Synthesis,Biophysical, and Biochemical Properties of PNA-DNA Chimeras

Abstract

Three PNA-DNA chimeric dimer synthons (tT, upT and uhT, see Sch. 1) have been synthesized in solution and used to make T₂₀-analogue chimeras applying standard solid-phase DNA synthesis protocol. Duplex forming ability of chimeras with dA₂₀ and their hydrolyses by 3′- and 5′-exonucleases (snake venom and bovine spleen phosphodiesterase, respectively) have been investigated.     

A PRELIMINARY LIMNOLOGICAL INVESTIGATION OF TWELVE SOUTHERN AFRICAN GEOTHERMAL WATERS

SUMMARY

The ionic composition and algal flora of twelve geothermal waters in southern South West Africa and north-western South Africa are described, many for the first time. Water temperatures ranged from 24,9 to 66 °C and salinity values indicated moderate mineralization. A trend of increasing sodium and sulphate dominance with increasing water temperature was evident. Green algae were confined to springs with low water temperatures (below 31 °C) while diatoms and blue-green algae were recorded in all the springs, at temperatures up to 66 °C. Flexibacteria (Chlcroflexus) were recorded only in the hotter springs, above 40 °C.     

Thermal properties of rhodopsin: insight into the molecular mechanism of dim-light vision

Rhodopsin has developed mechanisms to optimize its sensitivity to light by suppressing dark noise and enhancing quantum yield. We propose that an intramolecular hydrogen-bonding network formed by ～20 water molecules, the hydrophilic residues, and peptide backbones in the transmembrane region is essential to restrain thermal isomerization, the source of dark noise. We studied the thermal stability of rhodopsin at 55 °C with single point mutations (E181Q and S186A) that perturb the hydrogen-bonding network at the active site. We found that the rate of thermal isomerization increased by 1-2 orders of magnitude in the mutants. Our results illustrate the importance of the intact hydrogen-bonding network for dim-light detection, revealing the functional roles of water molecules in rhodopsin. We also show that thermal isomerization of 11-cis-retinal in solution can be catalyzed by wild-type opsin and that this catalytic property is not affected by the mutations. We characterize the catalytic effect and propose that it is due to steric interactions in the retinal-binding site and increases quantum yield by predetermining the trajectory of photoisomerization. Thus, our studies reveal a balancing act between dark noise and quantum yield, which have opposite effects on the thermal isomerization rate. The acquisition of the hydrogen-bonding network and the tuning of the steric interactions at the retinal-binding site are two important factors in the development of dim-light vision.     

Pilus backbone protein PitB of Streptococcus pneumoniae contains stabilizing intramolecular isopeptide bonds

Streptococcus pneumoniae type 2 pili are recently identified fimbrial structures extending from the bacterial surface and formed by polymers of the structural protein PitB. Intramolecular isopeptide bonds are a characteristic of the related pilus backbone protein Spy0128 of group A streptococci. Based on the identification of conserved residues in PitB, we predicted two intramolecular isopeptide bonds in PitB. Using a combination of tandem mass spectrometry and Edman sequencing, we show that these bonds were formed between Lys₆₃-Asn₂₁₄ and Lys₂₄₃-Asn₃₇₂ in PitB. Mutant proteins lacking the intramolecular isopeptide bonds retained the proteolytic stability observed with the wild type protein. However, absence of these bonds substantially decreased the melting temperature of the PitB-derivatives, indicating a stabilizing function of these bonds in PitB of the pneumococcal type 2 pilus.     

Effects of deformability and thermal motion of lipid membrane on electroporation: by molecular dynamics simulations

Effects of mechanical properties and thermal motion of POPE lipid membrane on electroporation were studied by molecular dynamics simulations. Among simulations in which specific atoms of lipids were artificially constrained at their equilibrium positions using a spring with force constant of 2.0 kcal/(mol Ų) in the external electric field of 1.4 kcal/(mol Å e), only constraint on lateral motions of lipid tails prohibited electroporation while non-tail parts had little effects. When force constant decreased to 0.2 kcal/(mol Ų) in the position constraints on lipid tails in the external electric field of 2.0 kcal/(mol Å e), water molecules began to enter the membrane. Position constraints of lipid tails allow water to penetrate from both sides of membrane. Thermal motion of lipids can induce initial defects in the hydrophobic core of membrane, which are favorable nucleation sites for electroporation. Simulations at different temperatures revealed that as the temperature increases, the time taken to the initial pore formation will decrease.     

