Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans

RNA binding proteins control gene expression by the attenuation/antitermination mechanism. HutP is an RNA binding antitermination protein. It regulates the expression of hut operon when it binds with RNA by modulating the secondary structure of single-stranded hut mRNA. HutP necessitates the presence of l-histidine and divalent metal ion to bind with RNA. Herein, we report the crystal structures of ternary complex (HutP–l-histidine–Mg²⁺) and EDTA (0.5 M) treated ternary complex (HutP–l-histidine–Mg²⁺), solved at 1.9 Å and 2.5 Å resolutions, respectively, from Geobacillus thermodenitrificans. The addition of 0.5 M EDTA does not affect the overall metal-ion mediated ternary complex structure and however, the metal ions at the non-specific binding sites are chelated, as evidenced from the results of structural features.     

Spermatozoa input concentrations and RNA isolation methods on RNA yield and quality in bull (Bos taurus)

Sperm RNA can be used to understand the past spermatogenic process, future successful fertilization, and embryo development. To study the sperm RNA composition and function, isolation of good quality RNA with sufficient quantity is essential. The objective of this study was to assess the influence of sperm input concentrations and RNA isolation methods on RNA yield and quality in bull sperm. The fresh semen samples from bulls (n = 6) were snap-frozen in liquid nitrogen and stored at −80 °C. The sperm RNA was isolated using membrane-based methods combined with TRIzol (RNeasy + TRIzol and PureLink + TRIzol) and conventional methods (TRIzol, Double TRIzol, and RNAzol RT). Based on fluorometric quantification, combined methods resulted in significantly (P < 0.05) higher total RNA yields (800–900 ng/30–40 × 10⁶) as compared with other methods and yielded 20 to 30 fg of RNA/spermatozoon. The quality of RNA isolated by membrane-based methods was superior to that isolated by conventional methods. The sperm RNA was observed to be intact as well as fragmented (50–2000 bp). The study revealed that the membrane-based methods with a cocktail of lysis solution and an optimal input concentration of 30 to 40 million sperm were optimal for maximum recovery of RNA from bull spermatozoa.     

Environmentally friendly microwave ionic liquids synthesis of hybrids from cellulose and AgX (X = Cl,Br)

The purpose of this article was to explore an environmentally friendly strategy to synthesis of biomass-based hybrids. Herein, microwave-assisted ionic liquids method was applied to fabricate the hybrids from cellulose and AgX (X = Cl, Br) using cellulose and AgNO₃. The ionic liquids act simultaneously as a solvent, a microwave absorber, and a reactant. Ionic liquids provided Cl⁻ or Br⁻ to the synthesis of AgCl or AgBr crystals; thus no additional reactant is needed. The products are characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectrometry (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and differential thermal analysis (DTA). The cellulose–Ag/AgCl hybrid and cellulose–Ag/AgBr hybrid were also obtained by using cellulose–AgCl and cellulose–AgBr hybrids as precursors. This environmentally friendly microwave-assisted ionic liquids method is beneficial to the hybrids with high dispersion.     

The synthesis and characterization of mixed ligand Ru(II) complexes with dipyrido(2,3-a:3′,2′-j)phenazine (dpop′) and 2,3,5,6-tetra(2-pyridyl)-pyrazine (tppz)

The synthesis of the mixed ligand mono metallic [Ru(dpop′)(tppz)]²⁺ and bimetallic [(dpop′)Ru(tppz)Ru(dpop′)]⁴⁺ (dpop′ = dipyrido(2,3-a:3′,2′-j)phenazine; tppz = 2,3,5,6 tetra-(2-pyridyl)pyrazine) complexes is described. The [Ru(dpop′)(tppz)]²⁺ complex display an intense absorption at 518 nm which is assigned to a Ru(dπ) → dpop′ (π∗) MLCT transition, and at 447 nm which is assigned to a Ru(dπ) → tppz(π∗) MLCT transition. It undergoes emission at RT in CH₃CN with λ_em = 722 nm. The bimetallic [(dpop′)Ru(tppz)Ru(dpop′)]⁴⁺ complex shows a low energy absorption shoulder near 635 nm assigned to a Ru(dπ) → tppz(π∗) MLCT transition and an intense peak at 542 nm due to Ru(dπ) → dpop′ (π∗) MLCT transition. The bimetallic complex also emits at RT in CH₃CN with λ_em = 785 nm. Cyclic voltammetry shows reversible Ru^+2/+3 oxidations at 1.68 V for the monometallic complex and Ru^+2/+3 oxidation couples at +1.94 and +1.70 V for the bimetallic complex.     

