Unusual Protonated Structure in the Homopurine · Homopyrimidine Tract of Supercoiled and Linearized Plasmids Recognized by Chemical Probes

Abstract

Plasmid pEJ4, which is a derivative of pUC19 containing an insert with 60-bp-long · homopurine homopyrimidine tract from sea urchin P. miliaris histone gene spacer, was studied by chemical probes of the DNA structure osmium tetroxide and glyoxal. The former probe reacts with pyrimidine bases, while the latter forms a stable product only with guanine residues. These probes can thus be applied as specific probes for the homopyrimidine and homopurine strands, respectively.

At pH 6.0 the site-specific modification of the homopurine · homopyrimidine tract by both probes was observed at native superhelical density of the plasmid. In the linear plasmid under the same conditions this modification was absent; it appeared, however, at more acid pH values. In supercoiled DNA the hypersensitivity of the homopurine homopyrimidine tract to osmium tetroxide did not substantially change when pH was decreased from 6.0 to 4.0. Changes in NaCl concentration at pH 4.5 did not influence the hypersensitivity to osmium tetroxide; at pH 6.0 this hypersensitivity decreased with increasing NaCl concentration. These results thus show that the chemical probes recognize an unusual protonated structure containing unpaired bases or non-Watson-Crick base pairs. At pH 5.6 the site-specific modification occurred at or near to the middle of the homopurine · homopyrimidine tract, suggesting that a hairpin may be involved in the unusual structure under the given conditions. From the models suggested so far for the unusual structure of homopurine · homopyrimidine tracts our results fit best the protonated triplex H form suggest by V.I. Lyamichev, S.M. Mirkin and M.D. Frank-Kamenetskii, J. Biomol. Struct. Dyn. 3, 667 (1986).     

Interaction of cobalt(II) and copper(II) hydroxamates with polyriboadenylic acid: An insight into RNA based drug designing

The polyadenylic acid [poly(A)] tail of mRNA plays a noteworthy role in the initiation of the translation, maturation, and stability of mRNA. It also significantly contributes to the production of alternate proteins in eukaryotic cells. Hence, it has recently been recognized as a prospective drug target. Binding affinity of bis(N-p-tolylbenzohydroxamato)Cobalt(II), [N-p-TBHA-Co(II)] (1) and bis(N-p-naphthylbenzohydroxamato)Copper(II), [N-p-NBHA-Cu(II)] (2) complexes with poly(A) have been investigated by biophysical techniques namely, absorption spectroscopy, fluorescence spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy, circular dichroism spectroscopy, viscometric measurements and through molecular docking studies. The intrinsic binding constants (K_b) of complexes were determined following the order of N-p-TBHA-Co(II)] > N-p-NBHA-Cu(II), along with hyperchromism and a bathochromic shift for both complexes. The fluorescence quenching method revealed an interaction between poly(A)-N-p-TBHA-Co(II)/poly(A)-N-p-NBHA-Cu(II). The mode of binding was also determined via the fluorescence ferrocyanide quenching method. The increase in the viscosity of poly(A) that occurred from increasing the concentration of the N-p-TBHA-Co(II)/N-p-NBHA-Cu(II) complex was scrutinized. The characteristics of the interaction site of poly(A) with N-p-TBHA-Co(II)/N-p-NBHA-Cu(II) were adenine and phosphate groups, as revealed by DRS-FTIR spectroscopy. Based on these observations, a partial intercalative mode of the binding of poly(A) has been proposed for both complexes. Circular dichroism confirmed the interaction of both the complexes with poly(A). The molecular docking results illustrated that complexes strongly interact with poly(A) via the relative binding energies of the docked structure as ?259.39eV and ?226.30eV for N-p-TBHA-Co(II) and N-p-NBHA-Cu(II) respectively. Moreover, the binding affinity of N-p-TBHA-Co(II) is higher in all aspects than N-p-NBHA-Cu(II) for poly(A).     

Specific cation effect on quenching reactions of excited tris(α,α-diimine)ruthenium(II) and tris(2,2-bipyridine)chromium(III) by tris(oxalato)- and tris(malnato)chromates(III) in aqueous solutions

Specific salt effects were studied on the quenching reaction of excited [Ru(N-N)₃]²⁺ (N-N=2,2^′-bipyridine (bpy), 1,10-phenanthrorine (phen)) and [Cr(bpy)₃]³⁺ by [Cr(ox)₃]³⁻ (ox=oxalate ion) and [Cr(mal)₃]³⁻ (mal=malonate ion) in aqueous solutions as a function of alkali metal ions which were added for adjustment of ionic strength. The value of k_q, quenching rate constants, and k₁, energy transfer rate constant in encounter complex, is changed by the cations as the order of Li⁺ > Na⁺ > K⁺ ≈ Rb⁺ ? Cs⁺, although diffusion rate constants are not changed by the co-existing cations. Among the quenching reactions investigated in this work, a ratio of k₁ values in the aqueous solutions whose ionic strength was adjusted with LiCl and KCl, k₁^LiCl/k₁^KCl, is larger for quenching systems of closely approached donor-acceptor pair than loosely bounded pair. These results indicate that co-existing alkali cation tunes the distance between donor and acceptor in encounter complex where energy transfer occurs.     