3,5-Lutidine coordinated zinc(II) aryl carboxylate complexes: Precursors for zinc(II) oxide

The reaction of Zn(κ²O,O′-OAc)₂·2H₂O with two equiv of 3,5-lutidine in methanol at room temperature for 12 h afforded [Zn(OAc)₂(3,5-lutidine)₂]· H₂O (1) in 91% yield. The acetate exchange reaction of 1 with two equiv of aryl carboxylic acids in methanol at room temperature for 12 h afforded [Zn(μ₂-κ¹O:κ¹O′-O₂CAr)₂(3,5-lutidine)]₂ [Ar = C₆H₅ (2) and C₆H₄Me-3 (3)], [Zn(OC(O)C₆H₄Me-2)₂(3,5-lutidine)₂] (4) and [Zn(κ²O,O′−O₂CC₆H₄Me-4)₂(3,5-lutidine)₂] (5) in ?90% yield. Complexes 1-5 were characterized by microanalytical, IR, solution (¹H and ¹³C) and solid-state cross-polarization magic angle spinning ¹³C NMR and X-ray diffraction data. The zinc atom in 1 is surrounded by nitrogen atom of two 3,5-lutidine and oxygen atom of two monodentate acetate moiety and thus attains a tetrahedral geometry. One of the acetate moieties is hydrogen bonded with a water molecule in the crystal lattice. Complexes 2 and 3 possess a dinuclear paddlewheel framework with a square pyramidal geometry around the zinc atom whereas 4 and 5 are mononuclear species with the zinc atom in tetrahedral and an octahedral geometry, respectively. Thermogravimetric analyses of 2-5 suggested ZnO as the decomposed product followed by the confirmation from the powder X-ray diffraction patterns. Enormous gas evolution resulting in porous ZnO during thermal decomposition was evidenced from scanning electron microscopic images.     

Novel heterometallic palladium-silver complex

The reaction between Pd₃(OOCMe)₆ and Ag₂(OOCMe)₂ afforded the first palladium-silver heterometallic acetate-bridged complex Pd^II[(μ-OOCMe)₂Ag^I(HOOCMe)₂]₂ (1). The molecular geometry and electronic structure of 1 were studied by single-crystal XRD and quantum-chemical DFT calculations. Thermal transformations of 1in vacuo and under Ar, H₂ produced PdAg alloy nanoparticles characterized with powder XRD and EXAFS.     

New copper(II), nickel(II) and zinc(II) complexes with 1,2,4-triazolo[1,5-a]pyrimidines and the chelating ligand 1,3-propanediamine: An unexpected coordination behavior for the 7-amine-derivative

Five new metal complexes with the metal ions Cu(II), Ni(II) and Zn(II) and containing 1,2,4-triazolo[1,5-a]pyrimidine derivatives and 1,3-propanediamine (tn) are described. The structural morphology of these coordination compounds depends on the triazolopyrimidine derivative used, being mononuclear for 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp) and 5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7(4H)-one (HmtpO), and 1D-polymeric for 7-amine-1,2,4-triazolo[1,5-a]pyrimidine (7atp). In the 7atp case, this ligand does not coordinate through N3 atom, as expected, but through N1, N4 and N71 in a bridging fashion. This unexpected coordination mode seems to be induced by the stability of the polynuclear metal complex in presence of tn ligand. All isolated metal complexes have been characterized by single-crystal X-ray diffraction, IR and UV-Vis spectroscopies, and EPR measurements. Moreover, luminescence measurements have been carried out for 7atp ligand and its polynuclear complex with Zn(II).     

Photoperiod modifies thermal reaction norms for growth and development in the red poplar leaf beetle Chrysomela populi (Coleoptera: Chrysomelidae)

Regression lines of development rate on temperature appeared significantly different between long (22 h) and short (12 h) day conditions and intersected each other at 23.8 °С. Thus, the rate of growth and development was higher at temperatures below the intersection point under short-day but above the intersection point it was higher under long day. Ecological relevance of this effect seems as follows: in autumn, as nights become longer and average daily temperature decreases, larvae have to speed up their development because it is only imago that overwinters. Conversely, midsummer offers long days and usually higher temperature, so again it is advantageous to develop as fast as possible in order to have at least one more generation per year. These results are compared with other studies showing interactions between photoperiod and temperature, and some possible general patterns are outlined. The lower thermal threshold for larval development depended on photoperiodic conditions; therefore rate isomorphy must be violated in this species. Development at higher temperatures generally resulted in smaller adults, as is usual with ectotherms according to the “temperature-size rule”, but body weight depended significantly on temperature only under short day. Our estimates of the lower temperature thresholds for growth and development in both cases did conform to the generalization made previously by Walters and Hassall (2006) in spite of another formula used by us. We briefly discuss this phenomenon and argue that relative position of these thresholds can be explained mathematically and per se may lack any biological sense.