Blend miscibility of cellulose propionate with poly(N-vinyl pyrrolidone-co-methyl methacrylate)

The blend miscibility of cellulose propionate (CP) with poly(N-vinyl pyrrolidone-co-methyl methacrylate) (P(VP-co-MMA)) was investigated. The degree of substitution (DS) of CP used ranged from 1.6 to >2.9, and samples for the vinyl polymer component were prepared in a full range of VP:MMA compositions. Through DSC analysis and solid-state ¹³C NMR and FT-IR measurements, we revealed that CPs of DS < 2.7 were miscible with P(VP-co-MMA)s of VP ≥ ∼10 mol% on a scale within a few nanometers, in virtue of hydrogen-bonding interactions between CP-hydroxyls and VP-carbonyls. When the DS of CP exceeded 2.7, the miscibility was restricted to the polymer pairs using P(VP-co-MMA)s of VP = ca. 10–40 mol%; the scale of mixing in the blends concerned was somewhat larger (ca. 5–20 nm), however. The appearance of such a “miscibility window” was interpretable as an effect of intramolecular repulsion in the copolymer component. Results of DMA and birefringence measurements indicated that the miscible blending of CP with the vinyl polymer invited synergistic improvements in thermomechanical and optical properties of the respective constituent polymers. Additionally, it was found that the VP:MMA composition range corresponding to the miscibility window was expanded by modification of the CP component into cellulose acetate propionate.     

Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera

We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A + T composition (79.3%–80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA^Gln and ND2 (64–87 bp), conserved ATACTAA motif between tRNA^{Ser (UCN)} and ND1, and characteristic features of the A + T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA^Asn/tRNA^{Ser (AGN)}, instead of the rearrangement tRNA^{Ser (AGN)}/tRNA^Asn, found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea + Noctuoidea + Geometroidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae + (Hesperiidae + (Pieridae + ((Lycaenidae + Riodinidae) + Nymphalidae)))) were strongly supported in all analyses (0.98–1 by BI and 96–100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.     

The complete mitochondrial genome of Taeniogonalos taihorina (Bischoff) (Hymenoptera: Trigonalyidae) reveals a novel gene rearrangement pattern in the Hymenoptera

The family Trigonalyidae is considered to be one of the most basal lineages in the suborder Apocrita of Hymenoptera. Here, we determine the first complete mitochondrial genome of the Trigonalyidae, from the species Taeniogonalos taihorina (Bischoff, 1914). This mitochondrial genome is 15,927 bp long, with a high A + T-content of 84.60%. It contains all of the 37 typical animal mitochondrial genes and an A + T-rich region. The orders and directions of all genes are different from those of previously reported hymenopteran mitochondrial genomes. Eight tRNA genes, three protein-coding genes and the A + T-rich region were rearranged, with the dominant gene rearrangement events being translocation and local inversion. The arrangements of three tRNA clusters, trnY–trnM–trnI–trnQ, trnW–trnL2–trnC, and trnH–trnA–trnR–trnN–trnS–trnE–trnF, and the position of the cox1 gene, are novel to the Hymenoptera, even the insects. Six long intergenic spacers are present in the genome. The secondary structures of the RNA genes are normal, except for trnS2, in which the D-stem pairing is absent.     

Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae)

Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A^u, B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π = 0.03343 and θ = 0.03536 for polyploid Ns genome sequences and π = 0.03886 and θ = 0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π = 0.0011 and θ = 0.0011. Nucleotide variation of diploid Aegilops speltoides (π = 0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π = 0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A^u, and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A^u, B, and D genomes were linked to T. urartu, A. speltoides, and A. tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum.     