Heterometallic complex formation on p-sulfonatothiacalix[4]arene platform resulting in pH- and redox-modification of [Ru(bpy)3] luminescence

The pH-dependent heterometallic complex formation with p-sulfonatothiacalix[4]arene (TCAS) as bridging ligand in aqueous solutions was revealed by the use of spectrophotometry, nuclear magnetic relaxation and fluorimetry methods. The novelty of the structural motif presented is that the appendance of emission metal center ([Ru(bpy)₃]²⁺) is achieved through the cooperative non-covalent interactions with the upper rim of TCAS. The second metal block (Fe(III), Fe(II) and Mn(II)), bound with the lower rim of TCAS in the inner sphere coordination mode is serving as quencher of [Ru(bpy)₃]²⁺ emission. The difference between the complex ability of Fe(III) and Fe(II) ions provides pH conditions for redox-dependent emission of [Ru(bpy)₃]²⁺.     

Photoinduced electron transfer and energy transfer reactions of hydroxo-(2,2′:6′,2″-terpyridine) platinum(II)

The luminescent complex [Pt(terpy)OH]BF₄ undergoes photoinduced electron transfer reactions with phenyl amine electron donors and nitrophenyl electron acceptors. Stern-Volmer analysis of the quenching of metal-to-ligand charge transfer phosphorescence (³MLCT) was used to calculate bimolecular rate constants for electron transfer. Rate constants vary from 10⁸ to >10¹⁰ M⁻¹ s⁻¹, depending on the thermodynamic driving force of the electron transfer reaction, with rate constants indicating that [Pt(terpy)OH]BF₄* is a powerful photo-oxidant. Aromatic triplet energy acceptors can also quench the ³MLCT emission.     

Changes of serum albumin affinity for aspirin induced by fatty acid

Saturated fatty acids such as myristic acid play an important role in the pathogenesis of cardiovascular disorders.

Using the quenching fluorescence method we examined the influence of myristate on the changes of transporting protein affinity towards aspirin—the most popular anticoagulant.

Our results showed that the presence of the myristic acid alters the stability of the anticoagulant–albumin complex. The ranges of [myristate]/[albumin] molar ratio at which the stability of drug–protein complex increases or decreases were determined. The differences in interaction between ligands and human or bovine serum albumins were identified. The competition in binding of ligands with these albumins was also described.     

Microbial metabolomics: past,present and future methodologies

Microbial metabolomics has received much attention in recent years mainly because it supports and complements a wide range of microbial research areas from new drug discovery efforts to metabolic engineering. Broadly, the term metabolomics refers to the comprehensive (qualitative and quantitative) analysis of the complete set of all low molecular weight metabolites present in and around growing cells at a given time during their growth or production cycle. This review focuses on the past, current and future development of various experimental protocols in the rapid developing area of metabolomics in the ongoing quest to reliably quantify microbial metabolites formed under defined physiological conditions. These developments range from rapid sample collection, instant quenching of microbial metabolic activity, extraction of the relevant intracellular metabolites as well as quantification of these metabolites using enzyme based and or modern high tech hyphenated analytical protocols, mainly chromatographic techniques coupled to mass spectrometry (LC-MSⁿ, GC-MSⁿ, CE-MSⁿ), where n indicates the number of tandem mass spectrometry, and nuclear magnetic resonance spectroscopy (NMR).     

三叶半夏组培快繁与优良单株的选育

本文利用组织培养技术实现了三种不同叶型三叶半夏的快速繁殖,并通过光合生理特征的比较对其优良单株进行了选育。结果表明：半夏能在分化培养基MS+6-BA 1.0 mg/L + NAA 0.2 mg/L+蔗糖3%+琼脂5.0 g/L和离体块茎诱导培养基（1/2 MS+IBA 0.03 mg/L+ NAA 0.01 mg/L+蔗糖5%+琼脂5.0 g/L+AC 0.3 g/L）上快速扩繁,继代繁殖系数为1:6.23,培养3个月后块茎的平均直径达0.88cm。 对其光合生理特征的研究结果表明：三叶半夏是一种典型的阴生植物,其光饱和点为700μmol·photons/s·m2;三种叶型的三叶半夏都存在着明显的光抑制现象,其中柳叶型最明显。本研究所选育的11个单株后代中,以桃叶2号（T2）的净光合速率和产量最高,柳叶2号（L2）对强光的耐受力最强。经过6个月的扩繁,本研究获得优良单株T2和L2离体块茎各1万颗。在温州乐清实验基地中经过1年的大田种植后得优良单株半夏块茎各100kg。     

On the use of the quenching of luminol luminescence to evaluate sod activity

Addition of horseradish peroxidase to a luminol solution (pH = 9.4) produces a burst of light followed by a steady luminescence that lasts for several minutes. This steady-state luminescence is readily quenched by SOD, with a concentration (the additive concentration needed to decrease by one-half the emitted luminescence intensity) of c.a. 4 ng/ml (14 mU/ml). The luminescence intensity decrease can then be employed to evaluate SOD activity in SOD-containing samples. However, the light intensity can also be quenched by additives, such as Trolox, that are able to trap luminol-derived intermediates. It is proposed that double quenching experiments must be performed in order to be able to relate the observed effect of an additive to its SOD-like activity.     

Influence of phosphate ion on the fluorescence of 3-fluorotyrosine

Summary 3-Fluorotyrosine fluorescence is quenched effectively by phosphate ions not only by a dynamic but also by a static mechanism owing to H-bond complex formation in ground state. 3-Fluorotyrosine pK_a values both in the ground and first excited state (8.3 and 4, respectively) are appreciably lower than those of tyrosine, thus promoting 3-fluorotyrosinate ion formation in the excited state. Additional emission owing to 3-fluorotyrosinate ion (near 350 nm) may be taken erroneously for tryptophan fluorescence.