamines, and soil chemistry in red spruce trees growing across the northeastern United States

Forest trees are constantly exposed to various types of natural and anthropogenic stressors. A major long-term goal of our research is to develop a set of early physiological and biochemical markers of stress in trees before the appearance of visual symptoms. Six red spruce (t Picea rubens Sarg.) stands from the northeastern United States were selected for collection of soil and foliage samples. All of the chosen sites had soil solution pH values below 4.0 in the Oa horizon but varied in their geochemistry. Some of these sites were apparently under some form of environmental stress as indicated by a large number of dead and dying red spruce trees. Samples of soil and needles (from apparently healthy red spruce trees) were collected from these sites four times during a two-year period. The needles were analyzed for perchloric acid-soluble polyamines and exchangeable inorganic ions. Soil and soil solution samples from the Oa and B horizons were analyzed for their exchange chemistry. The data showed a strong positive correlation between Ca and Mg concentrations in the needles and in the Oa horizon of the soil. However, needles from trees growing on relatively Ca-rich soils with a low exchangeable Al concentration and a low Al:Ca soil solution ratio had significantly lower concentrations of putrescine and spermidine than those growing on Ca-poor soils with a high exchangeable Al concentration and a high Al:Ca soil solution in the Oa horizon. The magnitude of this change was several fold higher for putrescine concentrations than for spermidine concentrations. Neither putrescine nor spermidine were correlated with soil solution Ca, Mg, and Al concentrations in the B horizon. The putrescine concentrations of the needles always correlated significantly with exchangeable Al (r²=0.73, t p0.05) and soil solution Al:Ca ratios (r²=0.91, t p0.01) of the Oa horizon. This suggests that in conjunction with soil chemistry, putrescine and/or spermidine may be used as a potential early indicator of Al stress before the appearance of visual symptoms in red spruce trees.