Effects of UV radiation and nitrate limitation on the production of biogenic sulfur compounds by marine phytoplankton

We tested the effects of UV radiation (UVR) and nitrate limitation on the production of dimethylsulfide (DMS), particulate dimethylsulfoniopropionate (DMSPp), and particulate dimethylsulfoxide (DMSOp) in natural seawater from the Gulf of Mexico and in phytoplankton cultures. DMS/Chl a ratios in PAR-only and PAR + UV-exposed seawater were 0.44–2.0 and 0.46–1.9 nmol DMS μg⁻¹ Chl a, respectively, whereas the ratios in cultures of Amphidinium carterae were 1.0–2.2 nmol μg⁻¹ in PAR-exposed samples and 0.91–2.1 nmol μg⁻¹ in PAR + UV-exposed samples. These results suggested that UVR did not substantially affect DMS/Chl a ratios in seawater and A. carterae culture samples. Similarly, UVR had no significant effect on DMSOp/Chl a in seawater samples (0.83–1.6 nmol DMSO μg⁻¹ Chl a for PAR + UV vs. 0.70–1.5 nmol μg⁻¹ for PAR-exposed seawater samples, respectively) or in A. carterae cultures (0.20–1.3 and 0.19–0.88 nmol DMSO μg⁻¹ Chl a in PAR + UV- and PAR-exposed cultures, respectively). In an experiment with the diatom, Thalassiosira oceanica, the culture was grown in high nitrate (30 μM) or low nitrate (6 μM) media and exposed to PAR-only or PAR + UV. The low nitrate, PAR-only samples showed an increase of intracellular dimethylsulfoniopropionate (DMSP) concentration from 2.1 to 15 mmol L⁻¹ in 60 h, but the increase occurred only after cultures reached the stationary phase. Cultures of T. oceanica grown under UVR had lower growth rates than those under PAR-only (μ′ = 0.17 and 0.32 d⁻¹, respectively) and perhaps did not experience severe nitrate limitation even in the low nitrate treatment. These results suggest that the elevated UVR in low nitrate environments could result in reduction of DMSP in some species, whereas DMSP concentrations would not be affected in eutrophic areas.     

Species-specificity of oospore dimensions in three ecorticate species of Chara (Charales,Charophyceae)

Dimensions of oospores such as length, width, fossa-breadth, length-to-width ratio and number of striae were considered for morphological identification of the members of Charales. Oospores were collected from natural stands of three species, viz. Chara braunii, C. corallina and C. wallichii in ponds in West Bengal (India). Oospore dimensions (length, width and fossa-breadth) correlated well: though the fossa breadth–length relation of C. braunii showed lower correlation coefficient (r² = 0.076, p < 0.001), all other five breadth or width–length relationships showed r² ≥ 0.23, p < 0.001. These bivariate patterns were significantly different among the species (one-way ANCOVA of length–width ratio to fossa-breadth: adjusted means and slopes both p < 0.001), C. braunii and C. corallina has similar length to width ratios, C. wallichii and C. corallina were similar in width, whereas the species differed in breadth and length in the order C. braunii, C. wallichii, and C. corallina.     

Correlation between grass carp (Ctenopharyngodon idella) resistance to grass carp reovirus and the genetic insert-deletion polymorphisms in promoter and intron of RIG-I gene

RIG-I (retinoic acid-inducible gene I) is an essential cytosolic pathogen recognition receptor that binds to a variety of viral RNA or DNA to induce type I interferons. In the present study, insert–deletion polymorphisms in promoter and introns of CiRIG-I (Ctenopharyngodon idella RIG-I) were explored, their associations with resistance/susceptibility to grass carp reovirus (GCRV) were analyzed. To this end, genomic sequence of CiRIG-I gene was obtained, and twenty pairs of primers were prepared for the detection of insert–deletion polymorphisms. Five insert–deletion mutations were found, a 2-bp mutation and an 8-bp mutation existed in the promoter and other three sizes in 74 bp, 146 bp and 53 bp were sited in the intron 8. After a challenge experiment, only the genotype and allele of − 740 insert–deletion mutation in the promoter and allele of 6804 insert–deletion mutation were significantly associated with resistance/susceptibility to GCRV among the five mutations (P < 0.05). To further identify this correlation, another independent challenge test was carried out. The result revealed that the cumulative mortality in ins/ins genotype individuals (43.75%) at − 740 insert–deletion mutation was significantly lower than that in ins/del (72.09%) and del/del (74.19%) genotypes (P < 0.05). Linkage disequilibrium and haplotype analysis showed 6610 insert–deletion mutation and 6804 insert–deletion mutation were linkage disequilibrium. The haplotype ins–ins (6610ins–6804ins) was significantly susceptible to GCRV, and ins–del (6610ins–6804del) was significantly resistant to GCRV (P < 0.05). Those could be potential gene markers for the future molecular selection of strains that are resistant to GCRV.     

Mineral nutrition and heterotrophy in the water conservative holoparasite Hydnora Thunb. (Hydnoraceae)

There are large gaps in our understanding of parasite–host nutrient relationships. Our goal was to evaluate transdermal water loss, parasite–host mineral relationships, and heterotrophy in the holoparasitic genus Hydnora. We estimated in situ transdermal water loss in Hydnora and measured nutrient profiles and δ¹³C and δ¹⁵N signatures for Hydnora and hosts in southern Africa and Madagascar. For comparison we also measured δ¹³C and δ¹⁵N for aerial hemiparasites at the same sites. Transdermal water loss in Hydnora ranged from 0.14 ± 0.02 to 0.38 ± 0.04 mg cm⁻² h⁻¹ and was comparable to transpiration rates for water conservative xerophytes. Concentrations of P and K were higher in Hydnora relative to CAM hosts; other mineral concentrations were significantly lower in the parasite or were not different. δ¹³C signatures of holoparasites and hemiparasites relative to their hosts reflected host metabolism and differences in commitment to heterotrophic C gain. Holoparasite δ¹³C values were significantly enriched (by 0.55‰ ± 0.23) compared to host shoot and depleted compared to host root tissues (by −0.97‰ ± 0.12). Holoparasite δ¹³C values were not significantly different compared to the estimated whole host δ¹³C value. δ¹⁵N values for holoparasites and hemiparasites were significantly correlated with hosts. The water conservative nature of Hydnora spp. combined with parasite–host mineral nutrition profiles are suggestive of active processes of solute uptake. Stable isotope fractionation in host tissues dictated significant differences between parasite and host (shoot and root) δ¹³C signatures. The confirmation of complete heterotrophy and the lack of a confounding transpiration stream may make Hydnora a promising model organism for the examination of parasite solute uptake.     

Seasonal acclimation in resting metabolism of the skink, Mabuya brevicollis (Reptilia: Scincidae) from southwestern Saudi Arabia

The resting metabolic rate (RMR) of seasonally-acclimated Mabuya brevicollis of various body masses was determined at 20, 25, 30, 35 and 40 °C, using open-flow respirometry. RMR (ml g⁻¹ h⁻¹) decreased with increasing mass at each temperature. RMRs increaProd. Type: FTPsed as temperature increased. The highest and lowest Q₁₀ values were obtained for the temperature ranges 20–25 °C and 30–35 °C for the summer-acclimated lizards. The exponent of mass “b” in the metabolism-body mass relation ranged from 0.41 to 0.61. b values were lower in the autumn and winter-acclimated lizards than in spring and summer-acclimated lizards. Seasonal acclimation effects were evident at all temperatures (20–40 °C) for M. brevicollis. Winter-acclimated skinks had the lowest metabolic rates at different temperatures. The pattern of acclimation exhibited by M. brevicollis may represent a useful adaptation for lizards inhabiting subtropical deserts to promote activity during their active seasons.     

Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms and susceptibility to ischemic stroke: A meta-analysis

Associations between 5,10-methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism and ischemic stroke have been reported (Ariyaratnam et al., 2007; Banerjee et al., 2007; Casas et al., 2004), but the results of these studies are inconsistent. To investigate the possible associations between the MTHFR gene polymorphism and ischemic stroke, we performed a meta-analysis. Nineteen case–control studies associated with MTHFR gene C667T involving 2223 cases and 2936 controls were included. Heterogeneity among studies was evaluated with I² and Egger's test and an inverted funnel plot was used to assess publication bias. Odds ratio (OR) was observed to identify the associations. Statistically significant association with ischemic stroke was identified for allele T polymorphism of MTHFR [fixed-effects OR = 1.28, 95% confidence interval (95% CI): 1.17–1.40, P < 0.00001] and marginally significant association was detected with genotype CT of MTHFR (fixed-effects OR = 1.13, 95% CI: 1.01–127, P = 0.04) and genotype TT of MTHFR (fixed-effects OR = 1.43, 95% CI: 1.20–1.70, P < 0.001). The results suggested that the MTHFR C667T genetic polymorphism was significantly associated with increased risk of ischemic stroke.     

Vegetation patterns and spontaneous regression of Caulerpa taxifolia (Vahl) C. Agardh in Malinska (Northern Adriatic,Croatia)

The green alga Caulerpa taxifolia was recorded at Malinska in 1994 and this actually represents the highest northern latitude (45°7′30″N) at which this invasive alga has been found in the world. The alga was widespread at four sites from which it was eradicated by suction pumps during 1996 and 1997. However, it immediately and intensively recolonized all but one site. Throughout 1998 and 1999 the renewed vegetation showed consistent seasonal patterns. The alga nearly disappeared in April and May while regenerating from over-wintering parts of the thalli in summer. The maximum development occurred in autumn and winter with values of biomass (around 200 g dry weight m⁻²) and frond number (around 2000 m⁻²) generally lower than those reported for the north-western Mediterranean. Values for the frond length (10–18 cm) were in the same range as those in the north-western basin. Throughout 1998 and 1999 the biomass was closely correlated to frond number and length (adjusted R² = 0.90). During the following years C. taxifolia entered a phase of regression. The total colonized area, which amounted to several thousands of square metres in 1998, spontaneously declined in 2000 and 2001 so that only several thalli were found in 2004 during a detailed survey of the settlement. No major changes in winter seawater temperatures, ranging from 9.5 to 10.5 °C, were observed in the area from 1994 to 2004. Thus, other unknown processes could likely play a role on specific vegetation patterns of C. taxifolia in Malinska. Accordingly, it is difficult to explain why the still surviving thalli did not proliferate during the favourable summer–autumn period.     

Effect of pre-incubation irradiance on survival of cryopreserved gametophytes of Undaria pinnatifida (Phaeophyta) and morphology of sporophytes formed from the gametophytes

Gametophyte strains originating from indigenous sporophytes of Undaria pinnatifida (Harvey) Suringar in Iwate Prefecture, Northeast Japan, were maintained for 9–10 months at 45 μmol photons m⁻² s⁻¹. Before cryopreservation in liquid nitrogen for more than 12 h (1–14 days) using a two-step cooling method with a mixture of cryoprotectants (10% l-proline and 10% glycerol), these were pre-incubated for 2, 4 and 8 months at 15 μmol photons m⁻² s⁻¹. After 1 week of thawing, no surviving gametophytes were detected in the strains without pre-incubation, but both the female and male gametophytes, pre-incubated for more than 4 months, showed high survival rates (43–60% for females and 64–100% for males). This revealed the induction of freezing tolerance by incubation at low irradiance. Thereafter, sporophytes derived from cryopreserved gametophytes and subcultured gametophytes, stored under pre-incubation conditions, were formed from the strain, and a morphological comparison was conducted with 10 characters (stipe length, stipe wet weight, blade length, blade wet weight, blade width, incision depth, blade thickness, sporophyll length, sporophyll wet weight, and sporophyll width). The morphology of the sporophytes formed from the cryopreserved gametophytes corresponded well with that of the subcultured gametophytes from the same strain. The results suggest that the cryopreservation method is applicable for preserving culture stocks of U. pinnatifida to be used in mariculture.     

Thermal preference,tolerance and oxygen consumption of adult white shrimp Litopenaeus vannamei (Boone) exposed to different acclimation temperatures

Final temperature preferendum of white shrimp adults were determined with acute and gravitation methods. The final preferendum was similar, independent of method (26.2–25.6 °C). A direct relationship was determined between the critical thermal maxima values and the acclimation temperatures (P<0.05). The end point of Critical Thermal Maxima (CTMax) for adults was defined as the loss of righting response (LRR). The acclimation response ratio (ARR) for adults of white shrimp had an interval of 0.36–0.76, values that agreed with others obtained for crustaceans from tropical and subtropical climates. The oxygen consumption rates increased significantly (P<0.05) from 39.6 up to 90.0 mg O₂ kg⁻¹ h⁻¹ wet weight (w.w.) as the acclimation temperature increased from 20 to 32 °C. The range of temperature coefficient (Q₁₀) of the white shrimp between 23 and 26 °C was the lower 1.60. The results obtained in this work are discussed in relation to the species importance in the reproductive scope and maintenance of breeders.     

Syntheses, characterizations and theoretical calculations of rhodium(III) 1,2-naphthoquinone-1-oxime complexes

Rhodium(III) complexes of 1,2-naphthoquinone-1-oxime (1-nqo) [Rh(1-nqo)L₂Cl₂] 1-3 [1, L = 4-methylpyridine (mpy); 2, L = 4-phenylpyridine (ppy); 3, L = 4-acetylpyridine (apy)] were prepared. The structure of complex 1 is analyzed by single crystal X-ray crystallography. All of the complexes were characterized by mass spectrometry, ¹H-¹H COSY NMR and FT-IR. UV-Vis absorption spectroscopy and cyclic voltammetry were employed to investigate the electronic transition behaviors of the complexes. The complexes displayed irreversible metal-localized two-electron reductions from Rh^III to Rh^I on the cyclic voltammogram. While the low-energy absorptions at λ_max of 488-490 nm on the UV-Vis spectra of the complexes were related to metal to 1-nqo ligand charge transfer [MLCT, dπ(Rh) → π∗(1-nqo)] and chloride to 1-nqo ligand charge transfer [LLCT, pπ(Cl) → π∗(1-nqo)] based on the theoretical calculations using time-dependent density functional theory (TD-DFT).     

RNA targeting by DNA binding drugs: Structural,conformational and energetic aspects of the binding of quinacrine and DAPI to A-form and H-form of poly(rC)·poly(rG)

A key step in the rational design of new RNA binding small molecules necessitates a complete elucidation of the molecular aspects of the binding of existing molecules to RNA structures. This work focuses towards the understanding of the interaction of a DNA intercalator, quinacrine and a minor groove binder 4′,6-diamidino-2-phenylindole (DAPI) with the right handed Watson–Crick base paired A-form and the left-handed Hoogsteen base paired H^L-form of poly(rC)·poly(rG) evaluated by multifaceted spectroscopic and viscometric techniques. The energetics of their interaction has also been elucidated by isothermal titration calorimetry. Results of this study converge to suggest that (i) quinacrine intercalates to both A-form and H^L-form of poly(rC)·poly(rG); (ii) DAPI shows both intercalative and groove-binding modes to the A-form of the RNA but binds by intercalative mode to the H^L-form. Isothermal calorimetric patterns of quinacrine binding to both the forms of RNA and of DAPI binding to the H^L-form are indicative of single binding while the binding of DAPI to the A-form reveals two kinds of binding. The binding of both the drugs to both conformations of RNA is exothermic; while the binding of quinacrine to both conformations and DAPI to the A-form (first site) is entropy driven, the binding of DAPI to the second site of A-form and H^L-conformation is enthalpy driven. Temperature dependence of the binding enthalpy revealed that the RNA–ligand interaction reactions are accompanied by small heat capacity changes that are nonetheless significant. We conclude that the binding affinity characteristics and energetics of interaction of these DNA binding molecules to the RNA conformations are significantly different and may serve as data for the development of effective structure selective RNA-based antiviral drugs.     

Synthesis, characterization and electrode adsorption studies of porphyrins coordinated to ruthenium(II) polypyridyl complexes

Two new porphyrins, meso-tris-3,4-dimethoxyphenyl-mono-(4-pyridyl)porphyrin (H₂MPy3,4DMPP) and meso-tris-3-methoxy-4-hydroxyphenyl-mono-(4-pyridyl)porphyrin (H₂MPy3M4HPP), and their ruthenium analogs obtained by coordination of [Ru(bpy)₂Cl]⁺ groups (where bpy = 2,2′-bipyridine) to the pyridyl nitrogens have been synthesized and studied by electronic absorption spectroscopy, cyclic voltammetry and spectroelectrochemistry. These ruthenated porphyrins couple Ru chromophores to porphyrins containing electroactive meso-substituents. The highest energy electronic absorption for the ruthenated complexes is assigned as a bpy(π) → bpy(π*) intraligand charge transfer while the next lowest energy electronic absorption is assigned as Ru(dπ) → bpy(π*) metal-to-ligand charge transfer (MLCT) transition. The Ru^III/II couples occur at approximately 0.95 V versus the SHE reference electrode in acetonitrile solutions. The first oxidation of the porphyrin is localized on the 3,4-dimethoxyphenyl and 3-methoxy-4-hydroxyphenyl substituents, respectively. Electroactive surfaces result from adsorption of these compounds onto glassy carbon electrodes followed by anodic cycling in acidic media.